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Reversible folding/unfolding of small α-helix in explicit solvent investigated by ABEEMσπ/MM

Science China Chemistry 2009年第11期52卷 1917-1924页

作者： LIU Cui & YANG ZhongZhi Chemistry and Chemical Engineering Faculty,Liaoning Normal University,Dalian 116029,China 1. Chemistry and Chemical Engineering Faculty Liaoning Normal University Dalian 116029 China

We have performed molecular dynamics simulations on the reversible folding/unfolding of small α-helix(short Ala based peptide Ala5) in explicit water solvent in terms of ABEEMσπ/MM.A dynamics analysis shows that the α-helical turn can be preserved up to a period of about 2 ns at 300 K,which supports the conclusions of Margulis et *** time trajectory of the root mean square deviation between the heavy atoms of the backbone and the helical reference structure indicate that "helix melting and formation occurs rapidly on a time scale of 0.1 ns at 300 K" is not a felicitous *** first quantificationally concluded that the helix nucleation can maintain 2 ns,1―1.5 ns and 0.8 ns for Ala5 at 300 K,400 K and 500 K,***,increasing temperature dose not alter the pathway of folding/unfolding,but change the *** analysis of structures in a "transition-state ensemble" shows that helix-to-coil transitions occurs predominantly through breaking of hydrogen bonds at the helix ends(92%),particularly at the C-terminus(50%).Hydrogen bonds' breaking and formation occurs on a time scale of 0.1 ns.

关键词： reversible folding/unfolding of protein Ala5 temperature hydrogen bond

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A network of conformational transitions in an unfolding process of HP-35 revealed by high-temperature MD simulation and a Markov state model

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Chinese Physics B 2018年第1期27卷 175-181页

作者：邵丹丹高恺夫 Institute of Biophysics and Department of Physics Central China Normal University

An understanding of protein folding/unfolding processes has important implications for all biological processes, in- eluding protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics （MD） simulations are uniquely suitable for it because of their atomic level resolution and accuracy. However, limited by computational ca- pabilities, nowadays even for small and fast-folding proteins, all-atom MD simulations of protein folding still presents a great challenge. An alternative way is to study unfolding process using MD simulations at high temperature. High temper- ature provides more energy to overcome energetic barriers to unfolding, and information obtained from studying unfolding can shed light on the mechanism of folding. In the present study, a 1000-ns MD simulation at high temperature （500 K） was performed to investigate the unfolding process of a small protein, chicken villin headpiece （HP-35）. To infer the folding mechanism, a Markov state model was also built from our simulation, which maps out six macrostates during the folding/unfolding process as well as critical transitions between them, revealing the folding mechanism unambiguously.

关键词： molecular dynamics simulation Markov state model folding/unfolding HP-35

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Molecular Mechanism of Self-assembly of Aromatic Oligoamides into Interlocked Double-helix Foldamers

Molecular Mechanism of Self-assembly of Aromatic Oligoamides...

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第十三届全国量子化学会议

作者： Dongbo Zhao Yigao Yuan Hanchen Wang Hao Dong Shuhua Li Kuang Yaming Honors School Nanjing University Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical EngineeringNanjing University

Foldamer, with a propensity to fold into a 3D structure in solution, has been a hot button in supramolecular chemistry, due to its similarity to the structures and functions of biopolymers. Central issue in foldamer science is to understand how the primary sequence of oligomer folds into ordered structure, and how the individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable. Despite of the increasing emergence of new foldamers, the detailed mechanism remains an open question. Taking an artificially synthesized arylamide oligoamide foldamer as illustration, we aim to dissect the folding and self-association mechanisms of the double-helix foldamer with quantum chemical computations and molecular modelling. Our results reveal that the dimerization of two single helical motifs is energetically favorable, and that the spontaneous self-assembly into an entwined dimer proceeds through an ″unwinding-inserting-threading-rewinding″ mechanism. The detailed mechanisms about folding and self-assembly in aromatic oligoamide foldamer we present here disclose how the sequence is associated with the well-ordered three-dimensional structure at atomic level, and therefore may have implications for designing new foldamers with versatile functions.

关键词： Supramolecular chemistry Foldamer folding/unfolding Self-assembly/disassembly

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