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Molecule of the Month Archive

Molecule of the Month

The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.

This feature provides an easy introduction to the RCSB PDB for all types of users, but especially for teachers and students. It is used in many classrooms to introduce structures to students, and is an integral part of the protein modeling event at the Science Olympiad. It is not intended to be a comprehensive index to entries in the PDB archive, nor necessarily represent the historical record. The structures used to illustrate each installment are chosen at the discretion of the authors. Goodsell described the creation of these articles and images in an interview with the RCSB PDB Newsletter.

Citation and usage information is available. High resolution TIFF images are also available.

Other institutions publish similar features, including the Protein of the Month at the European Bioinformatics Institute and Protein Spotlight at the Swiss Institute of Bioinformatics.

Molecule of the Month is translated into Japanese by PDBj.

The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology (2015) DS Goodsell, S Dutta, C Zardecki, M Voigt, HM Berman, SK Burley PLoS Biol 13(5): e1002140. doi: 10.1371/journal.pbio.1002140


Sorted by Year



  Glutamate-gated Chloride Receptors    (  ePub Version)

Glutamate-gated Chloride Receptors

Medical science is always looking for a magic bullet: an antibiotic that will kill a pathogen, but leave our own bodies untouched. The trick is to find targets that are unique to the pathogen, and then find a drug that attacks only them. For instance, penicillin attacks the machinery that builds bacterial cell walls (see the Molecule of the Month on Penicillin binding proteins), which are quite different than the membranes surrounding our own cells. This gets trickier, however, when we need to fight parasitic animals, since their molecules are quite similar to ours.

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  Two-component Systems    (  ePub Version)

Two-component Systems

Bacteria live at the mercy of their environment, much more so than we do. Our bodies help to buffer changes in temperature or resources, and we can always pick up and walk away if things get really bad. Bacteria don't have these options. They are tiny and are subject to large changes in conditions in their local surroundings, so they often must make due with what they have. To do this, they build a collection of several dozen sensors that probe the local conditions and decide how best to respond.

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  Amyloids    (  ePub Version)


Proteins have evolved to fold into a functional shape, or in cases where a flexible tether is needed, to remain consistently unfolded. In some cases, however, proteins aggregate to form unwanted structures, which can have dangerous consequences. The amyloid-beta precursor protein is a perfect example. In its normal form, it is a membrane-bound protein with folded regions connected by flexible tethers. But if the protein chain is broken, some of the resulting peptides aggregate into long fibrils, termed "amyloids," that can gum up the proper working of cells.

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  Tetrahydrobiopterin Biosynthesis    (  ePub Version)

Tetrahydrobiopterin Biosynthesis

Enzymes that perform unusual chemical reactions often need some assistance. The twenty natural amino acids have many different chemical properties that may be used to catalyze chemical reactions, but sometimes amino acids just aren't enough. In these cases, cofactors with special chemical properties provide the necessary chemical expertise and enzymes use them as tiny tools to perform their reactions. For instance, tetrahydrobiopterin is a cofactor used by several enzymes that juggle molecular oxygen, attaching it to amino acids and other molecules.

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  New Delhi Metallo-β-Lactamase    (  ePub Version)

New Delhi Metallo-β-Lactamase

The discovery of penicillin and other antibiotics marked a milestone in the history of humankind, giving us control over the ever-present danger of infectious disease. Within a few short years after this discovery, however, the bacterial world began to fight back, and strains of bacteria emerged that are resistant to the antibiotics. In the decades that followed, and continuing to this day, medical researchers have worked to discover new antibiotics, both natural and designed, to fight these resistant bacteria.

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  Receptor for Advanced Glycation End Products    (  ePub Version)

Receptor for Advanced Glycation End Products

Even the most innocuous things can be dangerous when used in excess. Sugar is the perfect example. Glucose is absolutely necessary to power our cells, so we need to eat a constant supply of food to stay alive. But if we overdo it, excess glucose can cause serious problems. This is particularly apparent in people with diabetes. Excess sugar in the blood, over many years, damages proteins around the body and leads to life-threatening medical problems.

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  Titin    (  ePub Version)


Titin is the largest protein chain in your body, with more than 34,000 amino acids. This titanic protein acts like a big rubber band in our muscles. It is attached at one end to the Z-disk (shown here at the top in blue), which organizes the thin actin filaments. The other end of titin is attached to the M-line (shown in red at the bottom), which organizes the thicker myosin filaments. In between, titin (shown in yellow) has a number of elastic elements that stretch and contract, holding the whole contractile apparatus in the proper shape as the muscle flexes.

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  Glucagon    (  ePub Version)


Too much glucose in the blood can lead to serious problems like diabetes, but too little glucose will also cause problems, starving cells throughout the body. Your body uses two main hormones, secreted by cells in the pancreas, to get the balance just right. Just after we eat, insulin is released, telling cells to take glucose out of the blood and store it for future use. Between meals, glucagon is released and has the opposite action, telling these same cells to release glucose for use in energy production and metabolism.

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  Phototropin    (  ePub Version)


Scientists have known for many years that plants respond to light, growing toward sources of light and protecting themselves from light that is too harsh. In many of these cases, plants are responding to the level of blue light. Blue light has several advantages over other colors. It is among the most energetic of the visible colors, and thus can have a greater effect on chromophore molecules that absorb light. For plants that live in water, blue light also penetrates deeper than other colors. Plants, as well many other types of organisms, use sensor proteins to see the level of blue light and respond to it.

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  Insulin Receptor    (  ePub Version)

Insulin Receptor

Cells throughout the body are fueled largely by glucose that is delivered through the bloodstream. A complex signaling system is used to control the process, ensuring that glucose is delivered when needed and stored when there is a surplus. Two hormones, insulin and glucagon, are at the center of this signaling system. When blood glucose levels drop, alpha cells in the pancreas release glucagon, which then stimulates liver cells to release glucose into the circulation. When blood glucose levels rise, on the other hand, beta cells in the pancreas release insulin, which promotes uptake of glucose for metabolism and storage. Both hormones are small proteins that are recognized by receptors on the surface of cells.

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  Cascade and CRISPR    (  ePub Version)

Cascade and CRISPR

Living organisms are under constant attack by viruses and have evolved an effective set of weapons to fight them. Bacteria and archaea take several approaches. They have several hardwired systems that fight the most common attackers. For instance, restriction enzymes stand ready to cut up the DNA of invading viruses. They also have a more adaptive system, akin to our own immune system, that can be tuned to protect against the viruses that are present at any given time. This system, termed CRISPR-Cas, stores information on current threats and provides the weapons to destroy them.

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  TAL Effectors    (  ePub Version)

TAL Effectors

Nature is full of surprises, and sometimes you can find treasures hidden in the most unlikely places. A few years ago, scientists found one of these treasures in a bacterium that attacks plants: a modular protein that can read the sequence of nucleotides in DNA. Structural understanding of this protein opens the door to all manner of applications in medicine and biotechnology. We can now customize a protein to read any DNA sequence that we desire, and thus target the protein to specific places in a genome. Already, these sequence-reading proteins are being used to create the tools for genome editing, as a possible way to correct genetic diseases.

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  Methyl-coenzyme M Reductase    (  ePub Version)

Methyl-coenzyme M Reductase

Methanogenic archaea produce about a billion tons of methane each year. Methanogens are tiny microbes similar to bacteria that colonize anaerobic environments such as the bottom of lakes and swamps or the gut of cows and humans. They feed on molecules like carbon dioxide, methanol and acetic acid that are produced by fermenting bacteria, and release methane as their waste product, bubbling up as marsh gas, or in the case of our own resident methanogens, less socially-acceptable gases.

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  Ebola Virus Proteins    (  PDF 2.7 MB,   ePub Version)

Ebola Virus Proteins

The genome of ebola virus contains instructions for building seven proteins, which assemble with the genomic RNA to form one of the deadliest viruses. Ebola virus is surrounded by a membrane stolen from an infected cell, and studded with ebola glycoproteins. A layer of matrix proteins support the membrane on the inside, and hold a cylindrical nucleocapsid at the center, which stores and delivers the RNA genome.

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  Apoptosomes    (  ePub Version)


"To be, or not to be"--that question is continually being asked by each of your cells. Your cells are preprogrammed to die on command. This is essential during development of large organisms like ourselves, where cells work together, growing and dying to shape our complicated bodies. It is also essential throughout our adult lives, to remove damaged or infected or cancerous cells. The machinery for cell death is always silently present in cells, but can be instantly mobilized if the choice is made to die.

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  Dynein    (  ePub Version)


Our cells rely on three main types of motors to move things around, all powered by ATP. Myosin moves along filaments of actin, and is the engine that powers muscle contraction as well as many more molecule-sized transport tasks inside the cell. Kinesin and dynein move along microtubules, in most cases transporting their cargo in opposite directions along the tubule. Together, these tiny molecular motors make sure that everything is in the right place at the right time.

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  Microtubules    (  ePub Version)


Microtubules are the railways of the cell. They are huge, sturdy filaments that extend through the cytoplasm, providing support and providing tracks for the motion of two types of protein motors: kinesin and dynein. These motors pull many types of cargo through the cell, ranging from small vesicles to entire mitochondria. They also play a starring role in the process of cell division, separating the duplicated chromosomes into two daughter cells.

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  GFP-like Proteins    (  ePub Version)

GFP-like Proteins

Twenty years ago, green fluorescent protein (GFP) was first used to reveal the location of proteins inside living cells, and since then, it has emerged as an invaluable tool for cell biologists. GFP is a small, stable, and brightly fluorescent protein. A gene encoding GFP can be added to a cell and used to synthesize GFP, which then creates its own internal chromophore that fluoresces when illuminated with ultraviolet light, without consuming cellular energy. And perhaps most importantly, GPF can be fused to another protein without perturbing its normal function, creating a highly visible tag that allows the protein of interest to be tracked throughout the cell.

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  Aquaporin    (  ePub Version)


Cell membranes are fairly waterproof, forming a barrier that resists the crossing of water molecules. Some cells, however, need to allow more water to flow through the membrane. For instance, the concentration of wastes in the kidneys and the internal pressure of the eye involve careful control of water. In these cases, cells use aquaporins to control the flow of water in and out of the cell.

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  RecA and Rad51    (  ePub Version)

RecA and Rad51

Breakage of DNA is bad news, so cells have powerful methods to fix damaged DNA. One method trims the broken ends and then reconnects them back together. This is fast and easy, but has the disadvantage of possibly incorporating errors during the repair. Cells also have a more accurate method to repair breaks that relies on duplicate copies of the genome. This process is called homologous recombination, and rebuilds the damaged areas using an intact copy as a template.

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  Neurotransmitter Transporters    (  ePub Version)

Neurotransmitter Transporters

Nerve cells communicate with one another in two ways. Some neurons send an electrical signal directly to their neighbors, which is very fast. Most neurons, however, use chemical signals to transmit their messages, releasing small neurotransmitter molecules that are recognized by receptors on neighboring neurons. Neurotransmitters have two important advantages: since thousands of molecules are released, they amplify the signal, and since many different types of neurotransmitters are used, they can encode a variety of different types of signals.

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  Broadly Neutralizing Antibodies    (  ePub Version)

Broadly Neutralizing Antibodies

Viruses like HIV and influenza have evolved sneaky methods for evading our immune system. The immune system searches for foreign molecules, but several viruses have found ways to hide their unique parts and masquerade as normal human molecules. They do this in many ways. As viral surface glycoproteins are synthesized in infected cells, they are decorated with the same sugar chains that coat human proteins, providing an effective camouflage. The conserved functional sites of the viral protein are hidden deep in a pocket surrounded by these sugars, and thus are difficult for antibodies to reach. In addition, these viruses have error-prone replication machinery, which creates a great diversity in the viral glycoproteins. So unfortunately, once the immune system has found antibodies to recognize the infecting virus, other viruses rapidly mutate to change the site that is recognized.

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  HIV Envelope Glycoprotein    (  ePub Version)

HIV Envelope Glycoprotein

Viruses are faced with a tricky problem: they need to get inside cells, but cells are surrounded by a protective membrane. Enveloped viruses like HIV and influenza, which are themselves surrounded by a similar membrane, solve this problem by fusing with the cell membrane. The envelope glycoprotein (Env) of HIV performs the many complex steps needed for membrane fusion. First, it attaches itself to proteins on the surface of the cell. Then, it acts like a spring-loaded mousetrap and snaps into a new conformation that drags the virus and cell close enough that the membranes fuse. Finally, the HIV genome is released into the cell, where it quickly gets to work building new viruses.

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  DNA Helicase    (  ePub Version)

DNA Helicase

Our genetic information is safely locked up inside the double helix of DNA. In order to use this information, the helix must be unwound to expose the bases, allowing polymerases access to build complementary DNA or RNA strands. Unwinding of DNA is trickier than you might expect. The interaction between bases is quite strong and there are many, many of them, so it takes appreciable energy to separate the strands. This is the job of DNA helicases: they are enzymes that pull apart the two strands in a DNA double helix.

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  SNARE Proteins    (  ePub Version)

SNARE Proteins

Small membrane-enclosed vesicles are used like cargo trucks to deliver proteins and other molecules inside and outside of cells. When these vesicles reach their proper destination, they fuse with a membrane and deliver their cargo. For instance, vesicles are used inside cells to transport digestive enzymes from the Golgi to their final location in lysosomes. They are also used to deliver molecules out of the cell: for example, neurotransmitters are released from vesicles that fuse with the cell membrane at nerve synapses. The 2013 Nobel Prize was awarded to three researchers who have revealed the central molecular machinery for this process of vesicle fusion.

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  Proteasome    (  ePub Version)


Proteasomes are the cell's protein recyclers. Proteins need to be destroyed for many reasons: they may be damaged, or they may be part of an invading virus, or they simply may not be needed any more. Proteasomes provide a controlled method for breaking down proteins safely within the environment of the cell. They chop obsolete or damaged proteins into small pieces, about 2 to 25 amino acids in length. Most of these are then completely broken down into amino acids by peptidases in the cell.

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  Designed Protein Cages    (  ePub Version)

Designed Protein Cages

Scientists are great tinkerers, and surprisingly, proteins can often be used like tinkertoys. The proteins found in cells have evolved to have a stable, folded structures. Scientists are now building on these stable proteins and making changes to engineer new functions. These functions include designing new enzymes, designing proteins with improved medicinal properties, and designing large complexes with a desired shape and size.

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  Ricin    (  ePub Version)


Ricin is one of the most deadly toxins that has been discovered. A single molecule can kill an entire cell. It's also a very common toxin. It's made by the castor bean plant, which can be found in gardens and wild areas around the world and is widely grown for the oil it produces. The seeds are laced with the toxin: about 8 beans can provide a lethal dose.

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  HIV Capsid    (  ePub Version)

HIV Capsid

Viruses come in many shapes and sizes, ranging from simple protein shells filled with RNA or DNA to membrane-enveloped particles that rival cells in complexity. HIV is one of these complex viruses, surrounded by a membrane and filled with a diverse collection of viral and cellular molecules. The genome of HIV, which is composed of two strands of RNA, is packaged inside a distinctive cone-shaped capsid, which protects the RNA and delivers it to the cells that HIV infects.

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  Serotonin Receptor    (  ePub Version)

Serotonin Receptor

Are you feeling happy today? Are you feeling hungry? Do you get migraines? All of these behaviors, and many more, are controlled in part by the neurotransmitter serotonin. Serotonin, a small molecule made from the amino acid tryptophan, was discovered for its role in the constriction of blood vessels. Most of the serotonin in your body is found in the digestive system where it helps to control the motions needed for digestion. However, the most dramatic effects of serotonin are in the brain. Less than one in a million neurons uses serotonin for communication, but these neurons help to control our emotions, moods and thoughts.

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  Dermcidin    (  ePub Version)


Bacteria are a constant threat, so our bodies have many defenses to protect us from infection. One of our first lines of defense is a collection of small peptides, termed antimicrobial peptides, that are secreted from our cells. These peptides are toxic to a broad spectrum of bacteria, binding to their membranes and disrupting their function.

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  Actinomycin    (  ePub Version)


Cells are master chemists, and many times the search for medical compounds begins by looking to nature. Many antibiotics have been found by studying the constant warfare between bacteria and fungi, and isolating the toxic molecules that they build to protect themselves. Actinomycin is the first natural antibiotic discovered that has anti-cancer activity. It was discovered in the bacterium Streptomyces antibioticus in 1940. Unfortunately, it is too toxic for general use, killing cancer cells but also poisoning the patient, but related molecules have subsequently been discovered, and are now widely used for cancer chemotherapy.

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  Erythrocruorin    (  ePub Version)


Hemoglobin comes in many shapes and sizes. In our blood, a hemoglobin with four chains carries oxygen from the lungs to cells throughout the body. Some plants build a single-chain hemoglobin to help protect sensitive nitrogen-fixing bacteria from oxygen, similar to the single chain myoglobin that stores oxygen in our muscle cells. Some bacteria also make simple forms of hemoglobin to help manage oxygen and other small molecules. Earthworms, however, are the champions when it comes to building huge hemoglobins. They, and a few other types of invertebrate animals, build enormous complexes of hemoglobin to carry their oxygen, termed erythrocruorins.

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  Proton-Gated Urea Channel    (  ePub Version)

Proton-Gated Urea Channel

The acid in your stomach helps to digest food, but it also helps protect you from bacterial infection. However, one type of bacteria, Helicobacter pylori, is able to live in the acidic environment of the stomach. It is one of the most common bacterial infections, found worldwide in half of the population. It causes a continued inflammation of the stomach, which leads in some cases to stomach ulcers and stomach cancer.

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  Transfer-Messenger RNA    (  ePub Version)

Transfer-Messenger RNA

Damaged messenger RNA poses a double danger to cells. If a messenger RNA is truncated, it will be missing its stop codon, so it will encode a faulty, truncated protein. Also, ribosomes get stalled at the end of these truncated messages and are unable to release the mRNA and move on to the next protein synthesis job. Bacteria possess an ingenious molecular method for solving both of these problems at the same time, that destroys the faulty protein and releases the ribosome all at once.

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  ABO Blood Type Glycosyltransferases    (  ePub Version)

ABO Blood Type Glycosyltransferases

Researchers have discovered that blood comes in several types, which define groups of people with compatible blood. The ABO system defines one of the major types determining groups of people who can donate blood to each other.

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  Vitamin D Receptor    (  ePub Version)

Vitamin D Receptor

Vitamins are exotic molecules that are essential for the proper function of cells, but somewhere along the process of evolution, our bodies have lost the ability to make them. So instead, we need to obtain them in our diet, or in a daily multivitamin tablet. These include vitamin A, which is used to build the light sensors in our eyes, a host of B vitamins used to build specialized tools for chemical reactions, and vitamin C, which plays an essential role in construction of collagen. Vitamin D is an exceptional case: our cells can make it, but only if there is enough sunlight.

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  Citric Acid Cycle    (  ePub Version)

Citric Acid Cycle

The citric acid cycle, also known as the Krebs cycle or the tricarboxylic acid cycle, is at the center of cellular metabolism, playing a starring role in both the process of energy production and biosynthesis. It finishes the sugar-breaking job started in glycolysis and fuels the production of ATP in the process. It is also a central hub in biosynthetic reactions, providing intermediates that are used to build amino acids and other molecules.

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  Pyruvate Dehydrogenase Complex    (  ePub Version)

Pyruvate Dehydrogenase Complex

A combination of crystallography, NMR spectroscopy and electron microscopy is revealing the secrets of pyruvate dehydrogenase complex. The complex performs a central step in energy production, catalyzing the reaction that links glycolysis with the tricarboxylic acid cycle. The reaction is performed in three separate steps by three separate enzymes, but all three enzymes are linked efficiently together into one large multienzyme complex.

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  cAMP-dependent Protein Kinase (PKA)    (  ePub Version)

cAMP-dependent Protein Kinase (PKA)

Phosphate groups are perfect chemical groups for modifying the function of proteins: they have a strong negative charge, they are fairly bulky, and they can form multiple hydrogen bonds. When a phosphate group is attached or removed to a protein, it may modify the shape and flexibility of the protein chain, or provide a readily-visible handle for recognition by other proteins. Cells take full advantage of these possibilities, and in a typical cell, phosphate groups are used to regulate the function of about one third of their proteins.

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  Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)    (  ePub Version)

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

Cells are great recyclers. They need to be, otherwise we would be faced with an insurmountable need for new molecular building blocks and enough energy to manage them. For instance, new messenger RNA chains are made constantly, transmitting information from the nucleus to build new proteins. Afterwards, these chains are broken down and the components are recycled. A complex set of salvage machinery is used to recycle these components.

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  Sliding Clamps    (  ePub Version)

Sliding Clamps

In our genome, it takes thousands of DNA nucleotides to encode the information for each protein, and even more to store all the regulatory information. So, when a cell needs to copy this information, it has to manage long, long stretches of DNA. As you might imagine, this is not easy in the chaotic environment of the cell.

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  Leptin    (  ePub Version)


The delivery of nutrients to cells throughout the body is controlled by a complex network of signaling molecules. Some of these signals happen without us really noticing, for instance, when insulin and glucagon control the level of glucose that is delivered through the blood after we eat. The signaling protein leptin, however, has a more apparent effect, acting within the system that makes us hungry when we need food.

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  Ras Protein    (  ePub Version)

Ras Protein

Cells are constantly sending messages, discussing nutrient levels and growth rates with other cells, and also managing the internal needs of the cell. These messages need to be clear and strong, so that they can be heard over the busy bustle inside the crowded cytoplasm. One way to strengthen signals is to link them to a process that is chemically irreversible, like the cleavage of ATP or GTP.

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  Rhodopsin    (  ePub Version)


Our eyes are biological cameras, complete with a deformable lens to focus light, an adjustable iris to control the exposure, and a retina that acts like a digital sensor to record the focused image. It is filled with amazing refinements, such as a layer of dark black cells behind the retina that reduce reflection and keep the image sharp. Rhodopsin plays the central role in this camera: it is the molecule that senses light.

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  Aminoglycoside Antibiotics    (  ePub Version)

Aminoglycoside Antibiotics

The discovery of streptomycin in 1944 provided the first effective treatment for tuberculosis. Ever since then, we have fought an escalating battle with bacteria using streptomycin and other aminoglycoside antibiotics. Researchers have discovered many natural aminoglycosides made by bacteria, and chemists have created entirely new antibiotics based on these effective natural defenses.

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  Messenger RNA Capping    (  ePub Version)

Messenger RNA Capping

In our cells, transcription is not just a simple process of reading DNA and building a complimentary RNA strand. Almost immediately after RNA polymerase begins, the cell is making changes. When the mRNA is only about 30 nucleotides long, the cell makes its first change: it connects a guanosine nucleotide to the end.

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  Complex I    (  ePub Version)

Complex I

Complex I, also known as NADH:quinone oxidoreductase, performs the first step in respiratory electron transport, the process that creates much of the energy that powers our cells. Complex I is a huge membrane-bound molecular machine that links two different reactions: the transport of electrons from NADH to ubiquinone, and the transport of protons across a membrane.

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  Toll-like Receptors    (  ePub Version)

Toll-like Receptors

The world is filled with bacteria and viruses, all eager to infect our cells. We have two lines of defense against this constant assault. Our first defense is the innate immune system, which stands guard against the most common attackers and mounts a quick defense when they are found. This innate system is found widely in animals, plants, and fungi, and for most, is the only line of defense. Vertebrate animals, however, have a second line of defense: the adaptive immune system. It is brought to bear if the problem is more severe, using custom-built antibodies and a powerful force of white blood cells to battle the invaders.

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  PDB Pioneers    (  ePub Version)

PDB Pioneers

Structural biology was born in 1958 with John Kendrew's atomic structure of myoglobin, and in the following decade, the field grew rapidly. By the early 1970's, there were a dozen atomic structures of proteins, and researchers were discovering that they had a goldmine of information.

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  O-GlcNAc Transferase    (  ePub Version)

O-GlcNAc Transferase

Cells use many methods to control their proteins, to make sure that they perform their jobs when and where they are needed. Some are brutally irreversible, such as the continuous breakdown of obsolete proteins by the ubiquitin/proteasome system. Others, such as the modulation of enzyme function by allosteric motions, are far more subtle and respond to the second-by-second needs of the cell. Often, chemical groups are added to amino acids in proteins to modulate their function. Phosphate groups are a familiar example: they are widely used to turn signaling proteins on and off, controlled by a diverse collection of kinases and phosphatases that add and remove these regulatory phosphate groups.

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  Rhomboid Protease GlpG    (  ePub Version)

Rhomboid Protease GlpG

Proteases, enzymes that cut protein chains, come in many shapes and sizes. The most familiar proteases, like trypsin and pepsin, are machines of destruction used to digest proteins in our diet. However, most of the proteases in our cells are used in a more delicate task. They regulate the action of other proteins by making specific cuts in their protein targets.

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  DNA Methyltransferases    (  ePub Version)

DNA Methyltransferases

Your body is built of skin cells, nerve cells, bone cells, and many other different types of cells. These cells are different shapes and sizes, and each type of cell builds a characteristic collection of proteins that are needed for its function. However, every cell in your body contains the same genetic information, encoded in strands of DNA. How does each cell decide which genes to use and which ones to ignore?

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  Glucansucrase    (  ePub Version)


We brush our teeth twice a day with fluoride toothpaste, use mouthwash, limit sugars in our diet...and we still get cavities. Cavities are caused by bacteria that consume some of the sugar in our diet, ferment it, and then release acids. These acids eat away at the hard minerals in our teeth. It seems like it would be easy to brush these bacteria away, and get rid of them once and for all. However, they have a trick to avoid this.

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  Cytochrome bc1    (  ePub Version)

Cytochrome bc1

Cells are masters at squeezing every drop of energy out of their food. They disassemble the molecules in food atom by atom, driving a variety of unusual energy transformations in the process. At the end, all of the hydrogen atoms have been separated from the food molecules and are used to turn the rotary motor of ATP synthase. To do this, the electrons are stripped from these hydrogen atoms and used to power huge protein pumps that transport protons across a membrane. These protons then power the rotation of ATP synthase as they return to their original positions.

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  Nanobodies    (  ePub Version)


Nature is full of exceptions, and sometimes they turn out to be exceptionally useful. In 1993, researchers discovered that camels, dromedaries and llamas have unusual antibodies composed of a single type of protein chain. Later, similar single-chain antibodies were discovered in sharks. This would have been just another biological oddity, but it turns out that these unusual molecules hold the key to better tools for biotechnology and medicine.

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  Integrase    (  ePub Version)


Retroviruses, such as HIV, are particularly insidious. Most viruses infect a cell, force it make many new copies of the virus, and then leave when the cell is used up. Retroviruses, however, take a long-term approach to infection. They enter cells and build a DNA copy of their genome.

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  Integrin    (  ePub Version)


Our bodies are composed of approximately ten trillion cells, which poses challenging problems for structure and communication. All of these cells must be connected strongly together, to allow us to stand and walk. The infrastructure holding us together, however, must also be malleable enough to allow repairs, to allow us to heal from wounds. These many cells must also communicate with each other, ensuring that each plays its own proper part. Many different molecules in our bodies are involved in this complex infrastructure of support and communication, and integrins play a central role.

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  Nitric Oxide Synthase    (  ePub Version)

Nitric Oxide Synthase

Nitroglycerin is a powerful explosive, detonating when exposed to heat or pressure. The same molecule, however, can save your life if you're experiencing a heart attack. A small dose of nitroglycerin will slowly break down and release nitric oxide (NO), which then spreads to the muscle cells surrounding blood vessels, telling them to relax. The curative properties of nitroglycerin have been used in this way for over a century, but scientists have only recently revealed how NO performs its job.

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  Adenovirus    (  ePub Version)


Viruses are one of the most dangerous enemies to our health, attacking cells and causing deadly diseases like AIDS and influenza. However, scientists are currently discovering ways to trick viruses into improving our health instead of causing disease. Adenovirus is one of the viruses being used in this work. It is found around the world, but it usually causes only mild disease when it infects cells. It can be life-threatening, however, in infants or people with weakened immune systems. Modified forms of the virus are being developed to cure genetic diseases, to fight cancer, and to deliver vaccines.

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  Inteins    (  ePub Version)


In most cases, each gene encodes a single protein, but cells have found ways around this limitation. Viruses, with their tiny genomes, often contain genes that encode long polyproteins, which are then chopped into a bunch of functional pieces by enzymes. Inteins are another way that cells make several proteins from one gene.

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  Riboswitches    (  ePub Version)


Why use two or more molecules when one will do? In our own cells, protein synthesis is controlled by thousands of regulatory proteins, which work together to decide when a particular protein will be made. Bacteria are masters of economy, however, and in some cases, they have figured out a way for messenger RNA to control itself, without the need for help by proteins.

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  Isocitrate Dehydrogenase    (  PDF 2.8 MB,   ePub Version)

Isocitrate Dehydrogenase

Sugar tastes great. This should be no surprise, though, since glucose is the central fuel used by oxygen-breathing organisms. Sugar is broken down in the central catabolic pathways of glycolysis and the citric acid cycle, and ultimately used to construct ATP. The enzymes in these pathways systematically break down glucose molecules into their component parts, capturing the energy of disassembly at each step. Isocitrate dehydrogenase performs the third reaction in the citric acid cycle, which releases one of the carbon atoms as carbon dioxide. In the process, two hydrogens are also removed. One of these, in the form of a hydride, is transferred to the carrier NAD (or NADP), and will be used later to power the rotation of ATP synthase.

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  Interferons    (  PDF 2.3 MB,   ePub Version)


Our cells have many defenses against viruses. When cells are infected, they build enzymes t hat slow protein synthesis, and thus also slow down viral growth, and they build enzymes to chop up double-stranded RNA, which is made primarily by viruses. Infected cells also alert the immune system by displaying pieces of the virus on their surfaces. In the worst cases, infected cells make the ultimate sacrifice and destroy themselves by apoptosis.

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  Crystallins    (  PDF 1.8 MB,   ePub Version)


As you read this Molecule of the Month, the light from the page is being focused in your eyes by a concentrated solution of crystallin proteins. The lenses in your eyes are built of long cells that, early in their development, filled themselves with crystallins and then made the major sacrifice, ejecting their nuclei and mitochondria and leaving only a smooth, transparent solution of protein. We then rely on these proteins to see for the rest of our lives.

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  Epidermal Growth Factor    (  PDF 2.1 MB,   ePub Version)

Epidermal Growth Factor

The cells in your body constantly communicate with each other, negotiating the transport and use of resources and deciding when to grow, when to rest, and when to die. Often, these messages are carried by small proteins, such as epidermal growth factor (EGF), shown here in red from PDB entry 1egf. EGF is a message telling cells that they have permission to grow. It is released by cells in areas of active growth, then is either picked up by the cell itself or by neighboring cells, stimulating their ability to divide. The message is received by a receptor on the cell surface, which binds to EGF and relays the message to signaling proteins inside the cell, ultimately mobilizing the processes needed for growth.

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  Parvoviruses    (  PDF 3.6 MB,   ePub Version)


Viruses are finely tuned to perform their deadly job. Many viruses are highly specific: they infect only a particular animal or plant, and may even only infect a few types of cells within their preferred hosts. However, viruses occasionally cross the line, and gain the ability to infect other hosts. This is often termed viral emergence, and has been sensationalized as a major threat to global health in books such as The Hot Zone. Fortunately, this type of switching occurs only rarely, but when it does, it can be a disaster.

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  Concanavalin A and Circular Permutation    (  PDF 2.2 MB,   ePub Version)

Concanavalin A and Circular Permutation

Evolution is a great tinkerer: once a successful plan is found, it is used again and again, often with many changes and improvements. This is easily seen in the living things around us. Most mammals have four limbs, which have evolved into all manner of arms and legs, and even into flippers and wings. Most plants are covered with leaves, which range from spiny needles to huge jungle fronds. Looking at protein sequences and structures, we see the same diversity generated through variation.

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  P-glycoprotein    (  PDF 2.8 MB,   ePub Version)


Our environment is filled with toxic substances that attack our molecular machinery. Our cells protect themselves from these dangers in many ways. In some cases, they use enzymes to convert them into harmless compounds. In other cases, they sequester them safely out of the way. For others, cells build specialized pumps that find toxins and eject them outside, for safe disposal.

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  Enhanceosome    (  PDF 2.1 MB,   ePub Version)


Take a moment to ponder the form of your body: the shape of your face, the color of your eyes, the length of your fingers, the perfect articulation of your bones and muscles, the way your hair grows curly or straight. Now let your imagination travel inward, and think of the complex shapes and functions of your different cells, and the teeming molecular world inside each one. Remarkably, this amazing structure and form and function is specified by information in the genome, which encodes a mere 20,000-25,000 protein-coding genes. One of the great puzzles being pieced together by scientists is the mechanism by which these genes, and the methods used to control their expression, specify all of these different aspects of life.

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  Ribosome    (  PDF 2.9 MB,   ePub Version)


Ribosomes are one of the wonders of the cellular world, and one of the many wonders you can explore yourself at the RCSB PDB. In 2000, structural biologists Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath made the first structures of ribosomal subunits available in the PDB, and in 2009, they each received the Nobel Prize for this work. Structures are also available for many of the other players in protein synthesis, including transfer RNA and elongation factors. Building on these structures, there are now hundreds of structures of entire ribosomes in the PDB, revealing the atomic details of many important steps in protein synthesis.

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  Antifreeze Proteins    (  PDF 1.4 MB,   ePub Version)

Antifreeze Proteins

Ice is a big problem for organisms that live in cold climates. Once the temperature dips below freezing, ice crystals steadily grow and burst cells. This danger, however, has not limited the spread of life on Earth to temperate regions. Organisms of all types--plants, animals, fungi and bacteria--have developed ways to combat the deadly growth of ice crystals. In some cases, they pack their cells with small antifreeze compounds like sugars or glycerol. But in cases where extra help is needed, cells make specialized antifreeze proteins to protect themselves as the temperature drops.

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  Designed DNA Crystal    (  PDF 3.4 MB,   ePub Version)

Designed DNA Crystal

DNA is a perfect raw material for constructing nanoscale structures. Since base-pairing has been selected by evolution to be highly specific, it is easy to design sequences that will link up with their proper mates. In this way, we can treat small pieces of DNA like Tinkertoys, designing individual components and then allowing them to assemble when we put them together. In addition, the chemistry of DNA synthesis has been completely automated, so custom pieces of DNA can be easily constructed, or even ordered from commercial biotech companies. This puts DNA nanotechnology in the hands of any modest laboratory, and many laboratories have taken advantage of this, creating nanoscale scaffolds, tweezers, polyhedra, computers, and even tiny illustrations composed entirely of DNA.

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  Sodium-Potassium Pump    (  PDF 2.4 MB,   ePub Version)

Sodium-Potassium Pump

Our bodies use a lot of energy. ATP (adenosine triphosphate) is one of the major currencies of energy in our cells; it is continually used and rebuilt throughout the day. Amazingly, if you add up the amount of ATP that is built each day, it would roughly equal the weight of your entire body. This ATP is spent in many ways: to power muscles, to make sure that enzymes perform the proper reactions, to heat your body. The lion's share, however, goes to the protein pictured here: roughly a third of the ATP made by our cells is spent to power the sodium-potassium pump.

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  Xanthine Oxidoreductase    (  PDF 2.7mb,   ePub Version)

Xanthine Oxidoreductase

Our diet includes a wide variety of different molecules. Many of these molecules are broken down completely and used to generate the metabolic energy that powers our cells. Others are disassembled piece-by-piece and recycled to build our own proteins and nucleic acids. The ones that are left over are broken down and discarded. Xanthine oxidoreductase, shown here from PDB entry 1fo4, is the last stop for extra purine nucleotides (ATP and GTP) in our cells. Purines are broken down in several steps, ultimately yielding uric acid, which is excreted from the body.

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  Sulfotransferases    (  PDF 2.4 MB,   ePub Version)


Cells are master chemists. They perform all manner of chemical reactions to build and modify their molecules. One of the chemical tricks used by many cells is to add sulfuryl groups to a molecule. Under typical cellular conditions, sulfuryl groups carry a negative charge, and they have lots of oxygen atoms that accept hydrogen bonds from other molecules. This makes sulfurylated molecules much more soluble and easy to recognize. To build molecules with sulfuryl groups, cells use a diverse collection of sulfotransferases. These enzymes take a sulfuryl group from the convenient carrier molecule PAPS (3'-phosphoadenosine-5'-phosphosulfate), and transfer it to the target molecule.

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  beta-Secretase    (  PDF 1.7 MB,   ePub Version)


Many of our proteins need to be shaped, folded and trimmed after they are made, to coax them into their proper functional form. A variety of specialized chaperones and proteases perform these tasks. Occasionally, however, these chaperones and proteases make mistakes that can have life-threatening consequences.

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  Vaults    (  PDF 4.6 MB,   ePub Version)


Our cells are filled with compartments, each performing a specific function. Some of these compartments, such as mitochondria and lysozomes, are very large and enclose many different molecular machines. Other intracellular compartments are smaller, such as the transport vesicles that shuttle proteins from site to site inside the cell. Most of these compartments, including mitochondria, lysozomes and transport vesicles, are surrounded by membranes. However, in special cases, cells build smaller compartments surrounded by a protein shell. In our own cells, vaults are a spectacular example of these protein-enclosed compartments.

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  Influenza Neuraminidase    (  PDF 436 KB,   ePub Version)

Influenza Neuraminidase

Influenza virus is continually changing and every decade or so, a dangerous new strain appears and poses a threat to public health. This year, there has been an outbreak of a new strain of H1N1 flu, more commonly known as swine flu. The H1N1 designation refers to the two molecules that cover the surface of the virus: hemagglutinin and neuraminidase. Together, these two molecules control the infectivity of the virus. Hemagglutinin plays the starring role as the virus approaches a cell, binding to polysaccharide chains on the cell surface and then injecting the viral genome into the cell. Neuraminidase, on the other hand, plays its major role after the virus leaves an infected cell. It ensures that the virus doesn't get stuck on the cell surface by clipping off the ends of these polysaccharide chains.

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  Oct and Sox Transcription Factors    (  PDF 1.9 MB,   ePub Version)

Oct and Sox Transcription Factors

The development of a complete human being from a single cell is one of the great miracles of life. A human egg cell contains about 30,000 genes that encode proteins, and of these, about 3,000 of these genes encode transcription factors. Transcription factors determine when genes will be turned on and turned off, orchestrating the many processes involved in the development of an embryo and the many tasks performed by each cell after a child is born. Amazingly, there is only about 1 transcription factor for every 10 genes, posing a puzzle: how does this limited set of proteins control the many genes and processes that must be regulated?

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  Hydrogenase    (  PDF 2.5 MB,   ePub Version)


Hydrogen gas is an unusual substance. Normally, it is stable and must be coaxed with powerful catalysts to enter into chemical reactions. But when mixed with oxygen, a tiny spark will set off an explosive chain reaction. Hydrogen gas holds great promise to be the greenest of green energy sources. It has many advantages: compared with many fuels, it releases a lot of energy for its weight, and the reaction forms only energy and pure water. It has substantial disadvantages, however. It is dangerous to store, and it is difficult to perform the reaction in a controlled, non-explosive manner. Currently, the fuel cells being developed for use in hydrogen-powered vehicles use costly platinum catalysts to perform this reaction. Researchers are now looking to nature for other alternatives.

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  Auxin and TIR1 Ubiquitin Ligase    (  PDF 1.9 MB,   ePub Version)

Auxin and TIR1 Ubiquitin Ligase

Plants, like animals, have hormones that deliver chemical messages between distant cells. Charles Darwin and his son discovered this over a century ago--they noticed that if they shined a light on the tips of grass shoots, the stems bend to bring the entire shoot towards the light. Somehow, a message was being sent from the tip down to the stem. You might also have observed the action of hormonal signals in plants: when you prune a tree to make it more bushy, you are modifying the traffic of plant hormones. Both of these effects are caused by the phytohormone auxin.

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  Tobacco Mosaic Virus    (  PDF 556 KB,   ePub Version)

Tobacco Mosaic Virus

Tobacco mosaic virus (TMV) has been at the center of virus research since its discovery over a hundred years ago. TMV was the first virus to be discovered. Late in the 19th century, researchers found that a tiny infectious agent, too small to be a bacterium, was the cause of a disease of tobacco plants. It then took 30 years of work before the nature of this mysterious agent became apparent. In a Nobel-prize-winning study, Wendell Stanley coaxed the virus to form crystals, and discovered that it was composed primarily of protein. Others quickly discovered that there was also RNA in the virus. Then, many prominent structural researchers (including J. D. Bernal, Rosalind Franklin, Ken Holmes, Aaron Klug, Don Caspar, and Gerald Stubbs) used X-ray diffraction and electron microscopy to probe the structure of the virus.

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  Hsp90    (  PDF 352 KB,   ePub Version)


When cells are challenged with extreme heat, they build a collection of protective proteins called heat shock proteins (typically abbreviated as "Hsp" with the approximate molecular weight afterwards). Many of these proteins are chaperones that work to keep cellular proteins folded and active when conditions get bad. They also play important roles in the normal life of the cell, helping proteins fold and limiting the dangerous aggregation of immature proteins. Some of these proteins, such as Hsp70 and Hsp60 are general chaperones. Hsp90, on the other hand, plays a more specific role.

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  Mechanosensitive Channels    (  PDF 440 KB,   ePub Version)

Mechanosensitive Channels

We are remarkably resistant to changes in our surrounding environment. Our bulky bodies allow us to weather extremes of heat and cold, and our skin protects us if we go for a swim in fresh water or salty water. If things get too uncomfortable, we can always get up and walk away, finding a warmer or cooler or drier place. Bacteria don't have as many options. They are tiny and they are immersed in water, so changes in the environment can pose life-threatening challenges. For instance, if it rains they may be suddenly surrounded by fresh water. This is dangerous because the water seeps into the cell through osmosis and increases the pressure inside. At other times, the bacterium may be shifted suddenly to salty conditions, which pulls water out and dehydrates the cell. Bacteria have methods for resisting these changes, so they can keep a steady, comfortable osmotic pressure inside.

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  Poly(A) Polymerase    (  PDF 396 KB,   ePub Version)

Poly(A) Polymerase

Most of the RNA found in our cells is built using our DNA genome as a template. In special cases, however, our cells also build RNA strands without a template. For instance, the end of (almost) every messenger RNA strand is composed of a long string of repeated adenosine nucleotides. These long poly(A) tails are not encoded in the genome. Instead, they are added after RNA polymerase finishes its normal process of transcription. After RNA polymerase releases the RNA strand, other enzymes add the finishing touches, editing out introns, adding a cap to the front end, and building the long poly(A) tail at the other end.

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  Ribonuclease A    (  PDF 284 KB,   ePub Version)

Ribonuclease A

Ribonuclease A is the enzyme that digests RNA in our food. Because is it small, stable, and easily purified, ribonuclease has been an important enzyme in biochemical research. It was used by Christian Anfinsen to prove that the sequence of amino acids determines the structure of a folded protein and it was used by Stanford Moore and William Stein to show that a specific arrangement of amino acids is used in the catalytic center of enzymes. Ribonuclease A was also the first enzyme synthesized by R. Bruce Merrifield, showing that biological molecules are simply chemical entities that may be constructed artificially. All of these central concepts, discovered with the help of ribonuclease, were awarded Nobel Prizes.

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  Selenocysteine Synthase    (  PDF 280 KB,   ePub Version)

Selenocysteine Synthase

If you have visited your local health food store or looked closely at the ingredients in your daily multivitamin, you may have noticed that the element selenium is often listed as one of the beneficial supplements. Selenium is a double-edged sword, however. In general, selenium compounds are toxic and have an unpleasant garlicy odor, but in trace amounts, selenium is essential for our health. Selenium atoms are similar to sulfur atoms, with similar properties, except that selenium compounds tend to be more reactive. In a few specialized proteins, this extra reactivity is just what is needed. For instance, by using a selenium atom instead of sulfur, thioredoxin reductase improves its rate of catalysis by 100 times, and formate dehydrogenases act 300 times faster.

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  Dengue Virus    (  PDF 332 KB,   ePub Version)

Dengue Virus

Dengue virus is a major threat to health in tropical countries around the world. It is limited primarily to the tropics because it is transmitted by a tropical mosquito, but even with this limitation, 50-100 million people are infected each year. Most infected people experience dengue fever, with terrible headaches and fever and rashes that last a week or two. In some cases, however, the virus weakens the circulatory system and can lead to deadly hemorrhaging. Researchers are now actively studying the virus to try to develop drugs to cure infection, and vaccines to block infection before it starts.

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  Lactate Dehydrogenase    (  PDF 396 KB,   ePub Version)

Lactate Dehydrogenase

Lactate dehydrogenase is a safety valve in our pipeline of energy production. Most of the time, our cells break down glucose completely, releasing the carbon atoms as carbon dioxide and the hydrogen atoms as water. This requires a lot of oxygen. If the flow of oxygen is not sufficient, however, the pipeline of energy production gets stopped up at the end of glycolysis. Lactate dehydrogenase is the way that cells solve this problem, at least temporarily.

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  Prions    (  PDF 356 KB,   ePub Version)


Prions are proteins that can adopt two different forms, a normal form and a misfolded form. This may not seem unusual, since many proteins are flexible and adopt different shapes. However, prions have another unusual characteristic: the misfolded form of the prion can force normal prions to change into the misfolded shape. In this way, a few misfolded prions can corrupt a whole population of normal prions, converting them one-by-one into the misfolded shape. This can have deadly consequences, as the levels of misfolded proteins build up. For instance, misfolding of the PrP prion causes fatal neural diseases in humans and other mammals. To make things worse, misfolded prions are infectious, so a small dose of misfolded prions can infect and corrupt an entire organism.

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  Adrenergic Receptors    (  PDF 236 KB,   ePub Version)

Adrenergic Receptors

Our bodies have many built-in defenses. Our immune system prowls through the body looking for infections by viruses and bacteria. Our blood is filled with molecules that form clots at the first sign of damage. Our nervous system is also hard-wired with instinctive defenses that stand ready to protect us in times of danger. You have probably experienced one of these defenses yourself--when you are startled or scared by an impending danger, you will feel a rush of energy flowing through your body. This has been termed the "flight or fight" response--your body is mobilizing its many resources to make you ready either to run away from danger, or stay and fight.

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  Cadherin    (  PDF 688 KB,   ePub Version)


Your body is composed of trillions of cells, all working together to keep you alive. As you might imagine, this requires a massive infrastructure to hold everything together. This infrastructure is built at many levels. Huge structures, like bones and tendons, are built to support and move the entire body. Many of the spaces between cells are supported by connective tissue, which is built from a collection of sturdy molecular cables and sheets. Finally, an intimate, molecule-sized infrastructure is used to adhere cells directly to their neighbors.

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  Small Interfering RNA (siRNA)    (  PDF 1.2 MB,   ePub Version)

Small Interfering RNA (siRNA)

Double-stranded RNA is often a sign of trouble. Our transfer RNA and ribosomes do contain little hairpins that are double-stranded, but most of the free forms of RNA, messenger RNA molecules in particular, are single strands. Many viruses, however, form long stretches of double-stranded RNA as they replicate their genomes. When our cells find double-stranded RNA, it is often a sign of an infection, and they mount a vigorous response that often leads to death of the entire cell. However, plant and animal cells also have a more targeted defense that attacks the viral RNA directly, termed RNA interference.

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  Circadian Clock Proteins    (  PDF 1 MB,   ePub Version)

Circadian Clock Proteins

Our cells contain tiny molecular clocks that measure out a 24-hour circadian rhythm. This clock decides when we get hungry and when we get sleepy. This clock can sense when the days are getting longer and shorter, and then trigger seasonal changes. Our major clock is housed in a small region of the brain, called the suprachiasmic nuclei. It acts as our central pacemaker, checking the cycles of light and dark outside, and then sending signals to synchronize clocks throughout the rest of the body.

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  Oxidosqualene Cyclase    (  PDF 1.6 MB,   ePub Version)

Oxidosqualene Cyclase

Cholesterol has gained a bad reputation in recent years. It is absolutely essential in our lives: it is needed to keep our membranes fluid and it is the raw material used to build a host of important molecules such as vitamin D and steroid hormones. However, elevated levels of cholesterol (for instance from a fat-rich diet) have been linked to the formation of atherosclerosis and heart disease. Today, doctors suggest that a combination of a healthy low-fat diet and exercise will keep these two faces of cholesterol in balance.

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  Multidrug Resistance Transporters    (  PDF 1.2 MB,   ePub Version)

Multidrug Resistance Transporters

Ever since the discovery of penicillin, we have lived our lives with far less fear of infectious disease. In the decades since then, a wide variety of drugs have been isolated from natural sources or synthesized by chemists, giving our doctors a large arsenal of antibiotics to fight infection. Bacteria, however, are dynamic evolving organisms, and they have developed many methods to fight back. In some cases, they develop ways to destroy antibiotic drugs directly, for instance, some bacteria make beta-lactamase enzymes that break down penicillin. In other cases, the bacteria change their own molecular machinery, making it invulnerable to the drugs. For instance, methicillin-resistant Staphylococcus bacteria use new, resistant enzymes to build their cell walls. If these methods don't work, bacteria also have a more general method. They build special pumps that transport many different antibiotics out of the cell before they can do their job.

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  Superoxide Dismutase    (  PDF 836 KB,   ePub Version)

Superoxide Dismutase

We can't live without oxygen. Our cells rely on oxygen as the final acceptor of electrons in respiration, allowing us to extract far more energy from food than would be possible without oxygen. But oxygen is also a dangerous compound. Reactive forms of oxygen, such as superoxide (oxygen with an extra electron), leak from the respiratory enzymes and wreak havoc on the cell. This superoxide can then cause mutations in DNA or attack enzymes that make amino acids and other essential molecules. This is a significant problem: one study showed that for every 10,000 electrons transferred down the respiratory pathway in Escherichia coli cells, about 3 electrons end up on superoxide instead of the proper place. To combat this potential danger, most cells make superoxide dismutase (SOD, shown here from PDB entry 2sod), an enzyme that detoxifies superoxide.

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  Citrate Synthase    (  PDF 936 KB,   ePub Version)

Citrate Synthase

Your body burns up a lot of food every day. However, cells don't burn food like a fireplace. Instead, food molecules are combined with oxygen molecules one-by-one, in many carefully controlled steps. In this way, the energy that is released can be captured in convenient forms, like ATP or NADH, which are then used elsewhere to power essential cellular functions. Our cells get most of their energy from a long series of reactions that combine oxygen and glucose, forming carbon dioxide and water, and creating lots of ATP and NADH in the process.

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  Anabolic Steroids    (  PDF 1 MB,   ePub Version)

Anabolic Steroids

Athletes are constantly striving for better performance in their sports. Most athletes stay in top shape through a rigorous training program in fitness and nutrition, giving them the strength and stamina to push their bodies to the physical limit. But some athletes also look to biochemistry to improve their performance even further. There are many ways to give nature an artificial boost. For instance, some athletes artificially increase the number of red blood cells in their blood, either by injecting purified cells or by using the blood-stimulating hormone erythropoietin. The extra red blood cells carry more oxygen to their straining muscles than in normal blood, giving them an edge in endurance. Similarly, many male athletes use steroid hormones like testosterone to spur their muscles into growth far beyond what is normally possible, giving them the edge in strength. These methods are controversial and regarded by many to be unethical, and thus are generally banned from organized sporting events. However, the many drug testing scandals currently in the news show that these methods are still in widespread use.

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  Thymine Dimers    (  PDF 1.1 MB,   ePub Version)

Thymine Dimers

Summer is here, and we're all heading outdoors to enjoy the sun. But remember to take your sunscreen, since too much sunlight can damage your cells. Small doses of sunlight are needed to create vitamin D, but larger doses attack your DNA. Ultraviolet light is the major culprit. The most energetic and dangerous wavelengths of UV light, termed UVC, are screened out (at least for now) by the ozone in the upper atmosphere. However, the weaker UV light, termed UVA and UVB, passes through the atmosphere and is powerful enough to cause chemical changes in the DNA.

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  Fatty Acid Synthase    (  PDF 1.4 MB,   ePub Version)

Fatty Acid Synthase

Fat, these days, is a bad word. But we can't survive without fats, and more particularly, without fatty acids. Fatty acids are small molecules composed of a long string of carbon and hydrogen atoms, with an acidic group at one end. They are used for two essential things in your body. First, they are used to build the lipids that make up all of the membranes around and inside your cells. Second, fatty acids are a concentrated source of energy, so they are often connected to glycerol to form fats, which is a compact way to store energy until it is needed. But as we all know, if we eat too much, this extra fat can build up!

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  Aconitase and Iron Regulatory Protein 1    (  PDF 1.19 MB,   ePub Version)

Aconitase and Iron Regulatory Protein 1

Aconitase is an essential enzyme in the tricarboxylic acid cycle and iron regulatory protein 1 interacts with messenger RNA to control the levels of iron inside cells. You might ask: what do these two proteins have in common? They were discovered and studied by different researchers, who gave them names that described their two very different functions. But surprisingly, when they looked at the amino acid sequence of these proteins, they turned out to be identical. The same protein is performing two very different jobs.

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  Clathrin    (  PDF 1.16 MB,   ePub Version)


With its intricate meshwork of protein braids and alluring symmetry, clathrin is sure to seize your attention. It was named in the 1960s for its clathrate (lattice of bars) appearance in electron micrographs, and to this day, this beautiful molecule invokes intensive study. Like many proteins, clathrin represents a perfect case of form following function; it performs critical roles in shaping rounded vesicles for intracellular trafficking.

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  Zinc Fingers    (  PDF 1.3 MB,   ePub Version)

Zinc Fingers

As you are browsing through the proteins in the PDB, you may notice something: most proteins are big. They contain hundreds of amino acids, even though most of the work is often done by a few amino acids on one side. Why are proteins so big? One reason that proteins are so large is that they must self-assemble inside cells. Proteins are built as floppy chains that fold all by themselves (or with a little help from chaperones) into stable, compact structures. These folded structures are stabilized by hydrogen bonds, charge-charge interactions and hydrophobic forces between the different amino acids, which all line up like pieces in a jigsaw puzzle when the protein folds. A single hydrogen bond or a few charge pairs would not be enough, but a chain of hundreds of amino acids has hundreds of interactions that together glue the protein into a stable structure.

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  Exosomes    (  PDF 1.1 MB,   ePub Version)


Our genetic information is stored safely inside the nucleus of each cell. However, most of the action in a typical cell occurs outside the nucleus: proteins are built in the cytoplasm, energy is produced in the mitochondria, and interactions with the environment occur at the cell surface. So, the nucleus needs a way to communicate with the rest of the cell. RNA molecules perform this job. They are the messengers that deliver genetic information from the nucleus to places where it is needed for synthesis and control.

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  Importins    (  PDF 1 MB,   ePub Version)


Inside your cells, the process of protein synthesis is separated into two compartments. The first half of the job, when DNA is transcribed into RNA, is performed in the nucleus. The second half is then performed outside the nucleus, when ribosomes translate the RNA to construct proteins in the cytoplasm. This separation requires a continuous traffic of molecules: new RNA molecules must be transported out of the nucleus and nuclear proteins, such as newly-synthesized histones or polymerases, must be transported back into the nucleus. Huge tube-shaped nuclear pores act as the highway connecting the nucleus and the cytoplasm, and importins and exportins (collectively known as karyopherins) ferry molecules back and forth through the pore.

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  Transposase    (  PDF 865 KB,   ePub Version)


In the 1940's, Barbara McClintock discovered that the genome is a dynamic, changing place. She was studying maize, and she found that the beautiful mosaic colors of the kernels did not follow typical laws of inheritance. When she looked inside the cells, she found that the chromosomes changed shape, swapping pieces from one chromosome to the next. From this work, she found that the color changes were caused by the removal of a particular piece of DNA from the general area of the gene that caused the color, allowing the gene to be expressed and create pigments. She called this process transposition, where a piece of DNA is cut out of one place and pasted into another location.

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  Fibrin    (  PDF 712 KB,   ePub Version)


When you cut yourself, you bleed, but the bleeding rapidly stops. Blood has a built-in emergency repair system that quickly blocks any damage to the circulatory system, creating a temporary patch that allows time for more permanent repairs. Three basic mechanisms are at work. First, platelets (small fragments of blood cells that circulate in the blood) clump at the site of the wound, forming a weak plug. Second, neighboring blood vessels constrict, reducing the amount of blood flowing into the area. Finally, the protein fibrin assembles into a tough network that clots the blood and forms an insoluble blockage. Together, these methods stop the loss of blood and create a sturdy scab to protect the area as you heal.

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  Cytochrome p450    (  PDF 735 KB,   ePub Version)

Cytochrome p450

If you have a headache and take a drug to block the pain, you'll notice that the effects of the drug wear off in a few hours. This happens because you have a powerful detoxification system that finds unusual chemicals, like drugs, and flushes them out of your body. This system fights all sorts of unpleasant chemicals that we eat and breathe, including drugs, poisonous compounds in plants, carcinogens formed during cooking, and environmental pollutants. The cytochrome p450 enzymes are our first line of defense in this chemical battle.

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  Elongation Factors    (  PDF 1.4 MB,   ePub Version)

Elongation Factors

At first glance, we might think that cells are primarily protein synthesis factories. Over half of the molecular machinery in a typical bacterial cell is dedicated to building new proteins. These include the DNA and messenger RNA, which provide the instructions, transfer RNA, which performs the translation of this information, and ribosomes, which do the major construction work. Protein synthesis also requires a flurry of protein factors to orchestrate each step. These include initiation factors that get it all started, release factors that finish each chain, and elongation factors that assist the many steps between the beginning and the end.

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  AAA+ Proteases    (  PDF 1.3 MB,   ePub Version)

AAA+ Proteases

How would you make a protein cutting machine that would be safe to use inside a cell? Digestive proteases like trypsin and pepsin are small and efficient–they diffuse up to proteins and start cutting. This would never work inside a cell. The cell needs to have more control, so that only obsolete or damaged proteins are destroyed. The AAA+ proteases are one solution to this problem. They use two tricks to ensure that only certain proteins are destroyed. First, they hide the protein destruction machinery inside a closed container, and second, they use a special protein pump to feed proteins into this destruction chamber.

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  Amyloid-beta Precursor Protein    (  PDF 866 KB,   ePub Version)

Amyloid-beta Precursor Protein

Like Dr. Jekyll and Mr. Hyde, some seemingly innocent proteins have evil alter egos. The amyloid-beta precursor protein is an important example. It is a large membrane protein that normally plays an essential role in neural growth and repair. However, later in life, a corrupted form can destroy nerve cells, leading to the loss of thought and memory in Alzheimer's disease.

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  Luciferase    (  PDF 904 KB,   ePub Version)


Do you remember the first time that you saw a firefly? If you live anywhere between the Rocky Mountains and the east coast of the US, you have probably chased fireflies since you were a child. If you live in other parts of the world, like me, you may have had the pleasure of discovering fireflies during a summer vacation. They are one of the delightful wonders of warm summer evenings.

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  Glucose Oxidase    (  PDF 300 KB,   ePub Version)

Glucose Oxidase

Diabetes is a worldwide health problem affecting hundreds of millions of people. Fortunately, with careful management of diet and medication, the many complications of diabetes can be reduced. Part of this treatment includes the monitoring of glucose levels in the blood, so that proper action may be taken if levels get too high. The enzyme glucose oxidase has made glucose measurement fast, easy, and inexpensive.

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  Hemagglutinin    (  PDF 310 KB,   ePub Version)


Influenza virus is a dangerous enemy. Normally, the immune system fights off infections, eradicating the viruses and causing a few days of miserable flu symptoms. Yearly flu vaccines prime our immune system, making it ready to fight the most common strains of influenza virus. But once every couple of decades, a new strain of influenza appears that is far more pathogenic, allowing it to spread rapidly. This happened at the end of World War I, and the resultant pandemic killed over 20 million people, more than twice the number of people that were killed in the war.

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  Tissue Factor    (  PDF 308 KB,   ePub Version)

Tissue Factor

Blood performs many essential jobs in your body: it transports oxygen and nutrients, it protects your cells from infection, and it carries hormones and other messages from place to place in your body. But since blood is a liquid that is pumped under pressure, we must protect ourselves from leaks. Fortunately, the blood has a built-in repair method that quickly stops up breaks in the blood circulatory system as soon as they happen. You see these repairs in action whenever you cut yourself: the blood thickens and forms a gooey clot, which then dries into a scab that seals and protects the cut until it can heal.

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  Alpha-amylase    (  PDF 412 KB,   ePub Version)


Glucose is a major source of energy in your body, but unfortunately, free glucose is relatively rare in our typical diet. Instead, glucose is locked up in many larger forms, including lactose and sucrose, where two small sugars are connected together, and long chains of glucose like starches and glycogen. One of the major jobs of digestion is to break these chains into their individual glucose units, which are then delivered by the blood to hungry cells throughout your body.

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  Topoisomerases    (  PDF 378 KB,   ePub Version)


Each of your cells contains about 2 meters of DNA, all folded into the tiny space inside the nucleus, which is a million times smaller. As you might imagine, these long, thin strands can get tangled very easily in the busy environment of the nucleus. To make things even more complicated, DNA is a double helix, which must be unwound to access the genetic information. If you have ever tried to unravel the individual fibers in a piece of rope, you will understand the knotty problems that this can cause. To help with these problems, your cells build several different topoisomerase enzymes that untangle and relax DNA strands.

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  ATP Synthase    (  PDF 334 KB,   ePub Version)

ATP Synthase

ATP synthase is one of the wonders of the molecular world. ATP synthase is an enzyme, a molecular motor, an ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine. It plays an indispensable role in our cells, building most of the ATP that powers our cellular processes. The mechanism by which it performs this task is a real surprise.

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  Acetylcholine Receptor    (  PDF 487 KB,   ePub Version)

Acetylcholine Receptor

Nerve cells need to be able to send messages to each other quickly and clearly. One way that nerve cells communicate with their neighbors is by sending a burst of small neurotransmitter molecules. These molecules diffuse to the neighboring cell and bind to special receptor proteins in the cell surface. These receptors then open, allowing ions to flow inside. The process is fast because the small neurotransmitters, such as acetylcholine or serotonin, diffuse rapidly across the narrow synapse between the cells. The channels open in milliseconds, allowing ions to flood into the cell. Then, they close up just as fast, quickly terminating the message as the neurotransmitters separate and are removed from the synapse.

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  Designer Proteins    (  PDF 363 KB,   ePub Version)

Designer Proteins

As we learn more and more about proteins and how they work, we naturally have the desire to use this knowledge and do some tinkering of our own. Since the early 1980's, scientists have been using the ever-expanding understanding of protein structure and function to redesign existing proteins, and more recently, to design entirely new proteins.

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  Cholera Toxin    (  PDF 373 KB,   ePub Version)

Cholera Toxin

Bacteria pull no punches when they fight to protect themselves. Some bacteria build toxins so powerful that a single molecule can kill an entire cell. This is far more effective than chemical poisons like cyanide or arsenic. Chemical poisons attack important molecules one by one, so many, many molecules of cyanide are needed to kill a cell. Bacterial toxins use two strategies to make their toxins far more deadly than this.

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  Neurotrophins    (  PDF 270 KB,   ePub Version)


Your brain is composed of 85 billion interconnected neurons. Individually, each neuron receives signals from its many neighbors, and based on these signals, decides whether to dispatch its own signal to other nerve cells. Together, the combined action of all of these neurons allows us to sense the surrounding world, think about what we see, and make appropriate actions.

Remarkably, this complicated structure is formed in nine short months as an embryo grows into a baby. Nerve cells start as typical, compact cells, but then they send out long axons and dendrites, connecting to other cells in the brain or even to entirely different parts of the body. Neurons in the growing brain test the connections with their neighbors, looking for the proper wiring. Half of the neurons are discarded during this process, in areas that get too crowded. The half that remain become the nervous system. Throughout the rest of life, these neurons typically do not reproduce, although they do send out more dendrites to neighboring cells as the nervous system grows or repairs damaged areas.

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  TATA-Binding Protein    (  PDF 405 KB,   ePub Version)

TATA-Binding Protein

The enzyme RNA polymerase performs the delicate task of unwinding the two strands of DNA and transcribing the genetic information into a strand of RNA. But how does it know where to start? Our cells contain 30,000 genes encoded in billions of nucleotides. For each gene, the cell must be able to start transcription at the right place and at the right time.

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  Carotenoid Oxygenase    (  PDF 312 KB,   ePub Version)

Carotenoid Oxygenase

Eat your carrots or you'll go blind! The biochemical reason for this childhood warning is that we need retinal, vitamin A, to form the pigment that absorbs light in our eyes. Unfortunately, our cells cannot make it for themselves, so we have to obtain it in our diet. We typically get our daily dose of vitamin A in two different ways. Retinal, or molecules similar to it, may be obtained directly when we eat meat. Alternatively, we can eat molecules that are easily transformed into retinal. This is where the carrots enter the story. They are full of beta-carotene, which our cells break in half to form two molecules of retinal.

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  Self-splicing RNA    (  PDF 278 KB,   ePub Version)

Self-splicing RNA

Nature is full of surprises, and you can be sure that once you think you understand something, Nature will come up with an exception. Twenty years ago, this was the case with enzymes. After decades of work, biochemists thought that proteins were the only molecules that catalyzed chemical reactions in the cell, so it came as a surprise when Thomas Cech and his coworkers discovered a natural RNA splicing reaction that occurs even when all of the proteins are removed. Since then, researchers have discovered many additional examples of ribozymes--RNA molecules that perform chemical tasks.

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  Kinesin    (  PDF 274 KB,   ePub Version)


Because cells are so tiny, many cellular processes use simple random diffusion to get materials from one place to another. For instance, when a molecule of glucose is broken down in glycolysis, the ten enzymes and all the intermediate pieces are thrown together in the cytoplasm, and by randomly bumping around, everything manages to find its proper place. For small molecules and proteins, random diffusion is fast enough to get the job done, but for some larger tasks, cells have to take a more active approach. This is where molecular motors come in. Cells make a variety of motors that drag large cellular objects to their proper destinations.

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  T-Cell Receptor    (  PDF 351 KB,   ePub Version)

T-Cell Receptor

Viruses are one of the major dangers that we face in everyday life, so our immune system has powerful methods to fight them. Our cells call for help when they become infected, by displaying little pieces of the viruses on their surface. When the immune system finds these viral peptides, it quickly kills the infected cell and the viruses inside. Last month, we saw how an infected cell displays viral peptides using MHC. This month, we will look at the T-cell receptor, the protein that recognizes these viral peptides.

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  Major Histocompatibility Complex    (  PDF 462 KB,   ePub Version)

Major Histocompatibility Complex

Viruses are insidious enemies, so we must have numerous defenses against them. Antibodies are our first line of defense. Antibodies bind to viruses, mobilizing blood cells to destroy them. But what happens if viruses slip past this defense and get inside a cell? Then, antibodies have no way of finding them and the viruses are safe...but not quite. Each cell has a second line of defense that it uses to signal to the immune system when something goes wrong inside. Cells continually break apart a few of their old, obsolete proteins and display the pieces on their surfaces. The small peptides are held in MHC, the major histocompatibility complex, which grips the peptides and allow the immune system to examine them. In this way, the immune system can monitor what is going on inside the cell. If all the peptides displayed on the cell surface are normal, the immune system leaves the cell alone. But if there is a virus multiplying inside the cell, many of the MHC molecules carry unusual peptides from viral proteins, and the immune system kills the cell.

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  Phenylalanine Hydroxylase    (  PDF 477 KB,   ePub Version)

Phenylalanine Hydroxylase

The proteins that make up the skin, muscle, hair, bones and other organs in your body are primarily composed of a set of 20 building blocks, called amino acids. Amino acids are the alphabet in the protein language: when combined in a specific order, they make up meaningful structures (proteins) with varied and specific functions. Amino acids have distinct shapes, sizes, charges and other characteristics. Many amino acids are synthesized in your body from breakdown products of sugars and fats, or are converted from other amino acids by the action of specific enzymes. However, a few of them, called essential amino acids, cannot be synthesized or converted in your body and have to be obtained from the food you eat. Phenylalanine is one such essential amino acid. It is closely related to another amino acid, tyrosine, which just has an additional hydroxyl (OH) group. Liver cells contain an enzyme called phenylalanine hydroxylase, which can add this group and convert phenylalanine to tyrosine. Thus as long as this enzyme is functional and there is a reasonable supply of phenylalanine, tyrosine can be synthesized in your body and does not have to be included in the food that you eat.

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  Ubiquitin    (  PDF 315 KB,   ePub Version)


Nothing lasts forever. Many proteins, in fact, don't last more than a few minutes. Our cells are continually building proteins, using them for a single task, and then discarding them. For instance, proteins that are used for signaling or control, such as transcription regulators and the cyclins that control division of cells, lead very brief lives, carrying their messages and then being thrown away. Specialized enzymes are also built just when they are needed, allowing cells to keep up with their minute-by-minute synthetic needs. This approach of planned obsolescence may seem wasteful, but it allows each cell to respond quickly to its constantly changing requirements.

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  Photosystem II    (  PDF 1.2 MB,   ePub Version)

Photosystem II

Three billion years ago, our world changed completely. Before then, life on Earth relied on the limited natural resources found in the local environment, such as the organic molecules made by lightning, hot springs, and other geochemical sources. However, these resources were rapidly being used up. Everything changed when these tiny cells discovered a way to capture light and use it to power their internal processes. The discovery of photosynthesis opened up vast new possibilities for growth and expansion, and life on the earth boomed. With this new discovery, cells could take carbon dioxide out of the air and combine it with water to create the raw materials and energy needed for growth. Today, photosynthesis is the foundation of life on Earth, providing (with a few exotic exceptions) the food and energy that keeps every organism alive.

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  G Proteins    (  PDF 293 KB,   ePub Version)

G Proteins

Cells communicate by passing small, disposable messages to one another. Some of these messengers travel to distant parts of the body through the blood, others simply diffuse over to a neighboring cell. Then, another cell picks the message up and reads it. Thousands of these messages are used in the human body. Some familiar examples include adrenaline, which controls the level of excitement, glucagon, which carries messages about blood sugar levels, histamine, which signals tissue damage, and dopamine, which relays messages in the nervous system.

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  Catalase    (  PDF 430 KB,   ePub Version)


Living with oxygen is dangerous. We rely on oxygen to power our cells, but oxygen is a reactive molecule that can cause serious problems if not carefully controlled. One of the dangers of oxygen is that it is easily converted into other reactive compounds. Inside our cells, electrons are continually shuttled from site to site by carrier molecules, such as carriers derived from riboflavin and niacin. If oxygen runs into one of these carrier molecules, the electron may be accidentally transferred to it. This converts oxygen into dangerous compounds such as superoxide radicals and hydrogen peroxide, which can attack the delicate sulfur atoms and metal ions in proteins. To make things even worse, free iron ions in the cell occasionally convert hydrogen peroxide into hydroxyl radicals. These deadly molecules attack and mutate DNA. One theory, still controversial, is that this type of oxidative damage accumulates over the years of our life, causing us to age.

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  Caspases    (  PDF 340 KB,   ePub Version)


Billions of cells in your body will die in the next hour. This is entirely normal--the human body continually renews itself, removing obsolete or damaged cells and replacing them with healthy new ones. However, your body must do this carefully. If cells are damaged, like when you cut yourself, they may swell and burst, contaminating the surrounding area. The body responds harshly to this type of cell death, inflaming the area by rushing in blood cells to clean up the mess. To avoid this messy problem, your cells are boobytrapped with a method to die cleanly and quickly on demand. When given the signal, the cell will disassemble its own internal structure and fragment itself into small, tidy pieces that are readily consumed by neighboring cells. This process of controlled, antiseptic death is called apoptosis.

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  DNA Ligase    (  PDF 330 KB,   ePub Version)

DNA Ligase

Human cells (with a few unusual exceptions) each contain their own set of 46 long strands of DNA. All of our genetic information is encoded in these strands, with thousands of genes strung along their length. The ordering of genes, and the proximity of one next to the other, can be important for the proper usage of the information, so it is important that our cells protect their DNA from breakage. If one strand in the DNA breaks, it is not a disaster, but it can lead to problems when the DNA double helix is unwound during the processes of transcription and replication. Breakage of both strands, on the other hand, is far more serious. To protect us from these dangers, our cells use DNA ligases to glue together DNA strands that have been broken.

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  Acetylcholinesterase    (  PDF 321 KB,   ePub Version)


Every time you move a muscle and every time you think a thought, your nerve cells are hard at work. They are processing information: receiving signals, deciding what to do with them, and dispatching new messages off to their neighbors. Some nerve cells communicate directly with muscle cells, sending them the signal to contract. Other nerve cells are involved solely in the bureaucracy of information, spending their lives communicating only with other nerve cells. But unlike our human bureaucracies, this processing of information must be fast in order to keep up with the ever-changing demands of life.

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  Serpins    (  PDF 346 KB,   ePub Version)


Our cells are often forced to work with dangerous machinery. For instance, cells build many machines for demolition, such as nucleases that break down DNA and RNA, amylases and related enzymes that break down carbohydrates, lipases that chew up lipids, and proteases that disassemble proteins. These destructive enzymes are needed in many capacities. They are used in digestion, to break food molecules into workable pieces. They are used in defense, to attack invading viruses and bacteria. They are used to break down defective or obsolete molecules inside cells. They are also used in signaling cascades, to activate signaling molecules instantly when a message is received. These enzymes are essential when used at the proper place and time, but can spell disaster if they get loose.

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  Growth Hormone    (  PDF 210 KB,   ePub Version)

Growth Hormone

As children grow, their height, weight and strength increase. Numerous factors influence this growth, including the genetic makeup of the child, nutrition and environmental factors. Specific messengers released by the body also stimulate and regulate growth. Growth hormone is one key growth signal released from the pituitary, a pea-sized gland located at the base of the brain. Lack of this hormone in children can cause them to remain shorter than average, while in its excess they may grow taller than most. Growth hormone continues its work in adults, playing an important role in repair and maintenance of different tissues in the body.

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  Calcium Pump    (  PDF 315 KB,   ePub Version)

Calcium Pump

Every time we move a muscle, it requires the combined action of trillions of myosin motors. Our muscle cells use calcium ions to coordinate this massive molecular effort. When a muscle cell is given the signal to contract from its associated nerves, it releases a flood of calcium ions from a special intracellular container, the sarcoplasmic reticulum, that surrounds the bundles of actin and myosin filaments. The calcium ions rapidly spread and bind to tropomyosins on the actin filaments. They shift shape slightly and allow myosin to bind and begin climbing up the filament. These trillions of myosin motors will continue climbing, contracting the muscle, until the calcium is removed.

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  Glycolytic Enzymes    (  PDF 970 KB,   ePub Version)

Glycolytic Enzymes

Glucose powers cells throughout your body. Glucose is a convenient fuel molecule because it is stable and soluble, so it is easy to transport through the blood from places where it is stored to places where it is needed. Glucose is packed with chemical energy, ready for the taking. In a test tube, you can burn glucose, forming carbon dioxide and water and a lot of light and heat. Our cells also burn glucose, but they do it in many small, well-controlled steps, so that they can capture the energy in more useable forms, such as ATP (adenosine triphosphate). Glycolysis (sugar-breaking) is the first process in the cellular combustion of glucose.

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  Carbonic Anhydrase    (  PDF 260 KB,   ePub Version)

Carbonic Anhydrase

Breathing is a fundamental function in life - ever wondered what really happens when we breathe? The air we breathe in has precious oxygen that fuels the breakdown of sugars and fat in our cells. In our lungs, oxygen diffuses into the blood, binds to hemoglobin and is transported to all the cells of our body (see the Molecule of the Month feature on hemoglobin). Carbon dioxide is a byproduct of sugar and fat breakdown in cells and needs to be removed from our body. Again, blood acts as a transport medium. Carbon dioxide diffuses out of cells and is transported in blood in a few different ways: less than 10% dissolves in the blood plasma, about 20% binds to hemoglobin, while the majority of it (70%) is converted to carbonic acid to be carried to the lungs. An enzyme present in red blood cells, carbonic anhydrase, aids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the same enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Although these reactions can occur even without the enzyme, carbonic anhydrase can increase the rate of these conversions up to a million fold.

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  Catabolite Activator Protein    (  PDF 3.6 MB,   ePub Version)

Catabolite Activator Protein

Bacteria love sugar. In particular, bacteria love glucose, which is easily digestible and quickly converted to chemical energy. When glucose is plentiful, bacteria ignore other nutrients in their environment, feasting on their favored source. But, when glucose is rare, they shift gears and mobilize the machinery needed to use other sources of energy.

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  Simian Virus 40    (  PDF 388 KB,   ePub Version)

Simian Virus 40

Simian virus 40 is an example of how simple a virus can be and still perform its deadly job. Viruses are tiny machines with a single purpose: to reproduce themselves. They enter cells and hijack their synthetic machinery, forcing them to create new viruses. SV40 does this with very little molecular machinery. It is enclosed by a spherical capsid composed of 360 copies of one protein, seen in PDB entry 1sva, and a few copies of two others. This capsid is just big enough to enclose a small circle of DNA 5243 nucleotides long, which contains the barest minimum of information needed to get into the cell and make new viruses.

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  Trypsin    (  PDF 405 KB,   ePub Version)


Proteins are tough, so we use an arsenal of enzymes to digest them into their component amino acids. Digestion of proteins begins in the stomach, where hydrochloric acid unfolds proteins and the enzyme pepsin begins a rough disassembly. The real work then starts in the intestines. The pancreas adds a collection of protein-cutting enzymes, with trypsin playing the central role, that chop the protein chains into pieces just a few amino acids long. Then, enzymes on the surfaces of intestinal cells and inside the cells chop them into amino acids, ready for use throughout the body.

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  Estrogen Receptor    (  PDF 345 KB,   ePub Version)

Estrogen Receptor

Estrogens are small, carbon-rich molecules built from cholesterol. This is quite different than larger hormones, such as insulin and growth hormone, which are sensed by receptors on the cell surface. Estrogens pass directly into cells throughout the body, so the cell can use receptors that are in the nucleus, right at the site of action on the DNA. When estrogen enters the nucleus, it binds to the estrogen receptor, causing it to pair up and form a dimer. This dimer then binds to several dozen specific sites in the DNA, strategically placed next to the genes that need to be activated. Then, the DNA-bound receptor activates the DNA-reading machinery and starts the production of messenger RNA.

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  Calmodulin    (  PDF 353 KB,   ePub Version)


Calcium is the most plentiful mineral element found in your body, with phosphorous coming in second. This probably doesn't come as a surprise, since your bones are strengthened and supported by about two kilograms of calcium and phosphorous. Your body also uses a small amount of calcium, in the form of calcium ions, to perform more active duties. Calcium ions play essential roles in cell signaling, helping to control processes such as muscle contraction, nerve signaling, fertilization and cell division. Through the action of calcium pumps and several kinds of calcium binding proteins, cells keep their internal calcium levels 1000-10,000 times lower than the calcium levels in the blood. Thus when calcium is released into cells, it can interact with calcium sensing proteins and trigger different biological effects, causing a muscle to contract, releasing insulin from the pancreas, or blocking the entry of additional sperm cells once an egg has been fertilized.

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  Src Tyrosine Kinase    (  PDF 312 KB,   ePub Version)

Src Tyrosine Kinase

Your body is a democratic nation of cells. Each cell is an individual with its own needs, but all of your cells work together to keep you alive. As you might imagine, this requires an incredible amount of cooperation. Cells are in constant communication to inform their neighbors of their needs and future plans. They send messages to each other, passing hormones and chemokines and other molecular messages from cell to cell. These messages are received by proteins in the cell membrane, which transmit the signal inside. There, a bewilderingly complex collection of proteins relays the message to all of the appropriate places inside the cell.

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  Green Fluorescent Protein (GFP)    (  PDF 262 KB,   ePub Version)

Green Fluorescent Protein (GFP)

The green fluorescent protein, shown here from PDB entry 1gfl, is found in a jellyfish that lives in the cold waters of the north Pacific. The jellyfish contains a bioluminescent protein-- aequorin--that emits blue light. The green fluorescent protein converts this light to green light, which is what we actually see when the jellyfish lights up. Solutions of purified GFP look yellow under typical room lights, but when taken outdoors in sunlight, they glow with a bright green color. The protein absorbs ultraviolet light from the sunlight, and then emits it as lower-energy green light.

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  Hemoglobin    (  PDF 2.0 MB,   ePub Version)


Ever wondered why blood vessels appear blue? Oxygenated blood is bright red: when you are cut, the blood you see is brilliant red oxygenated blood. Deoxygenated blood is deep purple: when you donate blood or give a blood sample at the doctor's office, it is drawn into a storage tube away from oxygen, so you can see this dark purple color. However, deep purple deoxygenated blood appears blue as it flows through our veins, especially in people with fair skin. This is due to the way that different colors of light travel through skin: blue light is reflected in the surface layers of the skin, whereas red light penetrates more deeply. The dark blood in the vein absorbs most of this red light (as well as any blue light that makes it in that far), so what we see is the blue light that is reflected at the skin's surface. Some organisms like snails and crabs, on the other hand, use copper to transport oxygen, so they truly have blue blood.

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  RNA Polymerase    (  PDF 278 KB,   ePub Version)

RNA Polymerase

RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins. In fact, most of the RNA in cells is found in ribosomes--our protein-synthesizing machines--and the transfer RNA molecules used to add each new amino acid to growing proteins. In addition, countless small RNA molecules are involved in regulating, processing and disposing of the constant traffic of messenger RNA. The enzyme RNA polymerase carries the weighty responsibility of creating all of these different RNA molecules.

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  lac Repressor    (  PDF 511 KB,   ePub Version)

lac Repressor

DNA is filled with information. Our own DNA contains the instructions for building tens of thousands of different proteins and RNA, which perform all the different functions that keep us alive. As discovered by Watson and Crick fifty years ago, this genetic information is stored in the sequence of adenine, thymine, cytosine and guanine bases in the DNA. Their model of the DNA double helix showed how the information is read by separating the two strands of DNA and then pairing the exposed surfaces of the bases with appropriate partners, such that adenine always pairs with thymine and cytosine pairs with guanine.

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  Potassium Channels    (  PDF 561 KB,   ePub Version)

Potassium Channels

All living cells are surrounded by a membrane that separates the watery world inside from the environment outside. Membranes are effective barriers for small ions (as well as for large molecules like proteins and DNA), providing a novel opportunity: differences in ion levels may be used for rapid signaling. For instance, a cell can raise the level of potassium ions inside it. Then, at a moment's notice, potassium can be released through channels in the membrane, creating a large change in the potassium level that will be felt throughout the cell. This process is used in all types of cells - bacteria, plants and animals. Two common examples of ion channels at work are seen in muscle contraction (which is started by the release of calcium ions), and nerve signaling (which involves a complex flow of sodium and potassium ions).

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  Serum Albumin    (  PDF 257 KB,   ePub Version)

Serum Albumin

Think about how convenient it is to be able to eat. Each one of your ten trillion cells requires a constant supply of nourishment. But we don't have to worry about this--we merely eat our dinner and our body does the rest. The food is digested and the useful pieces are delivered to cells throughout the body, using the bloodstream as the delivery system. Delivery of water-soluble molecules, like sugar, is easy. They float in the watery bloodstream and are picked up by cells along the way. Other important nutrients, however, are not soluble in water, so special carriers must be made to chaperone them to hungry cells.

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  Cytochrome c    (  PDF 339 KB,   ePub Version)

Cytochrome c

Cytochrome c, shown here from PDB entry 3cyt, is a carrier of electrons. Like many proteins that carry electrons, it contains a special prosthetic group that handles the slippery electrons. Cytochrome c contains a heme group with an iron ion gripped tightly inside, colored red here. The iron ion readily accepts and releases an electron. The surrounding protein creates the perfect environment for the electron, tuning how tightly it is held. As shown on the next page, the protein also determines where cytochrome c fits into the overall cellular electronic circuit.

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  Ferritin and Transferrin    (  PDF 394 KB,   ePub Version)

Ferritin and Transferrin

Inside cells, extra iron ions are locked safely in the protein shell of ferritin, shown here from PDB entry 1fha. Ferritin is composed of 24 identical protein subunits that form a hollow shell. The bottom illustration shows the hollow shell cut in half, showing the chamber inside and a few of the pores that lead inside the shell. After entering the ferritin shell, iron ions are converted into the ferric state, where they form small crystallites along with phosphate and hydroxide ions. There is room to pack about 4500 iron ions inside.

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  Dihydrofolate Reductase    (  PDF 235 KB,   ePub Version)

Dihydrofolate Reductase

Dihydrofolate reductase is a small enzyme that plays a supporting role, but an essential role, in the building of DNA and other processes. It manages the state of folate, a snaky organic molecule that shuttles carbon atoms to enzymes that need them in their reactions. Of particular importance, the enzyme thymidylate synthase uses these carbon atoms to build thymine bases, an essential component of DNA. After folate has released its carbon atoms, it has to be recycled. This is the job performed by dihydrofolate reductase.

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  HIV Reverse Transcriptase    (  PDF 305 KB,   ePub Version)

HIV Reverse Transcriptase

Viruses are tricky. They use all sorts of unusual mechanisms during their attacks on cells. HIV is no exception. It is a retrovirus, which means that it has the ability to insert its genetic material into the genome of the cells that it infects. But, infectious HIV particles carry their genome in RNA strands. Somehow, during infection, the virus needs to make a DNA copy of its RNA genome. This is very unusual, because all of the normal cellular machinery is designed to make RNA copies from DNA, but not the reverse. DNA is normally only created using other DNA strands as a template. This tricky reversal of synthesis is performed by the enzyme reverse transcriptase, shown here from PDB entry 3hvt. Inside its large, claw-shaped active site, it copies the HIV RNA and creates a double-stranded DNA version of the viral genome. This then integrates into the cell's DNA, and later instructs the cell to make additional copies of the virus.

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  Chaperones    (  PDF 456 KB,   ePub Version)


This is not a trivial problem. Cells cannot merely wait for proteins to fold properly. Misfolded proteins often have carbon-rich amino acids on their surfaces, instead of tucked safely inside. These carbon-rich patches associate strongly with similar patches on other proteins, forming large aggregates. Random aggregates are death to cells: diseases such as sickle cell anemia, mad cow disease, and Alzheimer's disease are caused by unnatural aggregation of proteins into cell-clogging fibrils.

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  p53 Tumor Suppressor    (  PDF 348 KB,   ePub Version)

p53 Tumor Suppressor

Our cells face many dangers, including chemicals, viruses, and ionizing radiation. If cells are damaged in sensitive places by these attackers, the effects can be disastrous. For instance, if key regulatory elements are damaged, the normal controls on cell growth may be blocked and the cell will rapidly multiply and grow into a tumor. p53 tumor suppressor is one of our defenses against this type of damage. p53 tumor suppressor is normally found at low levels, but when DNA damage is sensed, p53 levels rise and initiate protective measures. p53 binds to many regulatory sites in the genome and begins production of proteins that halt cell division until the damage is repaired. Or, if the damage is too severe, p53 initiates the process of programmed cell death, or apoptosis, which directs the cell to commit suicide, permanently removing the damage.

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  Glutamine Synthetase    (  PDF 1.1 MB,   ePub Version)

Glutamine Synthetase

Our cells are continually faced with a changing environment. Think about what you eat. Some days you might eat a lot of protein, other days you might eat a lot of carbohydrate. Sometimes you may eat nothing but chocolate. Your body must be able to respond to these different foods, producing the proper enzymes for capturing the nutrients in each. The same is doubly true for small organisms like bacteria, which do not have as many options in choosing their diet. They must eat whatever food happens to be close by, and then mobilize the enzymes needed to use it.

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  Penicillin-binding Proteins    (  PDF 243 KB,   ePub Version)

Penicillin-binding Proteins

Bacteria pose a continual threat of infection, both to humans and to other higher organisms. Thus, when looking for new ways to fight infection, it is often productive to look at how other plants, animals and fungi protect themselves. This is how penicillin was discovered. Through a chance observation in 1928, Alexander Fleming discovered that colonies of Penicillium mold growing in his bacterial cultures were able to stave off infection. With more study, he found that the mold was flooding the culture with a molecule that killed the bacteria, penicillin.

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  Anthrax Toxin    (  PDF 488 KB,   ePub Version)

Anthrax Toxin

Anthrax is a household word, in spite of the fact that anthrax is not a common disease. For humans, anthrax is difficult to contract. It is not transmitted from person to person--it is usually contracted when people come into contact with infected animals or their products. But recently, anthrax has gained the potential to be a major threat through bioterrorism. It is an effective weapon because it forms sturdy spores that may be stored for years, that rapidly lead to lethal infections when inhaled.

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  Bacteriorhodopsin    (  PDF 358 KB,   ePub Version)


Sunlight powers the biological world. Through photosynthesis, plants capture sunlight and build sugars. These sugars then provide all of the starting materials for our growth and energy needs. As seen in the Molecule of Month last October, photosynthesis requires a complex collection of molecular antennas and photosystems. However, some archaebacteria have found a simpler solution to capturing sunlight.

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  Nitrogenase    (  PDF 430 KB,   ePub Version)


Nitrogen is needed by all living things to build proteins and nucleic acids. Nitrogen gas is very common on the earth, as it comprises just over 75% of the molecules in air. Nitrogen gas, however, is very stable and difficult to break apart into individual nitrogen atoms. Usable nitrogen, in the form of ammonia or nitrate salts, is scarce. Often, the growth of plants is limited by the amount of nitrogen available in the soil. Small amounts of usable forms of nitrogen are formed by lightning and the ultraviolet light from the sun. Significant amounts of nitrogen are fed to plants in the form of industrial fertilizers. But the lion's share of usable nitrogen is created by bacteria, using the enzyme nitrogenase.

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  Thrombin    (  PDF 344 KB,   ePub Version)


Oxygen and nutrients are delivered throughout our bodies through the watery transport system of the blood. Using a liquid delivery method poses two challenges. First, it leaves the entire body open to infection, since bacteria and viruses will be quickly distributed everywhere that the blood goes. The immune system, with antibodies as the first line of defense, fights this danger. Second, there is the constant danger of damage to the blood circulatory system. Blood is pumped throughout the body under pressure, and any small leak could lead to a rapid emptying of the entire system. Fortunately, the blood carries an emergency repair system: the blood clotting system. When we are cut or wounded, our blood builds a temporary dam to block the damage, giving the surrounding tissues time to build a more permanent repair.

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  Glycogen Phosphorylase    (  PDF 365 KB,   ePub Version)

Glycogen Phosphorylase

Although it may not seem so during the holiday season, we do not have to eat continually throughout the day. Our cells do require a constant supply of sugars and other nourishment, but fortunately our bodies contain a mechanism for storing sugar during meals and then metering it out for the rest of the day. The sugars are stored in glycogen, a large molecule that contains up to 10,000 glucose molecules connected in a dense ball of branching chains. Your muscles store enough glycogen to power your daily activities, and your liver stores enough to feed your nervous system and other tissues all through the day and on through the night.

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  DNA    (  PDF 324 KB,   ePub Version)


Each of the cells in your body carries about 1.5 gigabytes of genetic information, an amount of information that would fill two CD ROMs or a small hard disk drive. Surprisingly, when placed in an appropriate egg cell, this amount of information is enough to build an entire living, breathing, thinking human being. Through the efforts of the international human genome sequencing projects, you can now read this information. Along with most of the biological research community, you can marvel at the complexity of this information and try to understand what it means. At the same time, you can wonder at the simplicity of this information when compared to the intricacy of the human body.

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  Photosystem I    (  PDF 580 KB,   ePub Version)

Photosystem I

Look around. Just about everywhere that you go, you will see something green. Plants cover the Earth, and their smaller cousins, algae and photosynthetic bacteria, can be found in nearly every corner. Everywhere, they are busy converting carbon dioxide into sugar, creating living organic molecules out of air using the energy of sunlight as power. This process, termed photosynthesis, provides the material foundation on which all life rests.

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  Antibodies    (  PDF 363 KB,   ePub Version)


Antibodies are our molecular watchdogs, waiting and watching for viruses, bacteria and other unwelcome visitors. Antibodies circulate in the blood, scrutinizing every object that they touch. When they find an unfamiliar, foreign object, they bind tightly to its surface. In the case of viruses, like rhinovirus or poliovirus presented last month in the Molecule of the Month, a coating of bound antibodies may be enough to block infection. Antibodies alone, however, are no match for bacteria. When antibodies bind to a bacterial surface, they act as markers alerting the other powerful defensive mechanisms available in the immune system.

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  Poliovirus and Rhinovirus    (  PDF 440 KB,   ePub Version)

Poliovirus and Rhinovirus

Viruses are biological hijackers. They attack a living cell and force it to make many new viruses, often destroying the cell in the process. Picornaviruses, or "little RNA viruses," are among the most simple viruses. They are composed of a modular protein shell, which seeks out and binds to a target cell surface, surrounding a short piece of RNA, which contains all of the information needed to co-opt the cell's machinery and direct the construction of new viruses. In spite of their simplicity, or perhaps because of it, the picornaviruses are also among the most important viruses for human health and welfare. Three familiar examples are shown here: poliovirus at the top (PDB entry 2plv), rhinovirus at the center (PDB entry 4rhv), and the virus that causes foot and mouth disease in livestock at the bottom (PDB entry 1bbt).

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  Actin    (  PDF 278 KB,   ePub Version)


The complex ultrastructure of cells--their shape and internal structure--and the many motions of cells are largely supported by filaments of actin. A tangle of cross-linked actin filaments fills the cytoplasm of animal, plant and fungal cells, forming a "cytoskeleton" that gives the cell shape and form and provides a scaffold for organization. Tightly bundled actin filaments provide a sturdy backbone to extrude structures from the cell surface, such as the pseudopods used by amoebas for crawling and the finger-like microvilli of intestinal cells, which extend into the digestive tract and absorb nutrients. As we saw last month, actin also forms the ladder on which myosin climbs, providing the infrastructure for muscle contraction and creating the motion that we experience in our daily lives. Actin is plentiful throughout the body as it performs these basic structural tasks: it may comprise 5 percent of the protein in a typical cell, or up to one fifth of the protein in special cases, such as muscle cells.

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  Myosin    (  PDF 331 KB,   ePub Version)


All of the different movements that you are making right now--your fingers on the computer keys, the scanning of your eyes across the screen, the isometric contraction of muscles in your back and abdomen that allow you to sit comfortably--are powered by myosin. Myosin is a molecule-sized muscle that uses chemical energy to perform a deliberate motion. Myosin captures a molecule of ATP, the molecule used to transfer energy in cells, and breaks it, using the energy to perform a "power stroke." For all of your voluntary motions, when you flex your biceps or blink your eyes, and for all of your involuntary motions, each time your heart beats, myosin is providing the power.

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  Cyclooxygenase    (  PDF 237 KB,   ePub Version)


What is the most commonly-taken drug today? It is an effective painkiller. It reduces fever and inflammation when the body gets overzealous in its defenses against infection and damage. It slows blood clotting, reducing the chance of stroke and heart attack in susceptible individuals. And, there is growing evidence that it is an effective addition to the fight against cancer. This wonder drug, with manifold uses in medicine, is aspirin. Aspirin has been used professionally for a century, and traditionally since ancient times. A similar compound found in willow bark, salicylic acid, has a long history of use in herbal treatment. But only in the last few decades have we understood how aspirin works, and how it might be improved.

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  Aminoacyl-tRNA Synthetases    (  PDF 445 KB,   ePub Version)

Aminoacyl-tRNA Synthetases

When a ribosome pairs a "CGC" tRNA with "GCG" codon, it expects to find an alanine carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins.

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  Transfer RNA    (  PDF 230 KB,   ePub Version)

Transfer RNA

Since the process of DNA-directed protein synthesis was discovered, scientists and philosophers have searched, more or less seriously, for a relationship between the triplet nucleic acid codons and the chemical nature of the amino acids. These attempts have been uniformly unsuccessful, but remain an occasional topic of speculation because of their possible insights into the origins of life. There does not appear to be a specific interaction between the codons and the amino acids themselves. Instead, the match is made by transfer RNA, the Rosetta Stone that translates the nucleotide language of codons into the amino acid language of proteins. This translation is physical and direct: at one end of each tRNA is an anticodon that recognizes the genetic code, and at the other end is the appropriate amino acid for that code.

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  Insulin    (  PDF 150 KB,   ePub Version)


Our cells communicate using a molecular postal system: the blood is the postal service and hormones are the letters. Insulin is one of the most important hormones, carrying messages that describe the amount of sugar that is available from moment to moment in the blood. Insulin is made in the pancreas and added to the blood after meals when sugar levels are high. This signal then spreads throughout the body, to the liver, muscles and fat cells. Insulin tells these organs to take glucose out of the blood and store it, in the form of glycogen or fat.

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  Alcohol Dehydrogenase    (  PDF 266 KB,   ePub Version)

Alcohol Dehydrogenase

Here's a toast to alcohol dehydrogenase. While recovering from the excesses of New Year's Eve, we might ponder the enzyme that ceaselessly battles the champagne that we consume. Alcohol dehydrogenase is our primary defense against alcohol, a toxic molecule that compromises the function of our nervous system. The high levels of alcohol dehydrogenase in our liver and stomach detoxify about one stiff drink each hour. The alcohol is converted to acetaldehyde, an even more toxic molecule, which is then quickly converted into acetate and other molecules that are easily utilized by our cells. Thus, a potentially dangerous molecule is converted, through alcohol dehydrogenase, into a mere foodstuff.

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  Pepsin    (  PDF 394 KB,   ePub Version)


During the holiday season, we often place greater demands on our digestive enzymes than at other times of the year. Our digestive system contains a host of tough, stable enzymes designed to seek out those rich holiday treats and break them into small pieces. Pepsin is the first in a series of enzymes that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.

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  Rubisco    (  PDF 265 KB,   ePub Version)


Carbon is essential to life. All of our molecular machines are built around a central scaffolding of organic carbon. Unfortunately, carbon in the earth and atmosphere is locked in highly oxidized forms, such as carbonate minerals and carbon dioxide gas. In order to be useful, this oxidized carbon must be "fixed" into more organic forms, rich in carbon-carbon bonds and decorated with hydrogen atoms. Powered by the energy of sunlight, plants perform this central task of carbon fixation. Inside plant cells, the enzyme ribulose bisphosphate carboxylase/oxygenase (rubisco) forms the bridge between life and the lifeless, creating organic carbon from the inorganic carbon dioxide in the air. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate, a short sugar chain with five carbon atoms. Rubisco then clips the lengthened chain into two identical phosphoglycerate pieces, each with three carbon atoms. Phosphoglycerates are familiar molecules in the cell, and many pathways are available to use it. Most of the phosphoglycerate made by rubisco is recycled to build more ribulose bisphosphate, which is needed to feed the carbon-fixing cycle. But one out of every six molecules is skimmed off and used to make sucrose (table sugar) to feed the rest of the plant, or stored away in the form of starch for later use.

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  Ribosomal Subunits    (  PDF 347 KB,   ePub Version)

Ribosomal Subunits

Protein synthesis is the major task performed by living cells. For instance, roughly one third of the molecules in a typical bacterial cell are dedicated to this central task. Protein synthesis is a complex process involving many molecular machines. You can look at many of these molecules in the PDB, including DNA, DNA polymerases, and RNA polymerases; a host of repressors, DNA repair enzymes, topoisomerases, and histones; tRNA and acyl-tRNA synthetases; and molecular chaperones. This month, for the first time, you can also look at the factory of protein synthesis in atomic detail.

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  Lysozyme    (  PDF 211 KB,   ePub Version)


Lysozyme protects us from the ever-present danger of bacterial infection. It is a small enzyme that attacks the protective cell walls of bacteria. Bacteria build a tough skin of carbohydrate chains, interlocked by short peptide strands, that braces their delicate membrane against the cell's high osmotic pressure. Lysozyme breaks these carbohydrate chains, destroying the structural integrity of the cell wall. The bacteria burst under their own internal pressure.

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  Restriction Enzymes    (  PDF 195 KB,   ePub Version)

Restriction Enzymes

Bacteria are under constant attack by bacteriophages, like the bacteriophage phiX174 described in an earlier Molecule of the Month. To protect themselves, many types of bacteria have developed a method to chop up any foreign DNA, such as that of an attacking phage. These bacteria build an endonuclease--an enzyme that cuts DNA--which is allowed to circulate in the bacterial cytoplasm, waiting for phage DNA. The endonucleases are termed "restriction enzymes" because they restrict the infection of bacteriophages.

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  Nucleosome    (  PDF 256 KB,   ePub Version)


This is an auspicious time for molecular biology. The wave of knowledge that began in 1944 with Avery's discovery of DNA as the genetic material, which lead naturally to the atomic model of DNA proposed by Watson and Crick, and continued through detailed experiments to determine the genetic code, is now cresting with the release of the first draft of the human genome. This molecular text, written through billions of years of evolution, will provide untold insights into the molecular processes that underlie every aspect of our lives.

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  HIV-1 Protease    (  PDF 215 KB,   ePub Version)

HIV-1 Protease

Drugs that attack HIV-1 protease are one of the triumphs of modern medicine. The AIDS epidemic started a few short decades ago-- before that, HIV was unknown. These drugs demonstrate the powerful tools that medical science has to combat a new disease. Already, researchers have discovered a panel of effective drugs which slow the growth of the virus to a standstill. Important problems still remain, however. In particular, an effective vaccine against HIV is not available. But today, HIV-infected individuals have potent options for treatment.

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  Cytochrome c Oxidase    (  PDF 244 KB,   ePub Version)

Cytochrome c Oxidase

Oxygen is an unstable molecule. If given a chance, it will break apart and combine with other molecules. This is the process of oxidation, seen in our familiar world as the rusting of iron in cars and nails. But, surprisingly, the unusual electronic properties of oxygen molecules make this reaction very slow. So, paper doesn't spontaneously burn up--flames must be kindled. All animals and plants, and many microorganisms, use the instability of oxygen to power the processes of life. The molecules in food are oxidized and the energy is used to build new molecules, to swim or crawl, and to reproduce. Food is not oxidized in a fiery flame, however. It is oxidized in many slow steps, each carefully controlled and designed to capture as much useable energy as possible. Cytochrome c oxidase controls the last step of food oxidation. At this point, the atoms themselves have all been removed and all that is left are a few of the electrons from the food molecules. Cytochrome c oxidase, shown here, takes these electrons and attaches them to an oxygen molecule. Then, a few hydrogen ions are added as well, forming two water molecules.

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  Collagen    (  PDF 346 KB,   ePub Version)


About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.

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  DNA Polymerase    (  PDF 261 KB,   ePub Version)

DNA Polymerase

DNA polymerase plays the central role in the processes of life. It carries the weighty responsibility of duplicating our genetic information. Each time a cell divides, DNA polymerase duplicates all of its DNA, and the cell passes one copy to each daughter cell. In this way, genetic information is passed from generation to generation. Our inheritance of DNA creates a living link from each of our own cells back through trillions of generations to the first primordial cells on Earth. The information contained in our DNA, modified and improved over millennia, is our most precious possession, given to us by our parents at birth and passed to our children.

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  Bacteriophage phiX174    (  PDF 200 KB,   ePub Version)

Bacteriophage phiX174

The 10,000th entry in the Protein Data Bank, the bacteriophage phiX174, is a perfect example of how the science of protein structure has progressed in four decades. In 1960, the world got its first look at the structure of a protein. That first structure was the small protein myoglobin, composed of one protein chain and one heme group--about 1260 atoms in all. By contrast, the 10,000th entry in the PDB contains 420 protein chains and over half a million atoms. Enormous structures like this are not uncommon in the Protein Data Bank. The stakes have risen dramatically since the structure of myoglobin was first revealed.

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  Myoglobin    (  PDF 138 KB,   ePub Version)


Any discussion of protein structure must necessarily begin with myoglobin, because myoglobin is where the science of protein structure really began. After years of arduous work, John Kendrew and his coworkers determined the atomic structure of myoglobin, laying the foundation for an era of biological understanding. That first glimpse at protein structure is available at the PDB, under the accession code 1mbn. Take a closer look at this molecule, or look directly at the PDB information for 1mbn. You will be amazed, just like the world was in 1960, at the beautiful intricacy of this protein.

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