H-bonds in Crambin: Coherence in an alpha helix

TL;DR

This study uses coherence analysis on molecular dynamics simulations of crambin to reveal that hydrogen bonds in alpha helices behave like linear systems, enabling better understanding of their allosteric interactions.

Contribution

It introduces coherence analysis as a novel method to study linear interactions in protein hydrogen bonds from molecular dynamics data.

Findings

High coherence (>0.9) between atom displacements in H bonds within alpha helices.

Unrelated atoms show low coherence (~0.02), indicating uncorrelated motions.

Alpha helix layers form linear systems, supporting harmonic analysis of molecular dynamics.

Abstract

We applied coherence analysis to molecular dynamics simulations of the plant protein crambin, a thionin storage protein found in Abyssinian cabbage. Coherence analysis was developed by engineers to identify linear interactions, without statistical assumptions. Coherence is greater than 0.9 between the displacement of oxygen and nitrogen atoms of H bonds in alpha helices for frequencies between 0.391 GHz and 5.08 GHz (corresponding reciprocally to times of 2.56 ns and 0.197 ns). These H bonds act much like a linear system. Unrelated atoms have uncorrelated motions and much smaller coherence, say 0.02. Groups of atoms (that form a layer of an alpha helix) were averaged and the coherence function of two groups was evaluated. Layers of the alpha helix form a linear system, suggesting that the harmonic analysis of classical molecular dynamics can successfully describe the allosteric interactions of the layers of an alpha helix.