Thermodynamics and structural properties of a confined HP protein determined by Wang-Landau simulation

Busara Pattanasiri,David P Landau,Thomas Wüst,Ying Wai Li,Wannapong Triampo

doi:10.1088/1742-6596/454/1/012071

Abstract

Understanding protein folding confined by surfaces is important for both biological sciences and the development of nanomaterials. In this work, we study the properties of a confined HP model protein by three different types of surfaces, namely, surfaces that attract: (a) all monomers; (b) only P monomers; and (c) only H monomers. The thermodynamic and structural quantities, such as the specific heat, number of surface contacts, and number of hydrophobic pairs, are obtained by using Wang-Landau sampling. The conformational "transitions", specifically, the debridging process and hydrophobic core formation, can be identified based on an analysis of these quantities. We found that these transitions take place at different temperatures, and the ground state configurations show variations in structural properties when different surface type is used. These scenarios are confirmed by snapshots of typical states of the systems. From our study, we conclude that the thermodynamics of these transitions and the structural changes depend on the combined actions of both the composition of the H monomers and the P monomers in the HP chain and the surface types.

Highlights

Proteins are important biological molecules that perform most of the vital functions in living cells
On an AMD Opteron 2.2 GHz CPU, a single simulation took around 3-21 hours, 5-20 hours, and 1-12 hours for the 36mer confined between non-specific surfaces, polar surfaces, and hydrophobic surfaces, respectively
Further decrease in temperature induces the hydrophobic core (H-core) formation, where the adsorbed, extended chain collapses to form a compact structure, in which the hydrophobic monomers cluster together inside and the polar monomers reside on the outside

Summary

Introduction

Proteins are important biological molecules that perform most of the vital functions in living cells. Some proteins provide structural support, while others are involved in defending the body from antigens, or in muscle contraction [1]. In order to perform their specific functions, proteins must fold to a correct three dimensional shape or conformation, known as the native state. Incorrect protein folding are shown to be associated with a number of diseases, including Alzheimers, Huntington’s, Parkinsons, prion and other degenerative diseases [2,3,4].

Methods

Results

Conclusion