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The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration. 相似文献
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Two new methods are assessed for determining the location of hydration sites around proteins from computer simulation. Current methods extract hydration sites from peaks in the water density constructed in the protein frame. However, the dynamic nature of the water molecules, the nearby protein residues, and the protein reference frame as a whole tend to smear out the water density, making it more difficult to resolve sites. Two techniques are introduced to better resolve the water density. The first is to construct the water density from the time-averaged position of each water molecule in the protein frame while the water remains within a given distance of this averaged position. The second technique is to construct the water density from the time-averaged position of each water in the reference frame only of the nearby residues. Criteria for determining hydration sites from the water density are examined. Both techniques are found to significantly improve the detail in the water density and the number of hydration sites detected. 相似文献
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The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase. 相似文献
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Hao Yi Xian Zhang Yunliang Zhao Lingyun Liu Shaoxian Song 《Surface and interface analysis : SIA》2016,48(9):976-980
Molecular dynamics simulations (MDS) of montmorillonite (001)/water interface system were used for studying the hydration shell on the montmorillonite surface in this work. The study was performed on the simulation of concentration profile and self‐diffusion coefficients. The results have shown that there was a hydration shell on the surface with the thickness of approximately 1.74 nm, which was composed of six ordered water molecule layers, including ordered layers and transition layers. The water molecules in the shell were closely and orderly arranged than those in bulk water, leading to a higher concentration of water molecules. Copyright © 2016 John Wiley & Sons, Ltd. 相似文献
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The solvent molecular distribution significantly affects the behavior of the solute molecules and is thus important in studying many biological phenomena. It can be described by the solvent molecular density distribution, g, and the solvent electric dipole distribution, p. The g and p can be computed directly by counting the number of solvent molecules/dipoles in a microscopic volume centered at r during a simulation or indirectly from the mean force F and electrostatic field E acting on the solvent molecule at r, respectively. However, it is not clear how the g and p derived from simulations depend on the solvent molecular center or the solute charge and if the g(F) and p(E) computed from the mean force and electric field acting on the solvent molecule, respectively, could reproduce the corresponding g and p obtained by direct counting. Hence, we have computed g, p, g(F), and p(E) using different water centers from simulations of a solute atom of varying charge solvated in TIP3P water. The results show that g(F) and p(E) can reproduce the g and p obtained using a given count center. This implies that rather than solving the coordinates of each water molecule by MD simulations, the distribution of water molecules could be indirectly obtained from analytical formulas for the mean force F and electrostatic field E acting on the solvent molecule at r. Furthermore, the dependence of the g and p distributions on the solute charge revealed provides an estimate of the change in g and p surrounding a biomolecule upon a change in its conformation. 相似文献
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Matthias Wohlgemuth Dr. Mitsuhiko Miyazaki Dr. Martin Weiler Prof. Makoto Sakai Prof. Otto Dopfer Prof. Masaaki Fujii Prof. Roland Mitrić 《Angewandte Chemie (International ed. in English)》2014,53(52):14601-14604
The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide. 相似文献
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Yang PK 《Journal of computational chemistry》2011,32(13):2783-2799
The electric dipole moment p ( r ) was computed as the integral of the permanent dipole moment of the solvent molecule μ( r ) weighted by the orientational probability distribution Ω( r ; O ) over all orientations, where O is the orientation of the solvent molecule at r . The relationship between Ω( r ; O ) and the potential of the mean torque was derived; p ( r ) is proportional to the electric field E ( r ) under the following assumptions: (1) the van der Waals (vdW) interaction is independent of the orientation of the solvent molecule at r ; (2) the solvent molecule and its electrical effect are modeled as a point dipole moment; (3) the solvent molecule at r is in a region far from the solute; and (4) μE( r ) ? kBT, where kB is Boltzmann's constant and T is absolute temperature. The errors caused by calculating near‐solute Ω( r ) and p ( r ) from E ( r ) are unclear. The results show that Ω( r ) is inconsistent with the value calculated from E ( r ) for water molecules in the first and second shells of solute with charge state Q = ±1 e, and a large variation in solvent molecular polarizability γmol(r), which appeared in the first valley of 4πr2E(r) for |Q| < 1 e. Nonetheless, p (r) is consistent with the values calculated from E (r) for |Q| ≤ 1 e. The implication is that the assumptions for calculating p ( r ) can be ignored in the calculation of the solvation free energy of biomolecules, as they pertain to protein folding and protein–protein/ligand interactions. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 相似文献
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The local maxima of water density in the space near the single-helical of Konjac glucomannan as well as the dominant conformation of the system was studied by molecular dyna-mics under the water environment. The results indicate that the hydration shell,potential energy,and its hydrogen bond network with water bridges of the left-handed single-helix conformation was favored compared to those of right-handed single-helix conformation. This work suggests that the left-handed single-helix conformation was the dominant conformation of KGM in the water environment. 相似文献
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Zwitterionic polymers as crucial antifouling materials exhibit excellent antifouling performance due to their strong hydration ability. The structure–property relationship at the molecular level still remains to be elucidated. In this work, the surface hydration ability of three antifouling polymer membranes grafting on polysiloxane membranes Poly(sulfobetaine methacrylate) (T4-SB), poly(3-(methacryloyloxy)propane-1-sulfonate) (T4-SP), and poly(2-(dimethylamino)ethyl methacrylate) (T4-DM) was investigated. An orderly packed, and tightly bound surface hydration layer above T4-SP and T4-SB antifouling membranes was found by means of analyzing the dipole orientation distribution, diffusion coefficient, and average residence time. To further understand the surface hydration ability of three antifouling membranes, the surface structure, density profile, roughness, and area percentage of hydrophilic surface combining electrostatic potential, RDFs, SDFs, and noncovalent interactions of three polymers’ monomers were studied. It was concluded that the broadest distribution of electrostatic potential on the surface and the nature of anionic SO3- groups led to the following antifouling order of T4-SB > T4-SP > T4-DM. We hope that this work will gain some insight for the rational design and optimization of ecofriendly antifouling materials. 相似文献
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The evaluation of water binding free energies around solute molecules is important for the thermodynamic characterization of hydration or association processes. Here, a rapid approximate method to estimate water binding free energies around (bio)macromolecules from a single molecular dynamics simulation is presented. The basic idea is that endpoint free‐energy calculation methods are applied and the endpoint quantities are monitored on a three‐dimensional grid around the solute. Thus, a gridded map of water binding free energies around the solute is obtained, that is, from a single short simulation, a map of favorable and unfavorable water binding sites can be constructed. Among the employed free‐energy calculation methods, approaches involving endpoint information pertaining to actual thermodynamic integration calculations or endpoint information as exploited in the linear interaction energy method were examined. The accuracy of the approximate approaches was evaluated on the hydration of a cage‐like molecule representing either a nonpolar, polar, or charged water binding site and on α‐ and β‐cyclodextrin molecules. Among the tested approaches, the linear interaction energy method is considered the most viable approach. Applying the linear interaction energy method on the grid around the solute, a semi‐quantitative thermodynamic characterization of hydration around the whole solute is obtained. Disadvantages are the approximate nature of the method and a limited flexibility of the solute. © 2016 Wiley Periodicals, Inc. 相似文献
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Giacomo Fiorin Fabrizio Marinelli José D. Faraldo-Gómez 《Journal of computational chemistry》2020,41(5):449-459
We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this “Multi-Map” variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich–Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA. 相似文献
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Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water. 相似文献
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受限于不同螺旋性的纳米碳管中水的分子动力学模拟 总被引：3，自引：0，他引：3
近年来将纳米碱米碳管引入到与生命过程息息相关的离子通道膜的研究逐渐成 为热点,而其中的关键就是要了解受限于膜孔道（碳管）中水分子的行为。采用分 子动力学模拟在300 K和1.01 * 10~5 Pa下对受限于（6,6）armchair型和（10, 0）zigzag型纳米碳管中的水进行了研究,得到了水分子在碳管中的局部密度分布 等静态性质以及水分子在碳管中的传递等动态性质,并对不同势能模型的模拟结果 作了比较。结果表明选择不同的势能模型并没有改变此体系的固有性质,即水分子 不仅能够进入到憎水性的（6,6）碳管中而且能形成一条稳定的由氢键相连的纵列 （single file）,而且在管中以纵列的形式进行同歇传递。此外,碳管螺旋性对 受限水的静态性质影响不大但对动态性质则有一定程度的影响,水分子在（10,0 ）zigzag型碳管中的传递能力要强于在（6,6）armchair型碳管中的能力。 相似文献
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Water molecules at protein-protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein-protein or protein-peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein-peptide interfaces (X-ray resolutions 相似文献
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《Chemistry (Weinheim an der Bergstrasse, Germany)》2006,12(1):72-75
This report examines the effect of a decrease in solvent viscosity on the simulated folding behaviour of a β‐peptide heptamer in methanol. Simulations of the molecular dynamics of the heptamer H‐β3‐HVal‐β3‐HAla‐β3‐HLeu‐(S,S)‐β3‐HAla(αMe)‐β3‐HVal‐β3‐HAla‐β3‐HLeu‐OH in methanol, with an explicit representation of the methanol molecules, were performed for 80 ns at various solvent viscosities. The simulations indicate that at a solvent viscosity of one third of that of methanol, only the dynamic aspects of the folding process are altered, and that the rate of folding is increased. At a viscosity of one tenth of that of methanol, insufficient statistics are obtained within the 80 ns period. We suggest that 80 ns is an insufficient time to reach conformational equilibrium at very low viscosity because the dependence of the folding rate of a β‐peptide on solvent viscosity has two regimes; a result that was observed in another computational study for α‐peptides. 相似文献
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Alexander Cumberworth Jennifer M. Bui Jörg Gsponer 《Journal of computational chemistry》2016,37(7):629-640
Implicit solvent models for biomolecular simulations have been developed to use in place of more expensive explicit models; however, these models make many assumptions and approximations that are likely to affect accuracy. Here, the changes in free energies of solvation upon folding of several fast folding proteins are calculated from previously run μs–ms simulations with a number of implicit solvent models and compared to the values needed to be consistent with the explicit solvent model used in the simulations. In the majority of cases, there is a significant and substantial difference between the values calculated from the two approaches that is robust to the details of the calculations. These differences could only be remedied by selecting values for the model parameters—the internal dielectric constant for the polar term and the surface tension coefficient for the nonpolar term—that were system‐specific or physically unrealistic. We discuss the potential implications of our findings for both implicit and explicit solvent simulations. © 2015 Wiley Periodicals, Inc. 相似文献