Molecular Dynamics of Water at the Protein−Solvent Interface

Molecular view of water dynamics near model peptides

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.

Hydration and Dewetting near Graphite−CH3 and Graphite−COOH Plates

The dynamics of water near the nanoscale hydrophobic (graphite-CH(3)) and hydrophilic (graphite-COOH) plates has been studied in detail with molecular dynamics simulations in this paper. It is shown that these designed surfaces (by growing a layer of methyl or carboxyl groups on top of graphite) can have a significant impact on the neighboring water dynamics, with the hydrophilic carboxyl surface having even more profound effects. The water hydrogen bond lifetime is much longer near both types of surfaces than that in the bulk, while on the other hand the water diffusion constant is much smaller than that in the bulk. The difference in the diffusion constant can be as large as a factor of 8 and the difference in the hydrogen bond lifetime can be as large as a factor of 2, depending on the distance from the surface. Furthermore, the water molecules in the first solvation shell of surface atoms show a strong bias in hydroxyl group orientation near the surface, confirming some of the previous findings. Finally, the possible water dewetting transition between two graphite-CH(3) plates and the effect of the strength of the solute-solvent attractions on the water drying transition are investigated. The relationship among the dewetting transition critical distance, van der Waals potential well depth, and water contact angle on the graphite-CH(3) surface is also analyzed on the basis of a simple macroscopic theory, which can be used to predict the dewetting transition critical distance.

Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.

Internal dynamics and protein–matrix coupling in trehalose-coated proteins

We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water-trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q(B) containing or Q(B) deprived reaction centre from R. sphaeroides. Experimental results, together with the outcome of molecular dynamics simulations, concurred to give a picture of how water-containing matrices control the internal dynamics of the embedded proteins. This occurs, in particular, via the formation of hydrogen bond networks that anchor the protein surface to the surrounding matrix, whose stiffness increases by lowering the sample water content. In the conclusion section, we also briefly speculate on how the protein-matrix interactions observed in our samples may shed light on the protein-solvent coupling also in liquid aqueous solutions.

Stability of proteins: Temperature, pressure and the role of the solvent

We focus on the various aspects of the physics related to the stability of proteins. We review the pure thermodynamic aspects of the response of a protein to pressure and temperature variations and discuss the respective stability phase diagram. We relate the experimentally observed shape of this diagram to the low degree of correlation between the fluctuations of enthalpy and volume changes associated with the folding-denaturing transition and draw attention to the fact that one order parameter is not enough to characterize the transition. We discuss in detail microscopic aspects of the various contributions to the free energy gap of proteins and put emphasis on how a cosolvent may either enlarge or diminish this gap. We review briefly the various experimental approaches to measure changes in protein stability induced by cosolvents, denaturants, but also by pressure and temperature. Finally, we discuss in detail our own molecular dynamics simulations on cytochrome c and show what happens under high pressure, how glycerol influences structure and volume fluctuations, and how all this compares with experiments.

Enzyme activity and flexibility at very low hydration

Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and 50% hydration by weight and at temperatures ranging from 120 to 300 K. At all temperatures and hydrations, significant quasielastic scattering intensity is found in the protein, indicating the presence of anharmonic, diffusive motion. As the hydration increases, a temperature-dependent dynamical transition appears and strengthens involving additional diffusive motion. The implication of these results is that, although the additional hydration-induced diffusive motion in the protein detected here may be related to increased activity, it is not required for the enzyme to function.

Properties of Spanning Water Networks at Protein Surfaces

The formation of a spanning two-dimensional hydrogen-bonded water network at the surface of proteins via a percolation transition enables their biological function. We show in detail how the spanning (percolating) water network appears at the surfaces of model hydrophilic spheres and at the surface of a single protein (lysozyme) molecule. We have found essential correlations of the linear extension, radius of gyration, and position of the center of mass of the largest water cluster with its size. The specific two-peak structure of the probability distribution of the largest cluster size allowed us to study various properties separately for spanning and nonspanning largest clusters. The radius of gyration of the spanning cluster always exceeds the radii of the spheres or the effective radius of the protein. Any spanning cluster envelops essentially more than half of the surface area. The temporal decay of the spanning networks shows a stretched exponential character. Their average lifetime at the percolation threshold is about the lifetime of a water-water hydrogen bond.

Supercooled Water in PVA Matrixes. II. A Molecular Dynamics Simulation Study and Comparison with QENS Results

Molecular dynamics (MD) simulations were carried out to elucidate the dynamic behavior of water confined in poly(vinyl alcohol), PVA, hydrogels. Model topology is supported by experimental network parameters, and simulation results are compared to an incoherent quasielastic neutron scattering (QENS) investigation carried out on PVA hydrogels. From the QENS dynamic scattering law (part I), a random jump model was adopted for the description of water diffusion to extract a microscopic diffusion coefficient and a residence time between two "jumps". In the present work, consistently with this framework, water diffusion parameters as diffusion coefficients and residence times have been evaluated using the mean square displacement of water in a time window of 10 ps and the time autocorrelation function of water hydrogen bonds. The calculated parameters are in good agreement with the experimental ones, giving confidence to this approach. Further developments are in progress to take into account a more realistic description of hydrogel structure in the molecular dynamics simulations.

Ultrafast surface solvation dynamics and functionality of an enzyme α-chymotrypsin upon interfacial binding to a cationic micelle

In this contribution we report studies on enzymatic activity of alpha-chymotrypsin (CHT) upon complexation with cationic cetyltrimethylammonium bromide (CTAB) micelle. With picosecond time resolution, we examined solvation dynamics at the interface of CHT-micelle complex, and rigidity of the binding. We have used 5-(dimethyl amino) naphthalene-1-sulfonyl chloride (dansyl chloride; DC) that is covalently attached to the enzyme at the surface sites. The solvation processes at the surface of CHT in buffer solution are found to be mostly in the sub-50 ps time scale. However, at the interface the solvation correlation function decays with time constant 150 ps (65%) and 500 ps (35%), which is significantly different from those found at the enzyme and micellar surfaces. The binding structure of the enzyme-micelle complex was examined by local orientational motion of the probe DC and compared with the case without micelle. The orientational dynamics of the probe DC in the complex reveals a structural perturbation at the surface sites of CHT upon complexation, consistent with other reported structural studies. We also found possible entanglement of charge transfer dynamics of the probe DC on the measured solvation processes by using time-resolved area normalized emission spectroscopic technique. The interfacial solvation process and complex rigidity elucidate the strong recognition mechanism between CHT and the micelle, which is important to understand the biological function of CHT upon complexation with the micelle.

Dynamics of Water Trapped between Hydrophobic Solutes

We describe the model dynamical behavior of the solvent between two nanoscopic hydrophobic solutes. The dynamics of the vicinal water in various sized traps is found to be significantly different from bulk behavior. We consider the dynamics at normal temperature and pressure at three intersolute distances corresponding to the three solvent separated minima in the free energy profile between the solutes with attractions. These three states correspond to one, two, and three intervening layers of water molecules. Results are obtained from a molecular dynamics simulation at constant temperature and pressure (NPT) ensemble. Translational diffusion of water molecules trapped between the two solutes has been analyzed from the velocity correlation function as well as from the mean square displacement of the water molecules. The rotational behavior has been analyzed through the reorientational dynamics of the dipole moment vector of the water molecule by calculating both first and second rank dipole-dipole correlation functions. Both the translational and reorientational mobilities of water are found to be much slower at the smaller separation and increases as the separation between solutes becomes larger. The occupation time distribution functions calculated from the trajectories also show that the relaxation is much slower for the smallest intersolute separation as compared to other wider separations. The sublinear trend in mean square displacement and the stretched exponential decay of the relaxation of dipolar correlation and occupation distribution function indicate that the dynamical behavior of water in the confined region between two large hydrophobic solutes departs from usual Brownian behavior. This behavior is reminiscent of the behavior of water in the vicinity of protein surface clefts or trapped between two domains of a protein.

Glassy behavior of a percolative water-protein system

We show that is possible to look at the glass transition as a percolation transition in phase space. This study has been carried out on a hydrated globular enzyme for which the thermodynamic transition and the percolative transition could have a functional significance. The approach adopted is based on the identity of roles played respectively by the glass transition temperature T(o) and the critical hydration threshold h(c) for the percolation of protons on the surface and through the protein, given that dynamical arrest is observed at temperatures and hydration below T(o) and h(c). Theoretical predictions for temperature dependence of the nonexponentiality parameter, beta(KWW) , appearing in the KWW relaxation function, indicate that at high temperatures, beta(KWW) remains insensitive to temperature changes, whereas in the vicinity of the glass transition, beta(KWW) is linearly increasing with temperature. The low temperature limit of beta(KWW) is about 1/3 and its temperature-independent behavior starts at 1.23 T(g): both predictions have been verified in the present study.

Sensitivity of Polar Solvation Dynamics to the Secondary Structures of Aqueous Proteins and the Role of Surface Exposure of the Probe

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.

Monolayer of Aerosol-OT Surfactants Adsorbed at the Air/Water Interface: An Atomistic Computer Simulation Study

An atomistic molecular dynamics (MD) simulation has been carried out to investigate the structural and dynamical properties of a monolayer of the anionic surfactant sodium bis(2-ethyl-1-hexyl) sulfosuccinate (aerosol-OT or AOT) adsorbed at the air/water interface. The simulation is performed at room temperature and at a surface coverage corresponding to that at its critical micelle concentration (78 A(2)/molecule). The estimated thickness of the adsorbed layer is in good agreement with neutron reflection data. The study shows that the surfactants exhibit diffusive motion in the plane of the interface. It is observed that the surfactant monolayer has a strong influence in restricting both the translational and reorientational motions of the water molecules close to the interface. A drastic difference in the dipolar reorientational motion of water molecules in the aqueous layer is observed with a small variation of the distance from the surfactant headgroups. It has been observed that the water molecules in the first hydration layer (region 1) form strong hydrogen bonds with surfactant headgoups. This results in the slower structural relaxation of water-water hydrogen bonds in the first hydration layer compared to that in the pure bulk water. Most interestingly, we notice that the water molecules present in the layer immediately after the first hydration layer form weaker hydrogen bonds and thus relax faster than even pure bulk water.

Anomalous behavior of water around sodium dodecyl sulphate micelles

The dynamics, structural properties, and energetics of hydration water around a sodium dodecyl sulphate micelle have been investigated using molecular dynamics simulation. A clear revelation of the slow dynamics of the hydration water has been made by separate measurements of the rotational and translational properties. Calculated diffusion coefficients fall within the range of experimentally observed quantities. The water-micelle head group (MHG) hydrogen bond is more stable (by an amount approximately 7.0 kcal/mol) compared to the water-water hydrogen bond. The difference in stability of the water monomers forming different numbers of hydrogen bonds (n=0,1,2) with the MHG has clearly been shown from the analyses of their rotational relaxation, residence times, as well as the energy of interaction with different components of the system. The singly hydrogen-bonded water species is the most abundant and stable. The entropy plays the key role in controlling the relative abundance of the different species.

Effect of graded hydration on the dynamics of an ion channel peptide: a fluorescence approach

Water plays an important role in determining the folding, structure, dynamics, and, in turn, the function of proteins. We have utilized a combination of fluorescence approaches such as the wavelength-selective fluorescence approach to monitor the effect of varying degrees of hydration on the organization and dynamics of the functionally important tryptophan residues of gramicidin in reverse micelles formed by sodium bis(2-ethylhexyl) sulfosuccinate. Our results show that tryptophans in gramicidin, present in the single-stranded beta6.3 conformation, experience slow solvent relaxation giving rise to red-edge excitation shift (REES). In addition, changes in fluorescence polarization with increasing excitation or emission wavelength reinforce that the gramicidin tryptophans are localized in motionally restricted regions of the reverse micelle. Interestingly, the extent of REES is found to be independent of the [water]/[surfactant] molar ratio (w(o)). We attribute this to heterogeneity in gramicidin tryptophan localization. Fluorescence intensity and mean fluorescence lifetime of the gramicidin tryptophans show significant reductions with increasing w(o) indicating sensitivity to increased polarity. Since the dynamics of hydration is related to folding, structure, and eventually function of proteins, we conclude that REES could prove to be a potentially sensitive tool to explore the dynamics of proteins under conditions of changing hydration.

Role of water mediated interactions in protein-protein recognition landscapes

The energy landscape picture of protein folding and binding is employed to optimize a number of pair potentials for direct and water-mediated interactions in protein complex interfaces. We find that water-mediated interactions greatly complement direct interactions in discriminating against various types of trap interactions that model those present in the cell. We highlight the context dependent nature of knowledge-based binding potentials, as contrasted with the situation for autonomous folding. By performing a Principal Component Analysis (PCA) of the corresponding interaction matrixes, we rationalize the strength of the recognition signal for each combination of the contact type and reference trap states using the differential in the idealized "canonical" amino acid compositions of native and trap layers. The comparison of direct and water-mediated contact potential matrixes emphasizes the importance of partial solvation in stabilizing charged groups in the protein interfaces. Specific water-mediated interresidue interactions are expected to influence significantly the kinetics as well as thermodynamics of protein association.

Water Structures of Differing Order and Mobility in Aqueous Solutions of Schizophyllan, a Triple-Helical Polysaccharide as Revealed by Dielectric Dispersion Measurements

Dielectric dispersion measurements were made on aqueous solutions of a triple-helical polysaccharide schizophyllan over a wide concentration range 10-50 wt % at -45 to +30 degrees C. In the solution state, three different water structures with the different relaxation times tau were found, namely, bound water (taul), structured water (taus), and loosely structured water (tauls) in addition to free water (tauP). Structured water is less mobile and loosely structured water is nearly as mobile as free water, but bound water with taul is much less mobile, thus taul >> taus >> tauls greater, similar tauP. The order-disorder transition accompanies the conversion between structured water and loosely structured water. However, the species with taus remains even in the disordered state and constitutes part of bound water in the entire temperature range. In the frozen state, in addition to bulk water formed by partial melting, two mobile species existed, which were assigned to liquidlike bound water and found to be a continuation of bound water in the solution state. These relaxation time data are discussed in connection with the entropy levels of the four structures deduced from heat capacity data (cf. Yoshiba, K.; et al. Biomacromolecules 2003, 4, 1348-1356).

Hydration dynamics near a model protein surface

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation for both the completely deuterated and completely hydrogenated leucine monomer. The NALMA-water system and the QENS data together provide a unique study for characterizing the dynamics of different hydration layers near a prototypical hydrophobic side chain and the backbone of which it is attached. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational and rotational water dynamics at the highest solute concentrations are found to be highly suppressed as characterized by long residential time and slow diffusion coefficients. The analysis of the more dilute concentration solutions models the first hydration shell with the 2.0 M spectra. We find that for outer layer hydration dynamics that the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis of the first hydration shell water dynamics shows spatially heterogeneous water dynamics, with fast water motions near the hydrophobic side chain, and much slower water motions near the hydrophilic backbone. We discuss the hydration dynamics results of this model protein system in the context of protein function and protein-protein recognition.

Conformational Transitions in Eosinophil Cationic Protein: A Molecular Dynamics Study in Aqueous Environment

Extensive molecular dynamics simulations have been performed on eosinophil cationic protein (ECP). The two structures found in the crystallographic dimer (ECPA and ECPB) have been independently simulated. A small difference in the pattern of the sidechain hydrogen bonds in the starting structure has resulted in interesting differences in the conformations accessed during the simulations. In one simulation (ECPB), a stable equilibrium conformation was obtained and in the other (ECPA), conformational transitions at the level of sidechain interactions were observed. The conformational transitions exhibit the involvement of the solvent (water) molecules with a pore-like construct in the equilibrium conformation and an opening for a large number of water molecules during the transition phase. The details of these transitions are examined in terms of intra-protein hydrogen bonds, protein-water networks and the residence times of water molecules on the polar atoms of the protein. These properties show some significant differences in the region between the N-terminal helix and the loop before the C-terminal strand as a function of different conformations accessed during the simulations. However, the stable hydrogen bonds, the protein-water networks, and the hydration patterns in most part of the protein including the active site are very much similar in both the simulations, indicating the fact that these are intrinsic properties of proteins.

Water network dynamics at the critical moment of a peptide’s β-turn formation: A molecular dynamics study

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of beta-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.

Protein-water interactions in ribonuclease A and angiogenin: A molecular dynamics study

It is known that water molecules play an important role in the biological functioning of proteins. The members of the ribonuclease A (RNase A) family of proteins, which are sequentially and structurally similar, are known to carry out the obligatory function of cleaving RNA and individually perform other diverse biological functions. Our focus is on elucidating whether the sequence and structural similarity lead to common hydration patterns, what the common hydration sites are and what the differences are. Extensive molecular dynamics simulations followed by a detailed analysis of protein-water interactions have been carried out on two members of the ribonuclease A superfamily-RNase A and angiogenin. The water residence times are analyzed and their relationship with the characteristic properties of the protein polar atoms, such as their accessible surface area and mean hydration, is studied. The capacity of the polar atoms to form hydrogen bonds with water molecules and participate in protein-water networks are investigated. The locations of such networks are identified for both proteins.

Probing protein-surfactant interaction by steady state and time-resolved fluorescence spectroscopy

The microenvironment of the probe coumarin 153 (C-153) in 1% bovine serum albumin (BSA) is more hydrophobic in nature compared to that in pure micelles or protein-surfactant complexes. In the native state of protein, we have not observed any solvation using C-153 as a probe but we have observed a slow dynamics on protein surface using 8-anilino-1-naphthalenesulfonic acid (ANS) as a probe. This may be due to the location of the probe (C-153) in the hydrophobic, solvent-inaccessible pocket of the BSA. Solvation dynamics in the BSA-surfactant (SDS) complexes in the solution phase is markedly different from that in pure micelles. This is may be due to the formation of 'necklace and bead' structure in the complexes. The rotational motion is also severely hindered in the surface of the protein.

Energetics of hydrogen bonds in peptides

Hydrogen bonds and their relative strengths in proteins are of importance for understanding protein structure and protein motions. The correct strength of such hydrogen bonds is experimentally known to vary greatly from approximately 5-6 kcal/mol for the isolated bond to approximately 0.5-1.5 kcal/mol for proteins in solution. To estimate these bond strengths, here we suggest a direct novel kinetic procedure. This analyzes the timing of the trajectories of a properly averaged dynamic ensemble. Here we study the observed rupture of these hydrogen bonds in a molecular dynamics calculation as an alternative to using thermodynamics. This calculation is performed for the isolated system and contrasted with results for water. We find that the activation energy for the rupture of the hydrogen bond in a beta-sheet under isolated conditions is 4.76 kcal/mol, and the activation energy is 1.58 kcal/mol for the same beta-sheet in water. These results are in excellent agreement with observations and suggest that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.

Static water structure detected by heat capacity measurements on aqueous solutions of a triple-helical polysaccharide schizophyllan

Heat capacity measurements were made on aqueous solutions of a triple-helical polysaccharide schizophyllan by precision adiabatic calorimetry over a wide range of concentrations 30.45-90.93 wt % at temperatures between 5 and 315 K. The heat capacity curves obtained were divided into four groups depending on the weight fraction of schizophyllan w regions I-IV. In region I, triple-helices with the sheath of bound water, structured water, and loosely structured water forming layers around the helix core are embedded in free water. In region II, there is no free water, and loosely structured water decreases until it vanishes, but structured water stays constant with increasing w. In region III, bound water remains unaffected, but structured water decreases with increasing w by overlapping each other. Finally, in region IV, only schizophyllan and bound water exist, the latter decreasing upon increasing w. The maximum thickness of each layer is 0.18(3) nm for bound water, 0.13(4) nm for structured water, and 0.23(6) nm for loosely structured water, and these layers of water are at the enthalpy levels of 53%, 93.7%, and nearly 100%, respectively, between ice (0%) and free water (100%).

Status of experiments probing the dynamics of water in confinement

In many relevant situations, water is not in its bulk form but is instead attached to some substrates or filling some cavities. We shall call water in the latter environment "confined or interfacial water" as opposed to bulk water. This confined water is essential for the stability and function of biological macromolecules. In this review paper, we present the more recent up to date account of the dynamics of confined water as compared with that of bulk water. Various techniques are used to study the dynamics of confined water. Among them, quasi-elastic and inelastic neutron scattering is a powerful tool to study translational and rotational diffusion as well as vibrational density of states of confined water. Various examples involving water confined in porous media, adsorbed on surface of ionic crystals, in the presence of organic solutes and at the surface of biological molecules are presented. The combined effects of the hydration level and the temperature on the retardation of the water molecules motions are discussed on the basis of phenomenological models as well as of power law fits based on the Mode Coupling Theory.

Effects of confinement on static and dynamical properties of water

Molecular-dynamics results on water confined in a silica pore are reviewed and discussed in connection with experiments performed on water in Vycor and with studies of water in contact with proteins. The properties of confined water are studied as a function of both temperature and hydration level. The interaction of water in the film close to the substrate with the silica atoms induces a strong distortion of the hydrogen bond network. At high hydration levels a double dynamical regime is observed. At low hydration an anomalous diffusion is found upon supercooling with a transition from a Brownian to a non-Brownian regime on approaching the substrate in agreement with results found in studies of water in contact with globular proteins.

Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation

The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.

Dynamics of bound and free water in an aqueous micellar solution: analysis of the lifetime and vibrational frequencies of hydrogen bonds at a complex interface

In order to understand the nature and dynamics of interfacial water molecules on the surface of complex systems, large scale, fully atomistic molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate (CsPFO) surfactant molecules have been carried out. The lifetime and the intermolecular vibrational frequencies of the hydrogen bonds that the water molecules form with the hydrophilic, polar head groups (PHG) of the surfactants are calculated. Our earlier classification [S. Balasubramanian et al., Curr. Sci. 84, 428 (2003); e-print cond-mat/0212097] of the interfacial water molecules, based on structural and energetic considerations, into bound and free types is further validated by their dynamics. Lifetime correlation functions of the water-surfactant hydrogen bonds show the long-lived nature of the bound water species. Surprisingly, the water molecules that are singly hydrogen bonded to the surfactants have a longer lifetime than those that form two such hydrogen bonds. The free water molecules that do not form any such hydrogen bonds behave similarly to bulk water in their reorientational dynamics. A few water molecules that form two such hydrogen bonds are orientationally locked in for durations of the order of a few hundreds of picoseconds; that is, much longer than their average lifetime. The intermolecular vibrational frequencies of these interfacial water molecules have been studied from the power spectra of their velocity autocorrelation function. We find a significant blue shift in the librational band of the interfacial water molecules, apart from a similar shift in the near neighbor bending modes, relative to water molecules in bulk. These blue shifts suggest an increase in rigidity in the structure around interfacial water molecules. This is in good agreement with recent incoherent, inelastic neutron scattering data on macromolecular solutions [S. Ruffle et al., J. Am. Chem. Soc. 124, 565 (2002)]. The results of the present simulations appear to be rather general and should be relevant to the understanding of the dynamics of water near any hydrophilic surface.

Static and dynamic water molecules in Cu,Zn superoxide dismutase

Understanding protein hydration is a crucial, and often underestimated issue, in unraveling protein function. Molecular dynamics (MD) computer simulation can provide a microscopic description of the water behavior. We have applied such a simulative approach to dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase, comparing the water molecule sites determined using 1.0 ns MD simulation with those detected by X-ray crystallography. Of the water molecules detected by the two techniques, 20% fall at common sites. These are evenly distributed over the protein surface and located around crevices, which represent the preferred hydration sites. The water mean residence time, estimated by means of a survival probability function on a given protein hydration shell, is relatively short and increases for low accessibility sites constituted by polar atoms. Water molecules trapped in the dimeric protein intersubunit cavity, as identified in the crystal structure, display a trajectory mainly confined within the cavity. The simulation shows that these water molecules are characterized by relatively short residence times, because they continuously change from one site to another within the cavity, thus hinting at the absence of any relationship between spatial and temporal order for solvent molecules in proximity of protein surface.

A quantitative model of ultraviolet matrix-assisted laser desorption/ionization including analyte ion generation

A quantitative model of ionization in ultraviolet matrix-assisted laser desorption/ionization (Knochenmuss, R. J. Mass Spectrom. 2002, 37, 867) is extended to include secondary ion-molecule reactions. Matrix-to-analyte charge-transfer reaction kinetics are described by a hard-sphere Arrhenius expression. The activation energy is derived from the reaction exoergicity using a nonlinear free energy relationship. The approach is applied to the specific case of proton-transfer reactions. With no adjustable parameters, the model correctly predicts the existence and characteristics of the matrix and analyte suppression effects, the shapes of the two-pulse time-delayed yield curves, and the dependence of analyte yields on laser fluence, molecular weight, relative concentrations, and reaction exoergicity.

Slaving: solvent fluctuations dominate protein dynamics and functions

Protein motions are essential for function. Comparing protein processes with the dielectric fluctuations of the surrounding solvent shows that they fall into two classes: nonslaved and slaved. Nonslaved processes are independent of the solvent motions; their rates are determined by the protein conformation and vibrational dynamics. Slaved processes are tightly coupled to the solvent; their rates have approximately the same temperature dependence as the rate of the solvent fluctuations, but they are smaller. Because the temperature dependence is determined by the activation enthalpy, we propose that the solvent is responsible for the activation enthalpy, whereas the protein and the hydration shell control the activation entropy through the energy landscape. Bond formation is the prototype of nonslaved processes; opening and closing of channels are quintessential slaved motions. The prevalence of slaved motions highlights the importance of the environment in cells and membranes for the function of proteins.

Ultrafast surface hydration dynamics and expression of protein functionality: alpha -Chymotrypsin

We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic alpha-chymotrypsin. The probe is the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs, when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, tau = 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%) and the slow component changes to a faster decay, tau = 28 ps. These results indicate that in the active state water molecules in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly structured. For the substrate-enzyme complex, the function and dynamics at the probe site are correlated, and the relevance to the enzymatic action is clear.