Effect of surface attractive strength on structural transitions of a confined HP lattice protein

26th IUPAP Conference on Computational Physics

物理学;计算机科学

Pattanasiri, Busara^1 ; Li, Ying Wai^2 ; Wust, Thomas^3 ; Landau, David P.^1

Center for Simulational Physics, Department of Physics and Astronomy, University of Georgia, Athens

GA

30602, United States^1

National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge

TN

37831, United States^2

Scientific IT Services, ETH Zürich IT Services, Zürich

8092, Switzerland^3

关键词: Conformational transitions;    Density of state;    Hydrophobic core;    Lattice proteins;    Lower temperatures;    Structural transitions;    Temperature decrease;    Wang-Landau sampling;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/640/1/012015/pdf
DOI  :  10.1088/1742-6596/640/1/012015

学科分类：计算机科学（综合）

来源: IOP

【 摘 要 】

We investigate the influence of surface attractive strength on structural transitions of a hydrophobic-polar (HP) lattice protein confined in a slit formed by two parallel, attractive walls. We apply Wang-Landau sampling together with efficient Monte Carlo updates to estimate the density of states of the system. The conformational transitions, namely, the debridging process and hydrophobic core formation, can be identified by analyzing the specific heat together with several structural observables, such as the numbers of surface contacts, the number of hydrophobic pairs, and radii of gyration in different directions. As temperature decreases, we find that the occurrence of the debridging process is conditional depending on the surface attractive strength. This, in turn, affects the nature of the hydrophobic core formation that takes place at a lower temperature. We illustrate these observations with the aid of a HP protein chain with 48 monomers.