Protein structure comparison based on fold evolution

Abstract

The paper presents a protein structure comparison algorithm that is capable to identify specific fold mutations between two proteins. The search for such mutations is based on structure evolution models suggesting that, similarly as sequences, protein folds (at least partially) evolve by a stepwise process, where each step comprises comparatively simple changes affecting few secondary structure elements. The particular fold mutations considered in this study are based on the work by Grishin [Gr01]. The algorithm uses structure representation by 3D graphs and is a modification of a method used in SSM structure alignment tool [KH04a]. Experiments demonstrate that our method is able automatically identify 85% of examples of fold mutations given by Grishin. Also a number of tests involving all-against-all comparisons of CATH struc- tural domains have been performed in order to measure comparative frequencies of different types of fold mutations and some statistical estimations have been obtained.