On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

TL;DR

This paper explores the relationship between protein secondary structures, backbone bond angles, and side-chain orientations, introducing new visualization methods and a universal energy model to accurately predict side-chain geometry from high-resolution structural data.

Contribution

It presents a novel visualization technique and a universal coarse-grained energy function for modeling side-chain geometry with atomic precision.

Findings

Correlation between tetrahedral deformations and secondary structure

Energy function accurately models side-chain geometry

Predicted structures closely match experimental data

Abstract

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\alpha$-C$_\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \.A in root-mean-square distance from the experimental X-ray structure.