Construction of side-chains in homology modelling: Application to the C-terminal lobe of rhizopuspepsin

Abstract

A detailed and rule-based side-chain modelling procedure for globular proteins is presented. It uses the conformational information contained in a homologous (template) structure as a starting point and includes recipes for atom placement and for checking and improving the atomic positions. The scheme does not rely on intuitive judgements or visual examination of the model during construction or refinement. It comprises four stages; the first three are relatively simple and the fourth is more complex. In the first stage, initial conformations for as many atoms as possible are transferred from the template structure based on the application of trends reported previously. Second, these trends are used to correct poor van der Waals overlaps. Third, the remaining side-chains atoms (those for which no information is contained in the template) are placed by evaluating their rigid rotation, van der Waals surfaces. The fourth stage consists of a hierarchial series of conformational checks. They involve the evaluation of individual residue energies in the absence and presence of the rest of the protein relative to statistical trends observed in the template structure, the comparison of hydrogen-bonding patterns and side-chain accessibilities in the model and template and brief energy minimization followed by an evaluation of the rigid rotation potential energy surfaces of each side-chain. The checks pinpoint “incorrectly” modelled side-chains, suggest conformational changes and provide a means for determining the portions of the model that are likely to be correct and those likely to be in error. The procedure developed in the paper is tested by modelling the side-chains of the C-terminal lobe of the aspartyl proteinase rhizopuspepsin, using the rhizopuspepsin backbone and the homologous protein, penicillopepsin, as a template for the side-chains. The resultant model was compared to the high-resolution X-ray structure of rhizopuspepsin. Using penicillopepsin data only (stage I), 58% of the χ 1 dihedrals and 44% of the χ 2 dihedrals were modelled correctly. Once poor van der Waals overlaps had been corrected and all of the atoms had been placed (stages II and III), 86% of the χ 1 dihedrals and 75% of the χ 2 dihedrals were correct. After the refinement had been completed (stage IV), 92% of the χ 1 dihedrals and 81% of the χ 2 dihedrals were correctly positioned. The incorrectly modelled side-chains were characterized by high accessibilities or elevated B-factors in the rhizopuspepsin and/or penicillopepsin X-ray structures or very broad or multiple minima on the side-chain rigid rotation potential energy surfaces.