Orientational correlation function for molecular liquids: The case of liquid water

Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure and folding. Here, using molecular dynamics simulation, we provide an explanation of recent x-ray and neutron solution scattering data that indicate that the density of water on the surface of lysozyme is significantly higher than that of bulk water. The simulationderived scattering profiles are in excellent agreement with the experiment. In the simulation, the 3-Å-thick first hydration layer is 15% denser than bulk water. About two-thirds of this increase is the result of a geometric contribution that would also be present if the water was unperturbed from the bulk. The remaining third arises from modification of the water structure and dynamics, involving approximately equal contributions from shortening of the average water-water O-O distance and an increase in the coordination number. Variation in the first hydration shell density is shown to be determined by topographical and electrostatic properties of the protein surface. On average, denser water is found in depressions on the surface in which the water dipoles tend to be aligned parallel to each other by the electrostatic field generated by the protein atoms.A characterization of protein hydration is essential for understanding protein structure, folding, and function. This characterization requires elucidating the effects of both the solvent on the protein and the protein on the solvent (1, 2). Concerning the latter effect, detailed information on ordering and dynamical properties of individual, highly perturbed, strongly bound water molecules has been furnished by highresolution x-ray crystallography and NMR spectroscopy (3-10). However, to obtain the data required for a complete thermodynamic description of protein hydration it is necessary to obtain a more global picture in which the solvent is described in terms of probability distributions. Recent work in this direction has used molecular dynamics (MD) simulation (11-13) and novel crystallographic methods (6,7,14) to enable radial distribution functions of water molecules around protein groups in crystals and related quantities to be obtained.It is of particular importance to determine how protein surface water is on average perturbed from the bulk. An intriguing result in this regard was reported by Svergun et al. (15), who combined small-angle scattering (SAS) of x-rays in H 2 O with that of neutrons in H 2 O and D 2 O to show that for lysozyme and other proteins the average density of the first hydration shell (0-3 Å from the surface) is significantly higher than that of bulk water. This finding is consistent with results from MD simulation (16) and the crystallographic work (14). The present article explains the physical origin of this effect. We use MD simulation of lysozyme in explicit water to determine the contributions to the hydration density profile. The MD allows detailed structural properties of the hydration water to be analyzed in the context of the SAS resul...

show abstract

“…The standard radial distribution function g(r) from this simulation is also shown in Fig. 1 and is also in good agreement with experiment (31).…”

Section: Resultssupporting

confidence: 70%

Is the first hydration shell of lysozyme of higher density than bulk water?

Merzel

Smith²

2002

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

352

276

View full text Add to dashboard Cite

show abstract

“…simulations of popular models [4, 13-15, 19, 22, 31, 37, 40] where in again the sum rule is maintained at every step of the dynamics and many bulk and other correlation properties [36] are well reproduced and are consistent with experiments [27,34,35,41].…”

Section: Introductionsupporting

confidence: 49%

Molecular mean field theory for liquid water

Anishetty

2012

Physica A: Statistical Mechanics and its Applications

View full text Add to dashboard Cite

show abstract

“…Detailed analyses of neutron-scattering data from liquid water, based on higher body correlation functions and using different analytical approaches, have consistently shown the dominance of the near tetrahedral hydrogen-bonding motif (e.g. Soper 1994Soper , 2001). Furthermore, conventional analysis of oxygen K-edge extended X-ray absorption fine-structure spectroscopy data, which is intimately related with the XANES data under discussion, but considerably less subject to uncertainties in the precise form of the atomic potential due to the higher energy of the photoelectron, shows that the local structure is fully consistent with the accepted fourfold coordinated models of water (Bowron et al 2000).…”

Section: So Why Might Water Be Special?mentioning

confidence: 99%

Water? What's so special about it?

Finney

2004

Phil. Trans. R. Soc. Lond. B

165

169

View full text Add to dashboard Cite

What is so special about water? Why does it have the properties it has, and how might these reasons be relevant to its apparent biological importance? By exploring the structure and dynamics of water, from the isolated molecule and its interactions, through its many crystalline phases and to its so-called anomalous liquid phase, some of its apparently unusual behaviour is rationalized. The way in which it interacts with some relatively simple interfaces is also discussed. As a result of this exploration, a checklist of possible molecular-level reasons for its biological importance is devised.

show abstract

Orientational correlation function for molecular liquids: The case of liquid water

Cited by 213 publications

References 14 publications

Is the first hydration shell of lysozyme of higher density than bulk water?

Is the first hydration shell of lysozyme of higher density than bulk water?

Molecular mean field theory for liquid water

Water? What's so special about it?

Contact Info

Product

Resources

About