’Knot’ to be undone, researchers discover unusual protein structure

Researchers funded by the National Institute of General Medical Sciences have determined the structure of a protein with a surprising feature in it: a knot. This is the first time a knot has been found in a protein from the most ancient type of single-celled organism, an archaebacterium, and one of only a few times a knot has been seen in any protein structure.

This very unusual protein shape finding is a result from the NIGMS Protein Structure Initiative, a 10-year effort to determine 10,000 unique protein structures using fast, highly automated methods. NIGMS, a component of the U.S. Department of Health and Human Services’ National Institutes of Health, provides $50 million per year to nine PSI research centers. The protein knot structure was solved at one of the PSI centers, the Midwest Center for Structural Genomics, which is directed by Andrzej Joachimiak, Ph.D., of Argonne National Laboratory in suburban Chicago.

The researchers describe the new protein structure in the journal Proteins. Their article will be published online Nov. 27 and in print in early December.

“It’s a surprising and different structure,” said NIGMS’ John Norvell, Ph.D., director of the Protein Structure Initiative. Protein folding theory previously held that forming a knot was beyond the ability of a protein. Joachimiak suggests that the newly discovered knot may stabilize the amino acid subunits of the protein.

Such discoveries are just what the PSI aims for. “The PSI approach is to solve thousands of unique protein structures,” said Norvell. “It’s a discovery-driven effort, a voyage into the unknown. We aren’t sure what we’ll find, but we expect to map a great diversity of protein structures.”

“This makes us want to find out why nature goes to the trouble of creating a knot instead of a more typical fold,” said Joachimiak.

One of the main goals of the PSI is to understand all of the possible shapes of proteins in nature. Scientists hope that understanding the full range of protein shapes will shed light on the mysterious process proteins use to fold into a three-dimensional structure from a linear chain of amino acid subunits. Ideally, scientists would like to be able to predict the shape of a protein from the sequence of the gene that codes for it. This ability could be immensely useful in understanding diseases and developing new drugs because a protein’s shape offers big clues to its function and can point to ways of controlling that function.

The “high-throughput” PSI approach is radically different from how scientists have approached protein structure determination in the past. Until recently, scientists focused on solving the structures of proteins with known functions.

The newly discovered knotted protein comes from a microorganism called Methanobacterium thermoautotrophicum. This organism is of interest to industry for its ability to break down waste products and produce methane gas. Scientists know which gene codes for the 268-amino acid protein, but they do not know the protein’s function. They speculate that it binds to RNA, a chemical cousin of the genetic material DNA, and helps process this molecule.

The PSI, currently in its pilot phase, expects to move into production phase by the end of 2005. By the end of the pilot phase, each center will aim to produce 100 to 200 new protein structures per year, adding greatly to the number of known structures. The PSI also expects to dramatically lower the average cost of solving a structure.

The paper describing the new structure was authored by scientists at Argonne National Laboratory and the University of Toronto. The nation’s first national laboratory, Argonne conducts basic and applied scientific research across a wide spectrum of disciplines, ranging from high-energy physics to climatology and biotechnology. The laboratory is operated by the University of Chicago as part of the U.S. Department of Energy’s national laboratory system.

NIGMS supports basic biomedical research and training nationwide. NIGMS-funded studies lay the foundation for advances in disease diagnosis, treatment and prevention. To learn more, visit the NIGMS Web site at www.nigms.nih.gov.

For information about the protein knot, contact Linda Joy in the NIGMS Office of Communications and Public Liaison at 301-496-7301 to speak with PSI director John Norvell, Ph.D, or Catherine Foster of Argonne National Laboratory at 630-252-5580 to speak with Andrzej Joachimiak, Ph.D.

REFERENCE

Zarembinski TI, Kim Y, Peterson K, Christendat D, Kharamsi A, Arrowsmith CH, Edwards AM, Joachimiak A. Deep trefoil knot implicated in RNA binding found in an archaebacterial protein. Proteins 2002; 50: 177-183.