Journal ArticleDOI
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more
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TLDR
The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.Abstract:
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...read more
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Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
TL;DR: This work shows that the conserved glutamic acid 242 near the active site of CcO undergoes a protonation state-dependent conformational change, which provides a valve in the pumping mechanism that ensures that at any point in time, the proton pathway across the membrane is effectively discontinuous, thereby preventing thermodynamically favorable proton back-leakage.
Journal ArticleDOI
Molecular dynamics simulations of sodium dodecyl sulfate micelles in water-the effect of the force field.
TL;DR: It is found that the Lennard-Jones (L-J) parameters for the sodium ions and the ionic oxygens of the SDS head group, as well as the water model, control the transition to bicelles, regardless of other L-J parameters.
Journal ArticleDOI
Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling.
TL;DR: Conformational changes occurring on the microsecond-millisecond time scale in basic pancreatic trypsin inhibitor (BPTI) are investigated using nuclear magnetic resonance spectroscopy to characterize the kinetics and mechanism of chemical exchange line broadening of the backbone of Cys 14, Lys 15, Cys 38, and Arg 39 in BPTI.
Gromacs User Manual Version 4.6
E. Apol,Rossen Apostolov,Herman J. C. Berendsen,A. van Buuren,Pär Bjelkmar,R. van Drunen,A. Feenstra,S. Fritsch,Gerrit Groenhof,Christoph Junghans,Peter M. Kasson,Per Larsson,P. Meulenhoff,Teemu Murtola,Szilárd Páll,Sander Pronk,Roland Schulz,Michael R. Shirts,A Sijbers,P. Tieleman,Berk Hess,D. van der Spoel,Erik Lindahl +22 more
Journal ArticleDOI
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.
Demian Riccardi,Peter König,Peter König,Xavier Prat-Resina,Haibo Yu,Marcus Elstner,Thomas Frauenheim,Thomas Frauenheim,Qiang Cui +8 more
TL;DR: An energetics motivated framework is established that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.
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.
Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
Journal ArticleDOI
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.