Protein fold recognition and dynamics in the space of contact maps.
We introduce an energy function for contact maps of proteins. In addition to the standard term, that takes into account pair-wise 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. We succeeded in identifying the structure of some proteins 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. We also introduced a dynamic Monte Carlo procedure in the space of contact maps, taking topological and polymeric constraints into account by restrictive dynamic rules. Various aspects of protein dynamics, including high-temperature melting and refolding, were simulated. Perspectives of application of the energy function and the method for structure checking and fold prediction are discussed.
Mirny
L
L
Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. mirny@husc.harvard.edu
Domany
E
E
D000596:Amino Acids / Q000737:chemistry; D007611:Aprotinin / Q000737:chemistry; D004268:DNA-Binding Proteins; D008956:Models, Chemical; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D012097:Repressor Proteins / Q000737:chemistry; D013049:Spectrin / Q000737:chemistry; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D000596:Amino Acids; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D013049:Spectrin; D007611:Aprotinin