关键词: 内禀无序蛋白/
构象/
序列/
分子模拟
English Abstract
Conformation of disordered peptides modulated by distributions of charged residues: Case study of random peptides composed of arginines and aspartic acids
Kang Wen-Bin1,2,3,Wang Jun1,
Wang Wei1
1.School of Physics, Nanjing University, Nanjing 210093, China;
2.Department of Mathematics and Physics, Hubei University of Medicine, Shiyan 442000, China;
3.Bio-X Research Center, Hubei University of Medicine, Shiyan 442000, China
Fund Project:Project supported by the National Basic Research Program of China (Grant No. 2013CB834100), the National Natural Science Foundation of China (Grant Nos. 11334004, 11174133, 81421091, 11774157), the 2017 National Training Program of Innovation and Entrepreneurship for Undergraduates, China (Grant No. 201710929002), and the Initial Project for Post-Graduates of Hubei University of Medicine, China (Grant No. 2011QDZR-11).Received Date:17 October 2017
Accepted Date:11 December 2017
Published Online:05 March 2018
Abstract:The relationship between the sequential and structural features of intrinsically disordered peptides (IDPs) has attracted much attention during the recent decade. One essential problem relating to sequence-structure relationship is how the distribution of charged residues affects the structure of IDP. In this work, we address this problem with simulations on a series of random peptides composed of arginine and aspartic acids. With the ABSINTH implicit solvation model, the structural ensembles are generated with Markov Chain Monte Carlo method and replica-exchange sampling. The relations between various structural features (including the gyration radius, the tail distance, the distance between residues, and asphericity) and the distribution of charged residues are analyzed. Several limit cases (with parts of interactions switched off) are also calculated for comparison. The conversion from extended conformations to compact structures is observed, following the demixing of negatively and positively charged residues along the sequence. For the cases with well-mixed charges, the intra-chain electrostatic repulsions and attractions are balanced, which results in a generic Flory random coil-like conformation. Differently, for the case with well-separated charged residues, the electrostatic attraction between residues distant along the sequence induces a semi-compact hairpin-like conformation. This is consistent with the observations of Pappu group. Our results suggest that the structural dependence on charge distribution would not be sensitive to the selection of amino acid, and is determined by the patterns of charges, which demonstrates the robustness of the mechanism that the charge distribution modulates the structural features in the IDP system. Our results may broaden our understanding of the sequence-structure relation of IDP system.
Keywords: intrinsically disordered protein/
structural ensemble/
sequence/
molecular simulation
