Molecule of the Month - 2003

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

Serum Albumin (by D.S. Goodsell)
Jan. 2003

Serum albumin is the carrier of fatty acids in the blood. Fatty acids are essential for two major things in your body. They are the building blocks for lipids, which form all of the membranes around and inside cells. They are also rich sources of energy, and may be broken down inside cells to form ATP... [MORE...]
Available in PDF Format [257 Kb].
Potassium Channels (by D.S. Goodsell and S. Dutta)
Feb. 2003
Membranes are effective barriers for small ions, providing a novel opportunity: differences in ion levels may be used for rapid signaling. For instance, a cell can raise the level of potassium ions inside. Then, at a moment's notice, potassium can be released through channels in the membrane, creating a large change in its level that will be felt throughout the cell. This idea is used in all types of cells... [MORE...]
Available in PDF Format [561 Kb].
lac Repressor (by D.S. Goodsell)
Mar. 2003
The lac repressor is part of a regulatory network--the lac operon--that was discovered in bacteria. It controls the production of three proteins that are involved in the metabolism of lactose. It is a tetramer of four identical subunits that normally binds tightly to a specific region in the bacterial DNA, termed the operator, that is next to a region that encodes three lactose-metabolizing proteins. When bound there, it blocks production of the proteins... [MORE...]
Available in PDF Format [511 Kb].
RNA Polymerase (by D.S. Goodsell)
Apr. 2003

RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins... [MORE...]
Available in PDF Format [278 Kb]
Hemoglobin (by D.S. Goodsell and S. Dutta)
May 2003
Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood. Each of the protein chains is similar in structure to myoglobin, the protein used to store oxygen in muscles and other tissues. However, the four chains of hemoglobin give it some extra advantages... [MORE...]
Available in PDF Format [2.0 Mb].
Green Fluorescent Protein (GFP) (by D.S. Goodsell)
Jun. 2003
The green fluorescent protein is found in a jellyfish that lives in the cold waters of the north Pacific. The jellyfish contains a bioluminescent protein-- aequorin--that emits blue light. The green fluorescent protein converts this light to green light, which is what we actually see when the jellyfish lights up... [MORE...]
Available in PDF Format [262 Kb].
Src Tyrosine Kinase (by D.S. Goodsell)
Jul. 2003
The Src protein is a signaling protein that specializes in messages that control the growth of cells. It sits just inside the cell membrane, where it assists in the passing of signals from various protein receptors to the proteins that turn "on" the engines of protein synthesis and cellular growth... [MORE...]
Available in PDF Format [312 Kb].
Calmodulin (by D.S. Goodsell and S. Dutta)
Aug. 2003
Calcium is the most plentiful mineral element found in your body, with phosphorous coming in second. As its name suggests, calmodulin is a CALcium MODULated proteIN. It is abundant in the cytoplasm of all higher cells and has been highly conserved through evolution. Calmodulin acts as an intermediary protein that senses calcium levels and relays signals to various calcium-sensitive enzymes, ion channels and other proteins... [MORE...]
Available in PDF Format [353 Kb].
Estrogen Receptor (by D.S. Goodsell)
Sep. 2003
Estrogens are small, carbon-rich molecules built from cholesterol. They pass directly into cells throughout the body, so the cell can use receptors that are in the nucleus, right at the site of action on the DNA. When estrogen enters the nucleus, it binds to the estrogen receptor, causing it to pair up and form a dimer. This dimer then binds to several dozen specific sites in the DNA, strategically placed next to the genes that need to be activated... [MORE...]
Available in PDF Format [345 Kb].
Trypsin (by D.S. Goodsell)
Oct. 2003
Trypsin uses a special serine amino acid in its protein-cutting reaction, and is consequently known as a serine protease. The serine proteases are a diverse family of enzymes, all of which use similar enzymatic machinery. In digestion, trypsin, chymotrypsin and elastase work together to chop up proteins... [MORE...]
Available in PDF Format [405 Kb].
Simian Virus 40 (by D.S. Goodsell)
Nov. 2003

Simian virus 40 is an example of how simple a virus can be and still perform its deadly job. Viruses are tiny machines with a single purpose: to reproduce themselves. They enter cells and hijack their synthetic machinery, forcing them to create new viruses. SV40 does this with very little molecular machinery. It is enclosed by a spherical capsid composed of 360 copies of one protein, seen in PDB entry 1sva, and a few copies of two others... [MORE...]
Available in PDF Format [388 Kb].
Catabolite Activator Protein (by D.S. Goodsell)
Dec. 2003

Catabolite activator protein (CAP) is activated by cyclic AMP and stimulates synthesis of the enzymes that break down non-glucose food molecules. It is composed of two identical subunits. When cyclic AMP binds, it changes the conformation of the protein slightly, making it perfect for binding to DNA. CAP binds to a specific DNA sequence, which is found next to the genes that are activated. When CAP binds to DNA, it coaxes RNA polymerase into place, beginning transcription... [MORE...]
Available in
PDF Format [3.6 Mb].