Article
Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology.
Center for Biophysical Modeling & Simulations and Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112.
Journal of Chemical Theory and Computation (impact factor:
5.22).
09/2010;
6(9):2566-2580.
DOI:10.1021/ct900579k
pp.2566-2580
Source: PubMed
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Cited In (0)
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Article: Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.
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ABSTRACT: A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than that of the overall rotational diffusion of ubiquitin and whose effects would not be apparent in experimentally derived order parameters. A coupled analysis of internal and overall motion yields simulated order parameters substantially closer to the experimentally determined values than is the case for a conventional analysis of internal motion alone. Improved agreement between simulation and experiment also is encouraging from the viewpoint of assessing the accuracy of long MD simulations.The Journal of Physical Chemistry B 06/2008; 112(19):6155-8. · 3.70 Impact Factor
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Keywords
chemically accurate framework
classical Transition State theory
full-dimensional reactive electronic potential energy surface
intramolecular proton transfer
kinetic isotope effect
level ab initio calculations
Path-Integral Quantum Transition State Theory
Quantum Instanton approach
reactive dynamics
two methods