Shot Range and High Order Correlations in Proteins

TL;DR

This study investigates dihedral angle correlations in proteins, revealing that short-range correlations dominate in stable structures while long-range correlations are more common in unstable regions, with implications for modeling protein conformations.

Contribution

The paper provides a detailed analysis of dihedral angle correlations in proteins, highlighting the limited significance of high-order correlations in stable structures and their prevalence in unstable regions.

Findings

Short-range correlations are prevalent in stable secondary structures.

Long-range correlations are observed in unstable loop regions.

High order dihedral correlations beyond third order are minimal in stable structures.

Abstract

The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral angles vary in a certain range. Each dihedral angle value can be described as a distribution, but only using the distribution can't describe the real conformation space. The reason is that the dihedral angle has correlation with others, especially the neighbor dihedral angles in primary sequence. In our study we analysis extensive molecular dynamics (MD) simulation trajectories of eleven proteins with different sizes and folds, we found that in stable second structure the correlations only exist between the dihedrals near to each other in primary sequence, long range correlations are rare. But in unstable structures (loop) long range correlations exist. Further we observed some characteristics of the short range correlations in different second structures ({\alpha}-helix, {\beta}-sheet) and we found that we can approximate good high order dihedral angle distribution good only use three order distribution in stable second structure which illustrates that high order correlations (over three order) is small in stable second structure.