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Structural View of Biology


Biomolecular structures allow us to understand the molecular nature of healthy cells and treat the underlying molecular causes of disease. Our cells contain thousands of molecules that must all work in concert to keep us healthy. When any of these molecules fails, or when a poison or pathogenic organism attacks these molecules, it may cause disease. Our bodies have many defenses against disease, and medical science has developed powerful drugs to assist these defenses.

The immune system protects us from infection by pathogenic organisms. There are many types of pathogens, including bacteria and viruses, and our immune system has many methods for fighting them. These include a collection of molecules for recognizing foreign molecules, like the molecules in bacteria, and a complex set of molecules that mobilize and coordinate attack by our defensive cells.

Scroll to a Molecule of the Month Feature in this subcategory:

  • Antibodies

    Antibodies

    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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    Discussed Structures
    antibody (immunoglobulin)
    antibody (immunoglobulin)
    antibody bound to antigen
    antibody bound to antigen
    catalytic antibody
    catalytic antibody
  • Broadly Neutralizing Antibodies

    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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    Discussed Structures
    HIV Envelope Glycoprotein
    HIV Envelope Glycoprotein
    Influenza Hemagglutinin with a Broadly Neutralizing Antibody
    Influenza Hemagglutinin with a Broadly Neutralizing Antibody
    Influenza Hemagglutinin with a Broadly Neutralizing Antibody
    Influenza Hemagglutinin with a Broadly Neutralizing Antibody
    Influenza Hemagglutinin with a Broadly Neutralizing Antibody
    Influenza Hemagglutinin with a Broadly Neutralizing Antibody
    Vaccine Protein for RSV
    Vaccine Protein for RSV
  • Dermcidin

    Dermcidin

    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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    Discussed Structures
    Dermcidin
    Dermcidin
    Defensin
    Defensin
  • Interferons

    Interferons

    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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    Discussed Structures
    interferon alpha
    interferon alpha
    interferon beta
    interferon beta
    interferon gamma
    interferon gamma
    interferon-gamma and receptor
    interferon-gamma and receptor
  • Major Histocompatibility Complex

    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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    Discussed Structures
    major histocompatibility complex
    major histocompatibility complex
    major histocompatibility complex
    major histocompatibility complex
    T-cell receptor and MHC
    T-cell receptor and MHC
    T-cell receptor and MHC
    T-cell receptor and MHC
  • Nanobodies

    Nanobodies

    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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    Discussed Structures
    nanobody bound to lysozyme
    nanobody bound to lysozyme
  • T-Cell Receptor

    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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    Discussed Structures
    T-cell receptor
    T-cell receptor
    T-cell receptor and MHC
    T-cell receptor and MHC
    T-cell receptor and MHC
    T-cell receptor and MHC
  • Toll-like Receptors

    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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    Discussed Structures
    Toll-like receptor TLR4 and MD-2 bound to lipopolysaccharide
    Toll-like receptor TLR4 and MD-2 bound to lipopolysaccharide
    Toll-like receptor TLR1/TLR2 bound to lipopeptide
    Toll-like receptor TLR1/TLR2 bound to lipopeptide
    Toll-like receptor TLR3 bound to double-stranded RNA
    Toll-like receptor TLR3 bound to double-stranded RNA
    Toll-like receptor TLR10 cytoplasmic domain
    Toll-like receptor TLR10 cytoplasmic domain

Please see our usage polices for citation and reprint information. Copies of the illustrations used in these features are available for download as high resolution TIFF images. Please note that the structures used to illustrate each installment are chosen at the discretion of the authors; the features are not intended to represent a historical record. The process behind the creation of this feature is described by the author.