COMPREHENSIVE ANALYSIS OF SEQUENCE-STRUCTURERELATIONSHIPS IN THE LOOP REGIONS OF PROTEINS

摘要

Local sequence-structure relationships in the loop regions of proteins were comprehen-sively estimated using simple prediction tools based on support vector regression (SVR).End-to-end distance was selected as a rough structural property of fragments, and theend-to-end distances of an enormous number of loop fragments from a wide variety ofprotein folds were directly predicted from sequence information by using SVR. We foundthat our method was more accurate than random prediction for predicting the struc-ture of fragments comprising 5, 9, and 17 amino acids; moreover, the extended loopfragments could be successfully distinguished from turn structures on the basis of theirsequences, which implies that the sequence-structure relationships were significant forloop fragments with a wide range of end-to-end distances. These results suggest thatmany loop regions as well as helices and strands restrict the conformational space of theentire tertiary structure of proteins to some extent; moreover, our findings throw lighton the mechanism of protein folding and prediction of the tertiary structure of proteinswithout using structural templates.