Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface

Rocchi, C.; Bizzarri, Anna Rita; Cannistraro, Salvatore

doi:10.1103/physreve.57.3315

Cited by 172 publications

(269 citation statements)

References 58 publications

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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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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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“…Such phenomena have been widely investigated by experiments [13][14][15][16][17][18] and by molecular simulations [19][20][21][22][23][24][25][26] for water in biological systems such as proteins and DNA.…”

Section: Introductionmentioning

confidence: 99%

Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

2005

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Atomistic molecular dynamics simulations are used to study generation 5 polyamidoamine (PAMAM) dendrimers immersed in a bath of water. We interpret the results in terms of three classes of water: buried water well inside of the dendrimer surface, surface water associated with the dendrimer-water interface, and bulk water well outside of the dendrimer. We studied the dynamic and thermodynamic properties of the water at three pH values: high pH with none of the primary or tertiary amines protonated, intermediate pH with only the primary amines protonated, and low pH with all amines protonated. For all pH values we find that both buried and surface water exhibit two relaxation times: a fast relaxation (∼1 ps) corresponding to the libration motion of the water and a slow (∼20 ps) diffusional component related to the escaping of water from one domain to another. In contrast for bulk water the fast relaxation is ∼0.4 ps while the slow relaxation is ∼14 ps. These results are similar to those found in biological systems, where the fast relaxation is found to be ∼1 ps while the slow relaxation ranges from 20 to 1000 ps. We used the 2PT MD method to extract the vibrational (power) spectrum and found substantial differences for the three classes of water. The translational diffusion coefficient for buried water is 11-33% (depending on pH) of the bulk value while the surface water is about 80%. The change in rotational diffusion is quite similar: 21-45% of the bulk value for buried water and 80% for surface water. This shows that translational and rotational dynamics of water are affected by the PAMAM-water interactions as well as due to the confinement in the interior of the dendrimer. We find that the reduction of translational or rotational diffusion is accompanied by a blue shift of the corresponding libration motions (∼10 cm -1 for translation, ∼35 cm -1 for rotation), indicating higher local force constants for these motions. These effects are most pronounced for the lowest pH, probably because of the increased rigidity caused by the internal charges. From the vibrational density of states we also calculate the enthalpies and entropies of the various waters. We find that water molecules are enthalpically favored near the PAMAM dendrimer: energy for surface water is ∼0.1 kcal/mol lower to that in the bulk, and ∼0.5-0.9 kcal/mol lower for buried water. In contrast, we find that both the buried and surface water are entropically unfavored: buried water is 0.9-2.2 kcal/mol lower than the bulk while the surface water is 0.1-0.2 kcal/mol lower. The net result is a thermodynamically unfavored state of the water surrounding the PAMAM dendrimer: 0.4-1.3 kcal/mol higher for buried water and 0.1-0.2 kcal/mol for surface water. This excess free energy of the surface and buried waters is released when the PAMAM dendrimer binds to DNA or metal ions, providing an extra driving force.

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“…The value of appears to depend on the thickness of the monitored layer. A typical example is water in hydration layers around plastocyanin, 31 where exponents = 1.7, = 1.5, and = 1.3 were found for layers with thicknesses of 4, 6, and 14 Å, respectively. Similar behavior, with Ϸ 1.5, was observed for water in a 6-Å-thick layer at the wall of a cylindrical silica cavity.…”

Section: -7mentioning

confidence: 99%

Water diffusion through a membrane protein channel: A first passage time approach

Hijkoop

Dammers

Malek

et al. 2007

The Journal of Chemical Physics

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Water diffusion through OmpF, a porin in the outer membrane of Escherichia coli, is studied by molecular dynamics simulation. A first passage time approach allows characterizing the diffusive properties of a well-defined region of this channel. A carbon nanotube, which is considerably more homogeneous, serves as a model to validate the methodology. Here we find, in addition to the expected regular behavior, a gradient of the diffusion coefficient at the channel ends, witness of the transition from confinement in the channel to bulk behavior in the connected reservoirs. Moreover, we observe the effect of a kinetic boundary layer, which is the counterpart of the initial ballistic regime in a mean square displacement analysis. The overall diffusive behavior of water in OmpF shows remarkable similarity with that in a homogeneous channel. However, a small fraction of the water molecules appears to be trapped by the protein wall for considerable lengths of time. The distribution of trapping times exhibits a broad power law distribution ͑ ͒ϳ −2.4 , up to = 10 ns, a bound set by the length of the simulation run. We discuss the effect of this distribution on the dynamic properties of water in OmpF in terms of incomplete sampling of phase space.

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Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface

Cited by 172 publications

References 58 publications

Biomolecular hydration: From water dynamics to hydrodynamics

Biomolecular hydration: From water dynamics to hydrodynamics

Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

Water diffusion through a membrane protein channel: A first passage time approach

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