Molecule of the Month - 2002

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

Thrombin (by D.S. Goodsell)
Jan. 2002

Oxygen and nutrients are delivered throughout our bodies through the watery transport system of the blood. Using a liquid delivery method poses two challenges; one is the constant danger of damage to the blood circulatory 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. Thrombin is at the center of this process... [MORE...]
Available in PDF Format [344 Kb].
Nitrogenase (by D.S. Goodsell)
Feb. 2002

Nitrogen is needed by all living things to build proteins and nucleic acids. Nitrogen gas is very common on the earth, comprising just over 3/4 of the molecules in air. Nitrogen gas, however, is very stable and difficult to break apart into individual nitrogen atoms. The lion's share of usable nitrogen is created by bacteria, using the enzyme nitrogenase... [MORE...]
Available in PDF Format [430 Kb].
Bacteriorhodopsin (by D.S. Goodsell)
Mar. 2002

Bacteriorhodopsin is a compact molecular machine that pumps protons across a membrane powered by green sunlight. It is built by halophilic (salt loving) bacteria, found in high-temperature brine pools. They use sunlight to pump protons outwards across their cell membranes, making the inside 10,000-fold more alkaline than the inside. These protons are then allowed to flow back inwards through another protein, ATP synthase, building much of the ATP that powers the cell... [MORE...]
Available in PDF Format [358 Kb].
Anthrax Toxin (by D.S. Goodsell)
Apr. 2002

Anthrax is caused by an unusually large bacterium, Bacillus anthracis. Once its spores lodge in the skin or in the lungs, it rapidly begins growth and produces a deadly three-part toxin. These toxins are designed for maximum lethality, and are frighteningly effective... [MORE...]
Available in PDF Format [488 Kb].
Penicillin-binding Proteins (by D.S. Goodsell)
May 2002

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... [MORE...]
Available in PDF Format [243 Kb]
Glutamine Synthetase (by D.S. Goodsell)
June 2002

The enzyme glutamine synthetase is a key enzyme controlling the use of nitrogen inside cells. Glutamine, as well as being used to build proteins, delivers nitrogen atoms to enzymes that build nitrogen-rich molecules, such as DNA bases and amino acids. It watches levels of amino acids like glycine, alanine, histidine and tryptophan, and levels of nucleotides like AMP and CTP. If too much of one of these molecules is made, glutamine synthetase senses this and slows production slightly... [MORE...]
Available in PDF Format [1.1 Mb].
p53 Tumor Suppressor (by D.S. Goodsell)
Jul. 2002

Our cells face many dangers, including chemicals, viruses, and ionizing radiation. 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... [MORE...]
Available in PDF Format [348 Kb].
Chaperones (by D.S. Goodsell)
Aug. 2002

Chaperones are proteins that guide proteins along the proper pathways for folding. They protect proteins when they are in the process of folding, shielding them from other proteins that might bind and hinder the process. Many chaperone proteins are termed "heat shock" proteins (with names like HSP-60) because they are made in large amounts when cells are exposed to heat... [MORE...]
Available in PDF Format [456 Kb].
Reverse Transcriptase (by D.S. Goodsell)
Sep. 2002

Reverse transcriptase performs a remarkable feat, reversing the normal flow of genetic information. It is used in the reproduction of a virus such as HIV. It is composed of two different subunits, but both are encoded by the same gene. After the protein is made, one of the subunits is clipped to a smaller size so that it can form the proper mate with one full-sized subunit... [MORE...]
Available in PDF Format [305 Kb].
Dihydrofolate Reductase (by D.S. Goodsell)
Oct. 2002

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... [MORE...]
Available in PDF Format [235 Kb].
Ferritin and Transferrin (by D.S. Goodsell)
Nov. 2002

Iron ions pose a great challenge in our modern biological environment. The water filling cells and the oxygen in the air together conspire to convert iron ions to the ferric state, which is highly insoluble, forming rust-like oxides. The cell must somehow shelter iron ions so that they may be stored and delivered in the necessary quantities. This is the job of ferritin and transferrin... [MORE...]
Available in PDF Format [394 Kb].
Cytochrome c (by D.S. Goodsell)
Dec. 2002

Cytochrome c 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. The iron ion readily accepts and releases an electron... [MORE...]
Available in PDF Format [339 Kb].