A molecular dynamics study of uranyl hydration

Molecular dynamics calculations were carried out in order to investigate the hydration structure of uranyl in aqueous solution. The CF1 model of flexible water molecules is used. This model allows one to investigate a hydrolysis reaction for water molecules in the first uranyl hydration shell. Charge redistribution effects on hydrolysis products are also taken into account. We found five ligands in uranyl hydration shell, which is of bipyramidal pentacoordinated structure. The charge redistribution effects resulted in ligands of four water molecules and one hydroxyl, which was found closer to uranium than the other ligands.     

A Nuclear Magnetic Resonance study of the reversible denaturation of hydrated lysozyme

The understanding of the physical processes that occur below the threshold of protein thermal denaturation is of fundamental importance. In this thermal region proteins undergo a reversible folding/unfolding process whose evolution depends upon temperature and time. When the kinetics of the folding is altered, the specific biological activity of the protein is altered as well and aggregation phenomena usually intervene. The most important role in driving these processes is played by the solvent and water is certainly the solvent par excellence. It is well known that proteins become biologically active with no less than a water monolayer covering their surface. The knowledge of the physical properties of this monolayer is of basic importance to prevent folding alterations. We present a proton Nuclear Magnetic Resonance study at very high resolution of the thermodynamic properties of lysozyme hydration water as a function of temperature and time in the thermal region of the reversible denaturation.     

Glass transition in biomolecules and the liquid-liquid critical point of water

Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also coincides with the maxima of the isobaric specific heat C_{P} and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.     

Ratiometric detection of Raman hydration shell spectra

The micro‐structure of hydration shell of solute in water is significant for understanding the properties of aqueous solutions. However the spectra of hydration shell are difficult to be obtained. Herein, a novel Raman ratio spectra, which is obtained through dividing the Raman spectra of aqueous solutions from the spectrum of water, was applied to deduce the spectra of hydration shell of organic (acetone‐D6) and inorganic compounds (NaNO₃, NaSCN, NaClO₄, Na₂SO₄, NaCl) in water. Those spectra of the hydration shell were employed to study the micro‐structures of the first hydration shells of anions, the number of water molecules in the first hydration shell of free anions and acetone‐D6, and the aggregation behavior of ions in the concentrated aqueous NaNO₃. The number of water molecules in the hydration shell was supported by our molecular dynamic simulations. The Raman ratio spectra can be widely employed to obtain the spectra of the first hydration shell, and it is helpful to understand the micro‐structure of aqueous solutions. Copyright © 2016 John Wiley & Sons, Ltd.     

Glassy dynamics of water at interface with biomolecules: A Mode Coupling Theory test

We study the slow dynamics of hydration water upon cooling in two different biological aqueous solutions, one containing a molecule of lysozyme and another with trehalose molecules. In particular we test if the glassy behaviour of these solutions fulfils the predictions of the popular Mode Coupling Theory of glassy dynamics. In particular we test the Time Temperature Superposition Principle and the matching of the exponents of the theory. Our results confirm that this theory is able to describe the dynamical behaviour of supercooled water also in non ideal cases as the ones under investigation in the region of mild supercooling.     

Dielectric modulation of biological water

We show that water constrained by vicinal hydrophobes undergoes a librational dynamics that lowers the dielectric susceptibility and induces a "redshift" of the relaxation frequency in the hydration shell. The results shed light on the way proteins enhance their intramolecular interactions as they fold or associate.     

Effect of unfolding on the thickness of the hydration layer of a protein

Properties of water in the hydration layer around a protein is intimately correlated with its function. A knowledge of the thickness of the hydration layer is important to understand its role in guiding the folding-unfolding of the protein. We have performed atomistic molecular dynamics simulations of the folded native and a partially unfolded molten globule structure of the villin headpiece subdomain or HP-36 in aqueous solution to estimate the effect of unfolding on the thickness of hydration layer around different segments of the protein. In particular, several dynamic properties of water around different segments of the folded native and the unfolded structure have been calculated by varying the thickness of the hydration layers. It is found that unfolding of a segment of the protein is correlated with the dynamics of water around it, i.e., within the first hydration layer. The effect of unfolding on water properties has been found to diminish when water molecules present beyond the first hydration layer were included in the calculations.      

Hydration characteristics of Ca2+ and Mg2+: a density functional theory,polarized continuum model and molecular dynamics investigation

In this work, density functional theory, Møller–Plesset second-order perturbation theory, and ab initio molecular dynamics (AIMD) were used to investigate hydrated characteristics of Mg²⁺ and Ca²⁺ as a function of coordination number in the first hydration shell (CN) and cluster size. It is generally accepted that the CNs of Mg²⁺ and Ca²⁺ are both six. Calculations show that the hydration of Mg²⁺ generally prefers six-coordinated structures, whereas the CN value of Ca²⁺ varies from 6 to 8 as the hydration proceeds. Moreover, the first hydration of Ca²⁺ is found to be more flexible than that of Mg²⁺, as indicated by the results of transition state calculations and AIMD simulations. In addition, the constraint of Mg²⁺ on the first hydration shell is obviously stronger than that of Ca²⁺, while the constraint on the inner hydration shells fades slightly faster for Mg²⁺ than Ca²⁺. It is also found that the charge transfer from central cation to water molecules is affected only by the first hydration shell for Mg²⁺, whereas by the first and second hydration shells for Ca²⁺. Based on hydration characteristics, approximatively saturated ion hydration shells for the hydration of Mg²⁺ and Ca²⁺ were proposed.     

The role of continuous and discrete water structures in protein function

Proteins have evolved to perform numerous roles as specific catalysts and nano-machines. Some of the mechanisms exploited by evolution are clear. Hydrophobicity drives the stabilization energy of folding, charges mediate long-range interactions and facilitate catalysis, and specific geometries and hydrogen bonding patterns facilitate molecular recognition and catalysis. In this work, we examine the energy landscape of protein dynamics in terms of the continuous and discrete water structures that control protein dynamics. We observe that the internal structures at the active site of proteins are constantly shaped by strong interactions with hydration shell and bulk water motions. By describing the energy landscape of proteins in terms of its three component motions; conformational, hydration and protonation, and electronic structure, it is possible to systematically understand protein function.     

Molecular dynamics computer simulation of the hydration of two simple organic solutes

The hydration of two simple organic solutes has been studied using the molecular dynamics (MD) computer simulation method. Results of the simulations of a single 1,4-dioxane or 1,3-dioxane molecule dissolved in 122 water molecules are compared with those of a MD simulation of an empty cavity of corresponding size in 216 water molecules. This yields the opportunity to trace the specific effects of the polar and dispersion solute-solvent interactions on the properties of the water molecules in the hydration shell of the solute.

The hydration shell properties of 1,4-dioxane (μ) = 0·14 D) are very similar to those of the corresponding cavity, whereas those of 1,3-dioxane (μ) = 1·91 D) show significant deviations. Earlier conclusions that water structure-making and water structure-breaking properties of 1,4-dioxane are about equally balanced, while 1,3-dioxane is definitely structure-breaking, are confirmed. Moreover, it is shown that a slower self-diffusion and reorientation of water molecules upon addition of a cosolvent does not necessarily point at structure-making properties, additional to those that are already induced by the cavity formation. The introduction of an empty cavity also slows down self-diffusion and molecular reorientation in the hydration shell.     

Slow dynamics of supercooled hydration water in contact with lysozyme: examining the cage effect at different length scales

ABSTRACT

We study by computer simulation the dynamics of hydration water in solution with lysozyme upon approaching the glassy state of water. We calculate the self-density correlation function at different wavelengths to test the Mode Coupling Theory (MCT) of glassy dynamics at different length scales. The results show a strict and clear relation of the behaviour of the structural relaxation with the cage effect. We find a good agreement with the predictions of the MCT in the short and medium scale range, while at increasing length scales the interaction of water molecules with the protein's substrate induces deviations from the MCT behaviour, as found in previous studies. Besides at low temperatures the slow dynamics deviates from MCT due to hopping processes, similar to the bulk, as witnessed by a crossover from a fragile behaviour to a strong behaviour. We show that this deviation is evident at all length scales. Interestingly, we find that in the fragile region the confining cage decreases in radius with temperature while in the strong region it appears stable.     

Hydration and protein dynamics: an ESR and ST-ESR spin labelling study of human serum albumin

Human serum albumin has been studied at low hydration level by the ESR spin labelling technique, under the assumption that a covalently bound spin-label is a reporter of the protein internal dynamics. At room temperature, the presence of a double component signal allowed us to monitor the influence of increasing hydration level on internal protein dynamics as well as on the superficial water dynamics. The ESR results have shown that the first 20 g of water per 100 g of protein activate the internal protein dynamics and that superficial water dynamics starts at higher hydration values. ESR experiments at low temperature have shown that at ?160°C ?T??80°C, the label experiences an increasing environmental polarity with increasing temperature in the samples with hydration values higher than about 20 g of water per 100 g of protein. The results are discussed in connection with both conformational substates of the protein and hydration water dynamics.     

Common features in the microscopic dynamics of hydration water on organic and inorganic surfaces

The microscopic dynamics of hydration water exhibits some universal features that do not depend on the nature of the hydrated surface. We show that the hydration level dependence of the dynamic transition in the mean squared atomic displacements measured by means of elastic neutron scattering is qualitatively similar for hydration water in inorganic and organic hosts. The difference is that the former are 'rigid', whereas the dynamics of the latter can be enhanced by the motions of the hydration water. The overall hydration level appears to be the main parameter governing the magnitude of the mean squared atomic displacements in the hydration water, irrespective of the details of the hydrated host.     

生物分子结合水的结构与动力学研究进展

生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.     

Water induced effects on the thermal response of a protein

A model protein and surrounding water have been investigated at different temperatures. We have detected an anomalous compression of the protein near the freezing point of water-a compression not obviously related to the negative thermal expansion of the solvent. Moreover, the physiological protein working temperature (T=300 K) appears to be related to the activation of exchange of vicinal water with the bulk and the concomitant absorption of heat by hydrophilic amino acids. The inferred activation was interpreted on the basis of degenerate tetrahedral order between the hydration shell and the bulk. The results support the notion that the dynamics of vicinal water makes a substantial contribution to the activity optimum of proteins.     

Onsets of anharmonicity in protein dynamics

Two onsets of anharmonicity are observed in the dynamics of the protein lysozyme. One at T approximately 100 K appears in all samples regardless of hydration level and is consistent with methyl group rotation. The second, the well-known dynamical transition at T approximately 200-230 K, is only observed at a hydration level h greater than approximately 0.2 and is ascribed to the activation of an additional relaxation process. Its variation with hydration correlates well with variations of catalytic activity suggesting that the relaxation process is directly related to the activation of modes required for protein function.     

Theoretical investigation of hydrogen atom transfer in the hydrated C–G base pair

Hydrogen atom transfer and the related electronic rearrangement in the hydrated C–G base pair have been studied in order to understand the role of the hydrogen bonds between the bases and those with the water molecules in these processes. The modification of hydrogen transfer due to the first shell and bulk hydration has been analysed. The different structures, when the hydrogen atom moves in a H-bond or in another bond, have been studied. Two naïve schemes, where the water molecules are only indirectly or directly involved in the hydrogen atom transfer, have been considered. The results support the idea that the actual mechanisms are more complex than these schemes. Hydration modifies the potential energy curves of both tautomers and zwitterionic structures, but does not generate new stable structures (minimum PES) of these types. We find a new stable structure due to both a reorganization of the two down water molecules and other global changes of the system. This new system is generated from a zwitterionic structure. The charges, during hydrogen transfer, of the hydrogen donor and of the hydrogen acceptor part of the base pair and of the hydrogen atoms between the bases have been determined and their modifications, due to the first shell and bulk hydration, have been analysed. The qualitative and quantitative behavior has been studied.