Residue Folding Degree—Relationship to Secondary Structure Categories and Use as Collective Variable

International Journal of Molecular Sciences

卷:22

Ryuhei Harada¹  Yasuteru Shigeta¹  Vladimir Sladek² 

[1] Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan;

[2] Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia;

关键词: protein folding;    secondary structure;    networks;    collective variables;    molecular dynamics;   

DOI  :  10.3390/ijms222313042

来源: DOAJ

【 摘 要 】

Recently, we have shown that the residue folding degree, a network-based measure of folded content in proteins, is able to capture backbone conformational transitions related to the formation of secondary structures in molecular dynamics (MD) simulations. In this work, we focus primarily on developing a collective variable (CV) for MD based on this residue-bound parameter to be able to trace the evolution of secondary structure in segments of the protein. We show that this CV can do just that and that the related energy profiles (potentials of mean force, PMF) and transition barriers are comparable to those found by others for particular events in the folding process of the model mini protein Trp-cage. Hence, we conclude that the relative segment folding degree (the newly proposed CV) is a computationally viable option to gain insight into the formation of secondary structures in protein dynamics. We also show that this CV can be directly used as a measure of the amount of $\alpha$-helical content in a selected segment.

【 授权许可】

Unknown