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Molecule of the Month - 2005

The "Molecule of the Month" 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 representative structures themselves.

Please note, the "Molecule of the Month" is not intended to be a comprehensive index to entries in the PDB, nor necessarily represent the historical record. The structures used to illustrate each installment are chosen at the discretion of the author of the "Molecule of the Month".

When using these images, please be sure to include the proper citation information, which can be found in the Structure Explorer for each PDB file referenced in each installment. A credit to the illustrator, David S. Goodsell of The Scripps Research Institute, should also be included.

Complete Molecule of the Month Index

Phenylalanine Hydroxylase (by D.S. Goodsell and S. Dutta)
Jan. 2005
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.. [MORE...]
Available in PDF Format [477 Kb].
Major Histocompatibility Complex (by D.S. Goodsell)
Feb. 2005
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. [MORE...]
Available in PDF Format [462 Kb].
T-Cell Receptor (by D.S. Goodsell)
Mar. 2005
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. [MORE...]
Available in PDF Format [351 Kb].
Kinesin (by D.S. Goodsell)
Apr. 2005
Kinesins are used for many tasks in cells. Typical cells contain an array of microtubules, all pointed from the center of the cell outwards to the surface. Kinesins are used to drag large objects, like lysozomes or endoplasmic reticulum, outwards away from the nucleus and towards the surface. Dyneins are used for the opposite function, to pull things inwards. Kinesins drag materials down the enormous length of nerve axons--this function is how kinesins were discovered. Kinesins are also used to slide microtubules next to one another, for instance, during the process of creating two separate systems of microtubules to separate chromosomes when the cell divides. [MORE...]
Available in PDF Format [274 Kb].
Self-splicing RNA (by D.S. Goodsell)
May 2005
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. [MORE...]
Available in PDF Format [278 Kb].
Carotenoid Oxygenase (by D.S. Goodsell)
June 2005

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. [MORE...]
Available in PDF Format [312 Kb].
TATA-Binding Protein (by D.S. Goodsell)
July 2005

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. [MORE...]
Available in PDF Format [405 Kb].
Neurotrophins (by D.S. Goodsell)
August 2005

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. [MORE...]
Available in PDF Format [270 Kb].
Cholera Toxin (by D.S. Goodsell)
September 2005

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. [MORE...]
Available in PDF Format [373 Kb].
Designer Proteins (by D.S. Goodsell)
October 2005

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. [MORE...]
Available in PDF Format [363 Kb].
Acetylcholine Receptor (by D.S. Goodsell)
November 2005

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. [MORE...]
Available in PDF Format [487 Kb].
ATP Synthase (by D.S. Goodsell)
December 2005

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. [MORE...]
Available in PDF Format [334 Kb].