The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation

Abseher, Roger; Schreiber, Hellfried; Steinhauser, Othmar

doi:10.1002/(sici)1097-0134(199607)25:3<366::aid-prot8>3.0.co;2-d

Cited by 107 publications

(130 citation statements)

References 2 publications

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“…This is in agreement with a previous study [88]. This bump (0.1 ps) is maximum for the bulk water and is shifted towards more negative values for the major and the minor groove water molecules, in agreement with previous observations [89,90]. This suggests that there are different forces at play on the waters occupying the major groove, the minor groove and the bulk region.…”

Section: Velocity Autocorrelation Of the Water Moleculessupporting

confidence: 91%

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

Samanta

Raghunathan

Mukherjee

2016

Journal of Molecular Graphics and Modelling

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Section: Velocity Autocorrelation Of the Water Moleculessupporting

confidence: 91%

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

Samanta

Raghunathan

Mukherjee

2016

Journal of Molecular Graphics and Modelling

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“…With 0 ϭ 2.1 ps at 20°C (30), this gives ͗ S ͘ ϭ 12 ps. Physical considerations (20) and molecular dynamics simulations (33)(34)(35) suggest that the distribution f( S ) is skewed toward longer S , and that it vanishes for S values somewhat shorter than 0 . A normalized distribution with these features is f( S ) ϭ ( S ͞ˆS 2 ) exp(Ϫ S ͞ˆS), which peaks at ˆS and has ͗ S Ϫ1 ͘ ϭ 2 ͗ S ͘ Ϫ1 .…”

Section: Resultsmentioning

confidence: 99%

Biomolecular hydration: From water dynamics to hydrodynamics

Halle

Davidovic²

2003

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

180

197

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Thermally driven rotational and translational diffusion of proteins and other biomolecules is governed by frictional coupling to their solvent environment. Prediction of this coupling from biomolecular structures is a longstanding biophysical problem, which cannot be solved without knowledge of water dynamics in an interfacial region comparable to the dry protein in volume. Efficient algorithms have been developed for solving the hydrodynamic equations of motion for atomic-resolution biomolecular models, but experimental diffusion coefficients can be reproduced only by postulating hundreds of rigidly bound water molecules. This static picture of biomolecular hydration is fundamentally inconsistent with magnetic relaxation dispersion experiments and molecular dynamics simulations, which both reveal a highly dynamic interface where rotation and exchange of nearly all water molecules are several orders of magnitude faster than biomolecular diffusion. Here, we resolve this paradox by means of a dynamic hydration model that explicitly links protein hydrodynamics to hydration dynamics. With the aid of this model, bona fide structure-based predictions of global biomolecular dynamics become possible, as demonstrated here for a set of 16 proteins for which accurate experimental rotational diffusion coefficients are available.T he translational and rotational motions of a protein molecule are three or more orders of magnitude slower than the relaxation of its linear and angular momenta and can therefore be described accurately by diffusion equations (1). Such global dynamics is thus characterized by isotropic translational (D T ) and rotational (D R ) diffusion coefficients, or by the corresponding tensors. The dynamic protein-solvent coupling is embodied in Einstein's fluctuation-dissipation theorem D T,R ϭ k B T͞ T,R (2). When this equation is combined with the results of macroscopic continuum hydrodynamics (3) for the friction coefficients of a sphere of radius a undergoing steady translation or rotation in a solvent of shear viscosity 0 , one obtains the celebrated Stokes-Einstein (SE) relationsMore elaborate expressions have been derived for ellipsoidal solutes (4). When applied to globular proteins, these expressions severely overestimate the diffusion coefficients. As an example, consider the rotation of hen egg-white lysozyme (HEWL). By using either the crystal structure or the partial specific volume in solution, one obtains a molecular volume of 16 nm 3 . Inserted into Eq. 1, this yields D R ϭ 42 s Ϫ1 in H 2 O at 20°C. If the elongated shape of HEWL is modeled by a prolate spheroid of aspect ratio 1.5, D R is reduced to 40 s Ϫ1 , still a factor 2 above the experimental value of 20 Ϯ 1 s Ϫ1 (5). Early workers attributed such discrepancies to ''bound'' water that migrates with the protein and therefore contributes to its hydrodynamic volume (6, 7). Measurements of transport coefficients like D T or D R thus became established as a method for quantifying protein hydration. Proteins, of course, do not have ellipsoid...

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“…If the hydration layer consisted of 'free' and 'bound' water molecules, as postulated, then one would expect bimodal distributions of residence times and rotational correlation times for hydration water. However, all simulations show that these distributions are unimodal (Abseher et al 1996;Luise et al 2000;Makarov et al 2000;Marchi et al 2002;Henchman & McCammon 2002). Also, from a structuralenergetic point of view, the notion of 'free' and 'bound' water molecules in the hydration layer is objectionable.…”

Section: Other Spectroscopic Probes Of Hydration Dynamicsmentioning

confidence: 99%

Protein hydration dynamics in solution: a critical survey

Halle

2004

Phil. Trans. R. Soc. Lond. B

492

576

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The properties of water in biological systems have been studied for well over a century by a wide range of physical techniques, but progress has been slow and erratic. Protein hydration-the perturbation of water structure and dynamics by the protein surface-has been a particularly rich source of controversy and confusion. Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. Recent oxygen-17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. The high mobility of hydration water ensures that all thermally activated processes at the protein-water interface, such as binding, recognition and catalysis, can proceed at high rates. The MRD-derived picture of a highly mobile hydration layer is consistent with recent molecular dynamics simulations, but is incompatible with results deduced from intermolecular nuclear Overhauser effect spectroscopy, dielectric relaxation and fluorescence spectroscopy. It is also inconsistent with the common view of hydration effects on protein hydrodynamics. Here, we show how these discrepancies can be resolved.

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The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation

Cited by 107 publications

References 2 publications

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

Biomolecular hydration: From water dynamics to hydrodynamics

Protein hydration dynamics in solution: a critical survey

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