Temperature Dependence of Protein Dynamics: Computer Simulation Analysis of Neutron Scattering Properties

Hayward, Jennifer A.; Smith, Jeremy C.

doi:10.1016/s0006-3495(02)75478-7

Cited by 89 publications

(113 citation statements)

References 40 publications

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“…A second inflection in atomic MSDs, which is hydration-independent, was observed at a temperature between 100 and 150 K (10,18). The low temperature inflection that occurs even in dry samples was also seen in molecular dynamics (MD) simulations (19) and has been attributed to the onset of methyl group rotations (20,21).…”

mentioning

confidence: 81%

Coupling of protein and hydration-water dynamics in biological membranes

Wood

Plazanet

Gabel

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

154

174

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The dynamical coupling between proteins and their hydration water is important for the understanding of macromolecular function in a cellular context. In the case of membrane proteins, the environment is heterogeneous, composed of lipids and hydration water, and the dynamical coupling might be more complex than in the case of the extensively studied soluble proteins. Here, we examine the dynamical coupling between a biological membrane, the purple membrane (PM), and its hydration water by a combination of elastic incoherent neutron scattering, specific deuteration, and molecular dynamics simulations. Examining completely deuterated PM, hydrated in H2O, allowed the direct experimental exploration of water dynamics. The study of natural abundance PM in D2O focused on membrane dynamics. The temperature-dependence of atomic mean-square displacements shows inflections at 120 K and 260 K for the membrane and at 200 K and 260 K for the hydration water. Because transition temperatures are different for PM and hydration water, we conclude that ps-ns hydration water dynamics are not directly coupled to membrane motions on the same time scale at temperatures <260 K. Molecular-dynamics simulations of hydrated PM in the temperature range from 100 to 296 K revealed an onset of hydration-water translational diffusion at Ϸ200 K, but no transition in the PM at the same temperature. Our results suggest that, in contrast to soluble proteins, the dynamics of the membrane protein is not controlled by that of hydration water at temperatures <260 K. Lipid dynamics may have a stronger impact on membrane protein dynamics than hydration water. molecular dynamics simulations ͉ neutron spectroscopy ͉ dynamical transition ͉ purple membrane ͉ bacteriorhodopsin P roteins are animated by a multitude of motions occurring on various length and time scales. In a current model, a protein is not characterized by a single three dimensional structure but, rather, by a large number of conformations, so-called conformational substates, that interconvert via molecular motions (1). Natively unfolded proteins reflect this conformational heterogeneity to an extreme degree. The developing concept of a free-energy landscape has put some order into the complex world of protein motions (1). The energy landscape is a highdimensional space, in which each conformational substate is defined by the coordinates of all atoms in the protein. The energy landscape is organized in a hierarchy of levels; the top level containing only a few substates that interconvert by relatively slow large-scale movements (2). Each substate at this level contains, itself, a larger number of substates, separated by smaller barriers that are sampled by more rapid motions. At the third level, the number of substates becomes very large and the barriers very small, and motions at this level have been proposed to take place on the ps-ns time scale (2). Which of the motions on different levels are crucial for biological function and whether and how they are correlated with each other are chall...

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mentioning

confidence: 81%

Coupling of protein and hydration-water dynamics in biological membranes

Wood

Plazanet

Gabel

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

154

174

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“…many hundreds of molecules) and long simulation times can now be addressed (e.g. Smith, 1991;Tarek et al, 2001;Tarek and Tobias, 2002;Hayward and Smith, 2002;Wood et al, 2007;Meinhold et al, 2007;Marrink et al, 2007). The dashed rectangle in Fig.…”

Section: Membrane Dynamicsmentioning

confidence: 99%

Applications of neutron and X-ray scattering to the study of biologically relevant model membranes

Pabst

Kučerka

Nieh

et al. 2010

Chemistry and Physics of Lipids

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Applications of Neutron and X-ray Scattering to the Study of Biologically Relevant Model MembranesPabst, G.; Kučerka, N.; Nieh, M.-P.; Rheinstädter, M.C.; Katsaras, J.This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Scattering techniques, in particular electron, neutron and X-ray scattering have played a major role in elucidating the static and dynamic structure of biologically relevant membranes. Importantly, neutron and X-ray scattering have evolved to address new sample preparations that better mimic biological membranes. In this review, we will report on some of the latest model membrane results, and the neutron and X-ray techniques that were used to obtain them. Crown

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“…Subsequently, a number of neutron scattering and other experimental and computer simulation studies on various biological systems have revealed that many proteins exhibit this temperature-dependent dynamical transition around 180-220K (12,13,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31).…”

Section: Dynamics Protein Glass Transitionmentioning

confidence: 99%

“…However, neutron scattering experiments and molecular dynamics simulations have shown signatures of anharmonic dynamics well below the ~220K dynamical transition (24,(29)(30)(31). The dynamic processes associated with this low-temperature anharmonicity, and how these motions may be related to global dynamical changes at the dynamical transition, have yet to be fully understood.…”

Section: Dynamics Protein Glass Transitionmentioning

confidence: 99%

Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with Computer Simulation

Smith

Krishnan

Petridis

et al. 2011

Dynamics of Soft Matter

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The combination of molecular dynamics simulation and neutron scattering techniques has emerged as a highly synergistic approach to elucidate the atomistic details of the structure, dynamics and functions of biological systems. Simulation models can be tested by calculating neutron scattering structure factors and comparing the results directly with experiments. If the scattering profiles agree the simulations can be used to provide a detailed decomposition and interpretation of the experiments, and if not, the models can be rationally adjusted. Comparison with neutron experiment can be made at the level of the scattering functions or, less directly, of structural and dynamical quantities derived from them. Here, we examine the combination of simulation and experiment in the interpretation of SANS and inelastic scattering experiments on the structure and dynamics of proteins and other biopolymers.2

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Temperature Dependence of Protein Dynamics: Computer Simulation Analysis of Neutron Scattering Properties

Cited by 89 publications

References 40 publications

Coupling of protein and hydration-water dynamics in biological membranes

Coupling of protein and hydration-water dynamics in biological membranes

Applications of neutron and X-ray scattering to the study of biologically relevant model membranes

Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with Computer Simulation

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