Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

摘要

Analysis of the geometric properties of a mean-field HP model on a squarelattice for protein structure shows that structures with large number of switchbacks between surface and core sites are chosen favorably by peptides as uniqueground states. Global comparison of model (binary) peptide sequences withconcatenated (binary) protein sequences listed in the Protein Data Bank and theDali Domain Dictionary indicates that the highest correlation occurs betweenmodel peptides choosing the favored structures and those portions of proteinsequences containing alpha-helices.