Journal ArticleDOI
Solvent mobility and the protein 'glass' transition.
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TLDR
A novel molecular dynamics simulation procedure with the protein and solvent at different temperatures has been used, showing the essential role of solvent in controlling functionally important protein fluctuations above 180 K.Abstract:
Proteins and other biomolecules undergo a dynamic transition near 200 K to a glass-like solid state with small atomic fluctuations. This dynamic transition can inhibit biological function. To provide a deeper understanding of the relative importance of solvent mobility and the intrinsic protein energy surface in the transition, a novel molecular dynamics simulation procedure with the protein and solvent at different temperatures has been used. Solvent mobility is shown to be the dominant factor in determining the atomic fluctuations above 180 K, although intrinsic protein effects become important at lower temperatures. The simulations thus complement experimental studies by demonstrating the essential role of solvent in controlling functionally important protein fluctuations.read more
Citations
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Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
Molecular dynamics simulations of biomolecules
TL;DR: A brief description of the origin and early uses of biomolecular simulations is presented, some recent studies that illustrate the utility of such simulations are outlined and their ever-increasing potential for contributing to biology is discussed.
Journal ArticleDOI
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis.
Katherine A. Henzler-Wildman,Ming Lei,Vu Hong Thai,S. Jordan Kerns,Martin Karplus,Dorothee Kern +5 more
TL;DR: It is shown that pico- to nano-second timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state.
Journal ArticleDOI
Control of the selectivity of the aquaporin water channel family by global orientational tuning.
Emad Tajkhorshid,Peter Nollert,Morten Østergaard Jensen,Larry J. W. Miercke,Joseph D. O'Connell,Robert M. Stroud,Klaus Schulten +6 more
TL;DR: Aquaporins are transmembrane channels found in cell membranes of all life forms and their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, is examined.
Journal ArticleDOI
Molecular Dynamics of Water at the Protein-Solvent Interface
TL;DR: In this article, a variety of structural and dynamical properties of protein hydration water are reviewed and compared with those of bulk and with corresponding experimental results, which can be traced back to the complexity of the overall protein−solvent energy landscape.
References
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Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
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Canonical dynamics: Equilibrium phase-space distributions
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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
Formation of glasses from liquids and biopolymers.
TL;DR: The onset of a sharp change in ddT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature.
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The energy landscapes and motions of proteins.
TL;DR: The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.