(1) Department of Chemistry, Harvard University, Cambridge MA, USA
(2)Department of Physics of Complex Systems,
Weizmann Institute of Science, Rehovot, Israel
FEDOMANY@WEIZMANN.weizmann.ac.il
We introduce an energy function for contact maps of proteins. In addition to the standard term, that takes into account pairwise interactions between amino acids, our potential contains a new hydrophobic energy term. Parameters of the energy function were obtained from a statistical analysis of the contact maps of known structures. The quality of our energy function was tested extensively in a variety of ways. In particular, fold recognition experiments revealed that for a fixed sequence the native map is identified correctly in an overwhelming majority of the cases tested. The successfully identified proteins include some cases that are known to pose difficulties for such tests (BPTI, spectrin and cro-protein). In addition, many known pairs of homologous structures were correctly identified, even when the two sequences had relatively low sequence homology. In addition we introduced a dynamic Monte Carlo procedure in the space of contact maps. Topological and polymeric constraints were taken into account by restrictive dynamic rules. Various aspects of protein dynamics, including high-temperature melting and refolding, were simulated.
KEY WORDS : contact maps, Monte Carlo dynamics, protein structure prediction, contact-map energy function, sequence specifity.