Glassy behavior of a protein

Iben, Icko; Braunstein, D.; Doster, Wolfgang; Frauenfelder, Hans; Hong, Mineui; Johnson, Jerald B.; Luck, Stanley; Ormos, Pál; Schulte, Alfons; Steinbach, Peter; Xie, Aihua; Young, Robert D.

doi:10.1103/physrevlett.62.1916

Cited by 416 publications

(348 citation statements)

References 31 publications

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“…Experimental measurements of the rebinding kinetics of CO to myoglobin indeed observed a stretched-exponential time dependence [5][6][7][8]. These observations led Frauenfelder et al [5[ to propose the existence of a hierarchy of motions occurring at various timescales, which results from an ensemble of nearly degenerate states separated by a hierarchical distribution of enthalpic energy barriers.…”

Section: Discussionmentioning

confidence: 99%

“…Proteins exhibit motions on a very wide range of timescales from picoseconds (ps) [1][2][3] to seconds [4] (as studied by hydrogen exchange experiments). Experimental studies on myoglobin suggest the existence of a hierarchy of motions occurring at various timescales and resulting from an ensemble of nearly degenerate states separated by a distribution of enthalpic energy barriers [5][6][7][8]. On longer timescales (milliseconds to seconds) many proteins seem to follow an energy-like funnel to the folded state [9,10].…”

Section: Introductionmentioning

confidence: 99%

“…In support of these observations Garcfa [29] showed that the fluctuations of a protein in solution are best described in terms of large-amplitude nonlinear motions. Molecular dynamics (MD) simulations, ligand recombination [30], pressure relaxation [7,8], time resolved X-ray crystallography [31 ] and vibrational echo studies [1][2][3] give information about the lower end of the funnel or energy landscape that is sampled in the folded state. Computational evidence (MD and Monte Carlo (MC) simulations) for the existence of these substates have been previously discussed in the literature [29,[32][33][34].…”

Section: Introductionmentioning

confidence: 99%

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Multi-basin dynamics of a protein in a crystal environment

Garcı́a

Blumenfeld

Hummer

et al. 1997

Physica D: Nonlinear Phenomena

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The dynamics of the small protein crambin is studied in the crystal environment by means of a 5.1 nanoseconds molecular dynamics (MD) simulation. The resulting trajectory is analyzed in terms of a small set of nonlinear dynamical modes that best describe the molecule's fluctuations. These modes are nonlinear in the sense that they describe a trajectory exhibiting multiple transitions among local minima at various timescales. Nonlinear modes are responsible for most of the protein atomic fluctuations. An ultrametric hierarchy of sampled local minima describes the protein trajectory when structures are classified in terms of their interconfigurational mean squared distance. Transitions among minima involve small changes in the relative atomic positions of many atoms in the protein. The character of the MD trajectory fits within the framework of rugged energy landscape dynamics. This MD simulation clarifies the unique statistical features of the barriers between minima in the energy-like configurational landscape. Longer timescale dynamics seem to sample transitions between minima separated by relatively higher barriers. The MD trajectory of the system in configurational space can be described in terms of diffusion of a particle in real space with a waiting time distribution due to partial trapping in shallow minima. A description of the dynamics in terms of an open Newtonian system (the protein) coupled to a stochastic system (the solvent and fast quasiharmonic modes of the protein) reveals that the system loses memory of its configurational space within a few picoseconds. The diffusion of the protein in configurational space is anomalous in the sense that the mean square displacement increases sublinearly with time, i.e., as a power law with an exponent that is smaller than unity.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multi-basin dynamics of a protein in a crystal environment

Garcı́a

Blumenfeld

Hummer

et al. 1997

Physica D: Nonlinear Phenomena

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“…Devoid of hydration water, proteins are inactive 10 and lack essential motions, thus implicitly suggesting a close relationship between protein and hydration water dynamics. The term 'slaving' has been used to express that water can impose its dynamical fingerprint on a protein 11,12 . Cryo-temperature dependent neutron scattering experiments revealed the solvent dependence of dynamical transitions in soluble proteins [13][14][15][16][17][18][19][20][21] and in RNA 22 and provided insights into the coupling between them.…”

Section: Introductionmentioning

confidence: 99%

From shell to cell: neutron scattering studies of biological water dynamics and coupling to activity

et al. 2009

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An integrated picture of hydration shell dynamics and of its coupling to functional macromolecular motions is proposed from studies on a soluble protein, on a membrane protein in its natural lipid environment, and on the intracellular environment in bacteria and red blood cells. Water dynamics in multimolar salt solutions was also examined, in the context of the very slow water component previously discovered in the cytoplasm of extreme halophilic archaea. The data were obtained from neutron scattering by using deuterium labelling to focus on the dynamics of different parts of the complex systems examined.

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“…[10][11][12][13] The motions below the transition are believed to be mostly harmonic whereas the mean-square displacements above the transition are dominated by anharmonic contributions. Below the transition the protein may be trapped in local potential energy minima or 'conformational substates' of the protein.…”

Section: Introductionmentioning

confidence: 99%

Temperature and timescale dependence of protein dynamics in methanol : water mixtures

Tournier

Réat

Dunn

et al. 2005

Phys. Chem. Chem. Phys.

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Experimental and computer simulation studies have suggested the presence of a transition in the dynamics of hydrated proteins at around 180-220 K. This transition is manifested by nonlinear behaviour in the temperature dependence of the average atomic mean-square displacement which increases at high temperature. Here, we present results of a dynamic neutron scattering analysis of the transition for a simple enzyme: xylanase in water : methanol solutions of varying methanol concentrations. In order to investigate motions on different timescales, two different instruments were used: one sensitive to B100 ps timescale motions and the other to Bns timescale motions. The results reveal distinctly different behaviour on the two timescales examined. On the shorter timescale the dynamics are dictated by the properties of the surrounding solvent: the temperature of the dynamical transition lowers with increasing methanol concentration closely following the melting behaviour of the corresponding water : methanol solution. This contrasts with the longer (ns) timescale results in which the dynamical transition appears at temperatures lower than the corresponding melting point of the cryosolvent. These results are suggested to arise from a collaborative effect between the protein surface and the solvent which lowers the effective melting temperature of the protein hydration layer. Taken together, the results suggest that the protein solvation shell may play a major role in the temperature dependence of protein solution dynamics.

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Glassy behavior of a protein

Cited by 416 publications

References 31 publications

Multi-basin dynamics of a protein in a crystal environment

Multi-basin dynamics of a protein in a crystal environment

From shell to cell: neutron scattering studies of biological water dynamics and coupling to activity

Temperature and timescale dependence of protein dynamics in methanol : water mixtures

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