No. 17
Spring 2003

Front Page

Message from the PDB

PDB Deposition Statistics

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PDB Focus: ADIT Annotators

New Features Available for Beta Testing: Biological Unit, Curated (Beta) mmCIF Files, Redundancy Reduction Cluster Data

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Structural Bioinformatics Book Includes Chapters on the PDB

PDB Paper Published in Nucleic Acids Research

New Distribution Procedure for Protein Data Bank CD-ROM Sets

PDB at the Biophysical Society Meeting

PDB Focus: David Goodsell and the Molecule of the Month

PDB Molecules of the Quarter: Serum Albumin, Potassium Channels, and lac Repressor

PDB Education Corner

Related Links: Education

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PDB Members & Statement of Support


© 2003 PDB


PDB Molecules of the Quarter: Serum Albumin, Potassium Channels, and lac Repressor

A sample of the molecules featured during this past quarter are included below:

PDB ID: 1e7i
Bhattacharya, A. A., Grune, T., Curry, S. (2000): Crystallographic Analysis Reveals Common Modes of Binding of Medium and Long-Chain Fatty Acids to Human Serum Albumin. J. Mol. Biol. 303, p. 721.
Serum Albumin: Carrying Fatty Acids

January, 2003 -- Think about how convenient it is to be able to eat. Each one of your ten trillion cells requires a constant supply of nourishment. But we don't have to worry about this--we merely eat our dinner and our body does the rest. The food is digested and the useful pieces are delivered to cells throughout the body, using the bloodstream as the delivery system. Delivery of water-soluble molecules, like sugar, is easy. They float in the watery bloodstream and are picked up by cells along the way. Other important nutrients, however, are not soluble in water, so special carriers must be made to chaperone them to hungry cells.

Serum albumin, shown in PDB entry 1e7i, 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. Thus, your body maintains a storehouse of fatty acids, stored as fat. When your body needs energy or needs building materials, fat cells release fatty acids into the blood. There, they are picked up by serum albumin and delivered to distant parts of the body.

Further information about serum albumin can be found at http://www.rcsb.org/pdb/molecules/pdb37_1.html.

Potassium Channels: Open and Shut

PDB ID: 1bl8
Doyle, D. A., Morais Cabral, J., Pfuetzner, R. A., Kuo, A., Gulbis, J. M., Cohen, S. L., Chait, B. T., MacKinnon, R. (1998): The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, p. 69.

February, 2003 -- All living cells are surrounded by a membrane that separates the watery world inside from the environment outside. Membranes are effective barriers for small ions (as well as for large molecules like proteins and DNA), 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 it. Then, at a moment's notice, potassium can be released through channels in the membrane, creating a large change in the potassium level that will be felt throughout the cell. This process is used in all types of cells - bacteria, plants and animals. Two common examples of ion channels at work are seen in muscle contraction (which is started by the release of calcium ions), and nerve signaling (which involves a complex flow of sodium and potassium ions).

When you smell a flower and know that it is a rose, or touch a hot object and immediately pull your hand away, nerves from your nose and hands use the release of ions to send signals to your brain and relay back the appropriate response. Nerve cells ready themselves for sending a signal by concentrating potassium ions inside and selectively pumping sodium ions out. This creates a difference in electrical potential across the cell membrane. To send a signal, sodium channels along the nerve open, allowing sodium to enter and reducing the voltage across the membrane. Potassium channels then open, letting the potassium ions out and re-establishing the original voltage. Other channels and pumps later reset the distribution of sodium and potassium ions inside and outside the cell. By clever design, both of these channels are sensitive to the voltage across the membrane, opening when the voltage changes. So, when the channels are opened at one end of a nerve cell, the flow of ions there instantly triggers channels further down the membrane to open. The result is a wave of channels opening that rushes down the nerve cell, carrying the nerve signal to the end.

Further information about potassium channels can be found at http://www.rcsb.org/pdb/molecules/pdb38_1.html.

lac Repressor: Blocking DNA

PDB ID: 1tlf
Friedman, A. M., Fischmann, T. O., Steitz, T. A. (1995): Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science 268, p. 1721.

PDB ID: 1efa
Bell, C. E., Lewis, M. (2000): A Closer View of the Conformation of the Lac Repressor Bound to Operator. Nat. Struct. Biol. 7, p. 209.

March, 2003 -- DNA is filled with information. Our own DNA contains the instructions for building tens of thousands of different proteins and RNA, which perform all the different functions that keep us alive. As discovered by Watson and Crick fifty years ago, this genetic information is stored in the sequence of adenine, thymine, cytosine and guanine bases in the DNA. Their model of the DNA double helix showed how the information is read by separating the two strands of DNA and then pairing the exposed surfaces of the bases with appropriate partners, such that adenine always pairs with thymine and cytosine pairs with guanine.

The genetic information encoded in the DNA strand is far from being the whole story. A simple set of protein blueprints would hardly be useful, because each of our cells would make all of the 30,000 proteins continually. But brain cells don't need to make hemoglobin, and red blood cells don't need to make acetylcholine receptors. Each cell needs to be able to control the construction of its proteins so that it only builds the proteins needed for its own function. To solve this problem, our DNA also contains a lot of regulatory information that specifies when and where each protein should be made. Unlike the genetic information, this regulatory information is read without unwinding the DNA double helix. Instead, an army of regulatory proteins--including the lac repressor-- feels along the surface of the DNA double helix, reading the parts of the bases that are exposed and looking for the appropriate instructions. Some of these proteins, when they find the appropriate instructions, bind to DNA and block the production of proteins that are encoded in the local area. Other regulators enhance the production of proteins, coaxing RNA polymerase to begin its function of transcribing messenger RNA. The nucleus is a flurry of these regulatory proteins, as they control the production of proteins that are currently needed and block synthesis of proteins that are not.

Further information about the lac repressor can be found at http://www.rcsb.org/pdb/molecules/pdb39_1.html.