The PDB has continued to implement its popular "Molecule of the Month" feature. Written and drawn by David S. Goodsell, an assistant professor of molecular biology at The Scripps Research Institute in La Jolla, California, these features provide an overview of significant milestones in the growth of the PDB's macromolecular structure data for a diverse audience. Here is a snapshot of information discussed in these articles:
Collagen: The First Protein Structure
April, 2000 -- 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.
Collagen is composed of three chains, wound together in a tight triple helix. Each chain is over 1400 amino acids long. A repeated sequence of three amino acids forms this sturdy structure. Every third amino acid is glycine, a small amino acid that fits perfectly inside the helix. Many of the remaining positions in the chain are filled by two unexpected amino acids: proline and a modified version of proline, hydroxyproline. We wouldn't expect proline to be this common, because it forms a kink in the polypeptide chain that is difficult to accommodate in typical globular proteins. But, it seems to be just the right shape for this structural protein.
Hydroxyproline, which is critical for collagen stability, is created by modifying normal proline amino acids after the collagen chain is built. The reaction requires vitamin C to assist in the addition of oxygen. Unfortunately, we cannot make vitamin C within our bodies, and if we don't get enough in our diet, the results can be disastrous. Vitamin C deficiency slows the production of hydroxyproline and stops the construction of new collagen, ultimately causing scurvy. The symptoms of scurvy--loss of teeth and easy bruising-- are caused by the lack of collagen to repair the wear-and-tear caused by everyday activities.
Collagen from livestock animals is a familiar ingredient for cooking. Like most proteins, when collagen is heated, it loses all of its structure. The triple helix unwinds and the chains separate. Then, when this denatured mass of tangled chains cools down, it soaks up all of the surrounding water like a sponge, forming gelatin.
Cytochrome c Oxidase: Oxygen and Life
May, 2000 -- 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 takes these electrons and attaches them to an oxygen molecule. Then, a few hydrogen ions are added as well, forming two water molecules.
The reaction of oxygen and hydrogen to form water is a favorable process, releasing a good deal of energy. In our familiar world, hydrogen and oxygen combine explosively, which is the reason that dirigibles are filled with helium instead of hydrogen. In our cells, however, the energy is carefully harnessed by cytochrome c oxidase to charge a battery, or perhaps more correctly, to charge a capacitor. Cytochrome c oxidase is a membrane protein. Most of the surface atoms are carbon and sulfur. In the cell, these atoms are buried inside a membrane. The regions at the top and bottom are covered with charged oxygen and nitrogen atoms. These regions, which prefer a watery environment, stick out on opposite faces of the membrane. This arrangement is perfect for the job performed by cytochrome c oxidase, which uses the reaction of oxygen to water to power a molecular pump. As oxygen is consumed, the energy is stored by pumping hydrogen ions from one side of the membrane to the other. Later, the energy can be used to build ATP or power a motor by letting the hydrogen ions seep back across the membrane.
HIV-1 Protease: A Target for AIDS Therapy
June, 2000 -- 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.
HIV-1 protease performs an essential step in the life cycle of HIV. Like many viruses, HIV makes many of its proteins in one long piece, with several proteins strung together. HIV-1 protease has the job of cutting this long 'polyprotein' into the proper protein-sized pieces. The timing of this step is critical. The intact polyprotein is necessary early in the life cycle, when it assembles the immature form of the virus. Then, the polyprotein must be cut into the proper pieces to form the mature virus, which can then infect a new cell. The cleavage reactions must be timed perfectly, allowing the immature virus to assemble properly before the polyprotein is broken. Because of its sensitive and essential function, HIV-1 protease is an excellent target for drug therapy. Drugs bind tightly to the protease, blocking its action, and the virus perishes because it is unable to mature into its infectious form.
The atomic structure of HIV-1 protease has made much of this work possible. The first structures were reported in 1989. A decade later, over one hundred structures are available in the PDB, including several genetic strains of the enzyme, complexes of the enzyme with many different drugs and inhibitors, and dozens of mutant enzymes. Hundreds more are stored in the proprietary databases of pharmaceutical companies, where they are used to test and refine new drug candidates. Overall, HIV-1 protease is now one of the best-studied enzymes known to medicine. It is an enigmatic enzyme, however, that still hides many of its secrets.
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