Contact Pair Dynamics During Folding of a Model Globular Protein, Hp-36

TL;DR

This study uses Brownian dynamics simulations to analyze contact pair formation during the folding of a model protein Hp-36, revealing multistage decay dynamics and identifying pairs that influence the folding rate.

Contribution

It introduces a contact pair distance time correlation function (CPCF) to characterize folding dynamics and links specific contact pairs to long-term folding behavior.

Findings

CPCF shows multistage decay with slow late-stage dynamics.

Certain contact pairs determine the long-time folding rate.

Model protein structure closely mimics native state with RMSD of 4.5 Å.

Abstract

The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to model the complex interaction potential. The resulting structure of the model protein mimics the native state of the real protein with a $RMSD$ of 4.5 \AA. A contact pair distance time correlation function (CPCF), $C_{P}^{ij}(t)$, is introduced which shows multistage decay, including a {\it slow late stage dynamics} for a few specific pairs. {\it These pairs determine the long time folding rate}. Dynamics can be correlated with the landscape, relative contact order and topological contact.