Journal ArticleDOI
Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results
Reads0
Chats0
TLDR
An extension of the technique of umbrella sampling to two dimensions is presented and applied to the study of the kinetic and thermodynamic properties of side chains in peptides in this paper, where four two-dimensional potential-of-mean-force surfaces for the two degrees of freedom χ1 and χ2 of the four phenylalanine residues in antamanide at 300 K are calculated using the stochastic dynamics simulation method with the molecular force field GROMOS.Abstract:
An extension of the technique of umbrella sampling to two dimensions is presented and applied to the study of the kinetic and thermodynamic properties of side chains in peptides. Four two-dimensional potential-of-mean-force surfaces for the two degrees of freedom χ1 and χ2 of the four phenylalanine residues in antamanide at 300 K are calculated using the stochastic dynamics simulation method with the molecular force field GROMOS. From these surfaces, time constants for the transitions between the favored conformations along χ1 and χ2 are calculated using transition state theory. The results are compared with experimental values determined by NMR. In addition, motionally averaged 3J-coupling constants are calculated from the rotamer probability distributions derived from the χ1, χ2 potential-of-mean-force surfaces using the generalized Karplus equations. The average values are compared to the experimental NMR results. It is shown that the two-dimensional umbrella-sampling approach is capable of providing d...read more
Citations
More filters
Journal ArticleDOI
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
Christian Bartels,Martin Karplus +1 more
TL;DR: In this paper, a new adaptive umbrella sampling technique for molecular dynamics simulations is described, which is achieved by using the weighted histogram analysis method to combine the results from different simulations, by a suitable extrapolation scheme to define the umbrella potential for regions that have not been sampled, and by a criterion to identify simulations during which the system was not in equilibrium.
Journal ArticleDOI
The alanine dipeptide free energy surface in solution
TL;DR: In this paper, three models of solvation were considered; (i) a simple scaling of electrostatic interactions, (ii) solvation energies determined by finite difference Poisson-Boltzmann calculations, and (iii) inclusion of explicit TIP3P solvent molecules.
Journal ArticleDOI
Conformational dynamics and distribution of nitroxide spin labels
TL;DR: These results are critically discussed in a unifying picture based on rotameric states of the group that carries the spin label andiencies in the current understanding of dynamics and conformations of spin labeled groups and of their influence on NMR observables are highlighted.
Journal ArticleDOI
Free Energy Surface, Reaction Paths, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase
TL;DR: In this paper, the authors applied molecular dynamics umbrella-sampling simulations and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to explore the free energy surface, reaction paths, and dideuterium kinetic isotope effect (KIE) of the β-oxidation of butyryl-coenzyme A by short-chain acyl-CoA dehydrogenase.
Journal ArticleDOI
Assessing the effect of conformational averaging on the measured values of observables
TL;DR: A general analytic formalism is proposed to determine the sensitivity of a spectroscopic observable to the underlying distribution of conformations and provides an expression for a weighted average across conformational substates that is independent of the averaging function used.
References
More filters
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
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
G.M. Torrie,John P. Valleau +1 more
TL;DR: In this paper, the authors describe the use of arbitrary sampling distributions chosen to facilitate the estimate of the free energy difference between a model system and some reference system, but the conventional Monte Carlo methods of obtaining such averages are inadequate for the free-energy case.
Journal ArticleDOI
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.
Journal ArticleDOI
Contact Electron‐Spin Coupling of Nuclear Magnetic Moments
TL;DR: In this article, the valence-bond theory for the contact electron-spin coupling of nuclear magnetic moments is used to calculate the proton−proton, proton-fluorine, and fluorine-florine coupling constants in ethanic and ethylenic molecules.
Related Papers (5)
An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
G.M. Torrie,John P. Valleau +1 more