Hydration-Coupled Dynamics in Proteins Studied by Neutron Scattering and NMR: The Case of the Typical EF-Hand Calcium-Binding Parvalbumin

Zanotti, Jean-Marc; Bellissent-Funel, Marie-Claire; Parello, Joseph

doi:10.1016/s0006-3495(99)77395-9

Cited by 131 publications

(124 citation statements)

References 86 publications

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“…Next we explore the hypothesis [50] that the observed glass transition in biomolecules [12,[51][52][53][54][55][56][57][58][59][60][61][62][63]71] is related to the liquid-liquid phase transition using MD simulations. Specifically, Kumar et al [50] studied the dynamic and thermodynamic behavior of lysozyme and DNA in hydration TIP5P water, by means of the software package GROMACS [64] for: (i) an orthorhombic form of hen egg-white lysozyme [65] and (ii) a Dickerson dodecamer DNA [66] at constant pressure P ¼ 1 atm, several constant temperatures T, and constant number of water molecules N (NPT ensemble).…”

Section: Glass Transition In Biomoleculesmentioning

confidence: 99%

The puzzling unsolved mysteries of liquid water: Some recent progress

Stanley

Kumar

et al. 2007

Physica A: Statistical Mechanics and its Applications

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Water is perhaps the most ubiquitous, and the most essential, of any molecule on earth. Indeed, it defies the imagination of even the most creative science fiction writer to picture what life would be like without water. Despite decades of research, however, water's puzzling properties are not understood and 63 anomalies that distinguish water from other liquids remain unsolved. We introduce some of these unsolved mysteries, and demonstrate recent progress in solving them. We present evidence from experiments and computer simulations supporting the hypothesis that water displays a special transition point (which is not unlike the ''tipping point'' immortalized by Malcolm Gladwell). The general idea is that when the liquid is near this ''tipping point,'' it suddenly separates into two distinct liquid phases. This concept of a new critical point is finding application to other liquids as well as water, such as silicon and silica. We also discuss related puzzles, such as the mysterious behavior of water near a protein. r

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Section: Glass Transition In Biomoleculesmentioning

confidence: 99%

The puzzling unsolved mysteries of liquid water: Some recent progress

Stanley

Kumar

et al. 2007

Physica A: Statistical Mechanics and its Applications

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“…A number of different experimental techniques like NMR, [1][2][3] time-resolved fluorescence spectroscopy, 4 neutron scattering, [5][6][7][8]11,18 ultrafast spectroscopy, 9 and IR absorption spectroscopy 10 have been used to study hydration water dynamics at the interface between a lipid bilayer membrane and bulk water. Most of these studies have been conducted a) Author to whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 99%

Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

Rønnest

Peters

Hansen

et al. 2016

The Journal of Chemical Physics

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Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes J. Chem. Phys. 140, 104901 (2014) Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-snglycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic potential within phospholipid membranes imply an enormous electric field of 10 8 -10 9 V m −1 , which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential for DMPG bilayers and found ∼1 V (∼2 · 10 8 V m −1 ) when in the fluid phase with a monovalent counter-ion and ∼1.4 V (∼2.8 · 10 8 V m −1 ) when in the gel phase with a divalent counter-ion. The number of water molecules for a fully hydrated DMPG membrane has been estimated to be 9.7 molecules per lipid in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) membranes but comparable to the number inferred for 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) membranes. Some of the properties of the DMPG membrane are compared with those of the neutral zwitterionic DMPC bilayer membrane at 303 K and 1 atm, which is the same reduced temperature with respect to the gel-to-fluid transition temperature as 310 K is for the DMPG bilayer membrane. C 2016 AIP Publishing LLC. [http://dx

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“…24 Neutron scattering experiments have shown protein dynamical amplitudes to increase upon hydration. [25][26][27] One possibility is that, in the absence of water, protein sidechains form hydrogen bonds with each other thus rigidifying the protein. Upon hydration, some of these hydrogen bonds would be transferred to water molecules, with the effect that the sidechains diffuse more freely in the solvent.…”

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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Hydration-Coupled Dynamics in Proteins Studied by Neutron Scattering and NMR: The Case of the Typical EF-Hand Calcium-Binding Parvalbumin

Cited by 131 publications

References 86 publications

The puzzling unsolved mysteries of liquid water: Some recent progress

The puzzling unsolved mysteries of liquid water: Some recent progress

Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

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

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