Temperature dependence of protein dynamics simulated with three different water models

The effect of variation of the water model on the temperature dependence of protein and hydration water dynamics is examined by performing molecular dynamics simulations of myoglobin with the TIP3P, TIP4P, and TIP5P water models and the CHARMM protein force field at temperatures between 20 and 300 K. The atomic mean-square displacements, solvent reorientational relaxation times, pair angular correlations between surface water molecules, and time-averaged structures of the protein are all found to be similar, and the protein dynamical transition is described almost indistinguishably for the three water potentials. The results provide evidence that for some purposes changing the water model in protein simulations without a loss of accuracy may be possible

STRUCTURE ET DYNAMIQUE DE PROTEINES PHOTOSYNTHETIQUES ETUDIEES PAR DIFFUSION DE NEUTRONS ET SIMULATION PAR DYNAMIQUE MOLECULAIRE

ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Liquid-like and solid-like motions in proteins

Recent analyses of molecular dynamics simulations of hydrated C-phycocyanin suggest that the internal single-particle dynamics of this protein can be decomposed into four almost decoupled motion types: (1) diffusion of residues ("beads") in an effective harmonic potential, (2) corresponding vibrations in a local potential well, (3) purely rotational rigid side-chain diffusion, and (4) residue deformations. Each residue bead is represented by the corresponding C[α] carbon atom on the main chain. The effective harmonic residue potential can be imagined as the envelope of many local wells which are separated by small energy barriers. The residue friction matrix is assumed diagonal and the individual friction constants can be related to the density of the surrounding atoms. In this article we show that our model can be applied to lysozyme in solution as well, the only difference being that the side-chain deformations are more important and seem to be strongly correlated with the side-chain rotations. Comparing the simulated coherent scattering function of C-phycocyanin to a neutron spin-echo spectrum we show that our model can also describe collective motions in proteins at the residue level

Harmonicity in slow protein dynamics

International audienceThe slow dynamics of proteins around its native folded state is usually described by diffusion in a strongly anharmonic potential. In this paper, we try to understand the form and origin of the anharmonicities, with the principal aim of gaining a better understanding of the principal motion types, but also in order to develop more efficient numerical methods for simulating neutron scattering spectra of large proteins. First, we decompose a molecular dynamics (MD) trajectory of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water into three contributions that we expect to be independent: the global motion of the residues, the rigid-body motion of the sidechains relative to the backbone, and the internal deformations of the sidechains. We show that they are indeed almost independent by verifying the factorization of the incoherent intermediate scattering function. Then, we show that the global residue motions, which include all large-scale backbone motions, can be reproduced by a simple harmonic model which contains two contributions: a short-time vibrational term, described by a standard normal mode calculation in a local minimum, and a long-time diffusive term, described by Brownian motion in an effective harmonic potential. The potential and the friction constants were fitted to the MD data. The major anharmonic contribution to the incoherent intermediate scattering function comes from the rigid-body diffusion of the sidechains. This model can be used to calculate scattering functions for large proteins and for long-time scales very efficiently, and thus provides a useful complement to MD simulations, which are best suited for detailed studies on smaller systems or for shorter time scales

C-Phycocyanin Hydration Water Dynamics in the Presence of Trehalose: An Incoherent Elastic Neutron Scattering Study at Different Energy Resolutions

We present a study of C-phycocyanin hydration water dynamics in the presence of trehalose by incoherent elastic neutron scattering. By combining data from two backscattering spectrometers with a 10-fold difference in energy resolution we extract a scattering law S(Q,ω) from the Q-dependence of the elastic intensities without sampling the quasielastic range. The hydration water is described by two dynamically different populations—one diffusing inside a sphere and the other diffusing quasifreely—with a population ratio that depends on temperature. The scattering law derived describes the experimental data from both instruments excellently over a large temperature range (235–320 K). The effective diffusion coefficient extracted is reduced by a factor of 10–15 with respect to bulk water at corresponding temperatures. Our approach demonstrates the benefits and the efficiency of using different energy resolutions in incoherent elastic neutron scattering over a large angular range for the study of biological macromolecules and hydration water