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Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study
Author(s) -
Nguyen Phuong H.,
Mu Yuguang,
Stock Gerhard
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20485
Subject(s) - molecular dynamics , energy landscape , chemistry , conformational isomerism , conformational ensembles , computational chemistry , azobenzene , folding (dsp implementation) , peptide , replica , maxima and minima , chemical physics , crystallography , molecule , organic chemistry , art , mathematical analysis , biochemistry , mathematics , engineering , electrical engineering , visual arts
A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced‐sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than ∼100‐ns length are either trapped in local minima (at 295 K) or—if run at high temperature—do not resemble the room‐temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and 3 J‐couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501–514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans ‐isomer of the azobenzene peptide exhibits a well‐defined structure, while the cis ‐isomer is a conformational heterogeneous system; that is, the trans ‐isomer occurs in 2 well‐defined conformers, while the cis ‐isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed. Proteins 2005. © 2005 Wiley‐Liss, Inc.