Molecules of the Quarter:
Collagen, Cytochrome c Oxidase, and HIV-1 Protease
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.
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.