Why do proteins coil up into spirals? A new answer to this question, which could aid the effort to identify the genetically determined shapes and functions of human proteins, will be published in the 20 July 2000 issue of the journal Nature. "We have discovered a simple explanation, based solely on principles of geometry, for the protein's preference for the helix as a major component of its overall structure," says Jayanth R. Banavar, professor of physics at Penn State and a member of the team of U.S. and Italian research physicists that made the discovery. The finding is expected to be useful in such wide-ranging research areas as structural genomics, pharmaceuticals, protein engineering, and materials science.
"We applied mathematical ideas about optimal shapes of strings with maximum 'thickness' to proteins, which are string-like in that they have an amino-acid backbone that curls and bends itself into a number of characteristic shapes, including the helix," Banavar says.
Proteins are the product of genes and also the structural stuff of cells and tissues. Like any tool, each protein's shape plays a large role in determining its function. Banavar and his colleagues asked in mathematical language what shape would lead to certain known properties of proteins. This approach is different from the intensive ongoing effort in biochemical research to understand what shape a protein is most likely to take based on each chemical bond that can form within its backbone's distinctive sequence of amino acids. "Many different amino-acid sequences fold into the same or similar structures, which suggests that the structure may be of more fundamental importance than the amino-acid sequences," Banavar says. "Our work yields a simple and logical way of looking at protein shapes independent of complex biochemical interactions."
"A fascinating question to think about is why proteins take on certain basic shapes in their folded states," says Amos Maritan
Contact: Barbara K. Kennedy