Protein Hydration Layer Research Articles

Impact of NaCl perturbation on physicochemical and structural properties of preheat–treated egg white protein modulating foaming property

This study aimed to investigate the mechanism of NaCl perturbed preheat–treated egg white proteins' (EWPs) physicochemical and structural properties to modulate the foaming property (FP). The results revealed that NaCl regulated the salinolysis (5 mM) – salt precipitation (50 mM) – gradual or complete coverage with hydrated Na+ of the hydration layer (100–300 mM) – enhanced Cl− hydration repulsion (500 mM) of EWP, showing a gradual decrease in aggregates particle size, and reversibility of structural freedom, including moleculer flexibility and surface hydrophobicity. Whereas preheating temperature affected the secondary structure rearrangement and tertiary conformation exposure, and excessive temperature reduced foaming capacity while enhanced foam stability, with a tight correlation between NaCl–mediated EWPs’ FP and the extent of Na+ covering the hydration layer. The findings provide a theoretical basis for processing factors to modulate the protein hydration layer to influence the functional properties.

Native and nonnative reactions in ethanolamine ammonia-lyase are actuated by different dynamics

We address the contribution of select classes of solvent-coupled configurational fluctuations to the complex choreography involved in configurational and chemical steps in an enzyme by comparing native and nonnative reactions conducted at different protein internal sites. The low temperature, first-order kinetics of covalent bond rearrangement of the cryotrapped substrate radical in coenzyme B12-dependent ethanolamine ammonia-lyase (EAL) from Salmonella enterica display a kink, or increase in slope, of the Arrhenius plot with decreasing temperature. The event is associated with quenching of a select class of reaction-actuating collective fluctuations in the protein hydration layer. For comparison, a nonnative, radical reaction of the protein interior cysteine sulfhydryl group with hydrogen peroxide (H2O2) is introduced by cryotrapping EAL in an aqueous H2O2 eutectic system. The low-temperature aqueous H2O2 protein hydration and mesodomain solvent phases surrounding cryotrapped EAL are characterized by using TEMPOL spin probe electron paramagnetic resonance spectroscopy, including a freezing transition of the eutectic phase that orders the protein hydration layer. Kinetics of the cysteine-H2O2 reaction in the EAL protein interior are monitored by DEPMPO spin trapping of hydroxyl radical product. In contrast to the native reaction, the linear Arrhenius relation for the nonnative cysteine-H2O2 reaction is maintained through the solvent-protein ordering transition. The nonnative reaction is coupled to the generic local, incremental fluctuations that are intrinsic to globular proteins. The comparative approach supports the proposal that select coupled solvent-protein configurational fluctuations actuate the native reaction, and suggests that select dynamical coupling contributes to the degree of catalysis in enzymes.

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

Controlling Amyloid Fibril Properties Via Ionic Liquids: The Representative Case of Ethylammonium Nitrate and Tetramethylguanidinium Acetate on the Amyloidogenesis of Lysozyme.

Protein aggregation into amyloid fibrils has been observed in several pathological conditions and exploited in nanotechnology. It is also key in several biochemical processes. In this work, we show that ionic liquids (ILs), a vast class of organic electrolytes, can finely tune amyloid properties, opening a new landscape in basic science and applications. The representative case of ethylammonium nitrate (EAN) and tetramethyl-guanidinium acetate (TMGA) ILs on lysozyme is considered. First, atomic force microscopy has shown that the addition of EAN and TMGA leads to thicker and thinner amyloid fibrils of greater and lower electric potential, respectively, with diameters finely tunable by IL concentration. Optical tweezers and neutron scattering have shed light on their mechanism of action. TMGA interacts with the protein hydration layer only, making the relaxation dynamics of these water molecules faster. EAN interacts directly with the protein instead, making it mechanically unstable and slowing down its relaxation dynamics.

The protein hydration layer in high glucose concentration: Dynamical responses in folded and intrinsically disordered dimeric states

This exposition reveals the effect of glucose as a molecular crowder on the solvent environment in proximity of the protein surface in putative folded (Ubiquitin) and intrinsically disordered (dimeric Amyloid beta) states. Atomistic simulations reveal markedly higher structural perturbation in the disordered systems due to crowding effects, while the folded state retains overall structural fidelity. Key hydrophobic contacts in the disordered dimer are lost. However, glucose induced crowding results in elevated hydration on surfaces of both protein systems. Despite evident differences in their structural responses, the hydration layer of both the folded and disordered states display a distinct enhancement in lifetimes of mean residence and rotational relaxation under the hyperglycemic conditions. The results are crucial in the light of emergent co-solvent induced biological phenomena in crowded media.

In situ investigation of lysozyme adsorption into polyelectrolyte brushes by quartz crystal microbalance with dissipation

A well understanding about protein adsorption into charged polymer brushes is of importance in the elucidation of mechanism and important phenomena (such as “chain delivery” effect) in protein adsorption on polymer-grafted ion exchange adsorbents. In this work, quartz crystal microbalance with dissipation (QCM-D) was introduced to in situ investigate lysozyme adsorption on QCM sensors grafted with poly(3-sulfopropyl methacrylate) ( p SPM) via atom transfer radical polymerization. It was achieved by analyzing frequency ( f ) and energy dissipation ( D ) shift simultaneously on p SPM-grafted sensors. The result showed that an initial decrease in Δ D was typical of lysozyme adsorption on p SPM-grafted sensor and more significant with an increase of chain length and grafting density. It was attributed to significant water release in the hydration layer of protein and polymer chains in lysozyme adsorption into p SPM brushes. On p SPM-grafted sensors with long and dense chains, furthermore, lysozyme transitioned from monolayer to multilayer adsorption and the maximum adsorbed amount was obtained to be 374.0 ng·cm −2 among all p SPM-grafted sensors in this work. The results in D - f plot further revealed that lysozyme adsorption into p SPM brushes increased the rigidity of adsorbed layer and little structure adjustment of adsorbed lysozyme. It was unfavorable for “chain delivery” effect for facilitated transport of adsorbed protein. This work provided valuable insight into protein adsorption in p SPM brushes and outlined a feasible approach to increasing mass transport in polymer-grafted ion exchange adsorbents.

Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response

The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.

Rotational dynamics of proteins in nanochannels: role of solvent’s local viscosity

Viscosity variation of solvent in local regions near a solid surface, be it a biological surface of a protein or an engineered surface of a nanoconfinement, is a direct consequence of intermolecular interactions between the solid body and the solvent. The current coarse-grained molecular dynamics study takes advantage of this phenomenon to investigate the anomaly in a solvated protein’s rotational dynamics confined using a representative solid matrix. The concept of persistence time, the characteristic time of structural reordering in liquids, is used to compute the solvent’s local viscosity. With an increase in the degree of confinement, the confining matrix significantly influences the solvent molecule’s local viscosity present in the protein hydration layer through intermolecular interactions. This effect contributes to the enhanced drag force on protein motion, causing a reduction in the rotational diffusion coefficient. Simulation results suggest that the direct matrix-protein non-bonded interaction is responsible for the occasional jump and discontinuity in orientational motion when the protein is in very tight confinement.

Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin.

Water dynamics on the protein surface mediate both protein structure and function. However, many questions remain about the role of the protein hydration layers in protein fluctuations and how the dynamics of these layers relate to specific protein properties. The fish eye lens protein γM7-crystallin (γM7) is found in vivo at extremely high concentrations nearing the packing limit, corresponding to only a few water layers between adjacent proteins. In this study, we conducted a site-specific probing of hydration water motions and side-chain dynamics at nine selected sites around the surface of γM7 using a tryptophan scan with femtosecond spectroscopy and NMR nuclear spin relaxation (NSR). We observed correlated fluctuations between hydration water and protein side chains on the time scales of a few picoseconds and hundreds of picoseconds, corresponding to local reorientations and network restructuring, respectively. These motions are heterogeneous over the protein surface and relate to the various steric and chemical properties of the local protein environment. Overall, we found that γM7 has relatively slower water dynamics within the hydration shell than a similar β-sheet protein, which may contribute to the high packing limit of this unique protein.

Entropy connects water structure and dynamics in protein hydration layer.

The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics. In particular, it was seen that regions of higher density exhibit faster water dynamics. This is analogous to the behavior of bulk water, where dynamics (diffusion coefficients) are connected to water structure (density and tetrahedrality) by excess (or pair) entropy, detailed in the Rosenfeld scaling relationship. Additionally, effects of protein surface topology and hydrophobicity on water structure and dynamics were evaluated using multiregression analysis, showing that topology has a somewhat larger effect on hydration layer structure-dynamics. Concave and hydrophobic protein surfaces favor a less dense and more tetrahedral solvation layer, akin to a more ice-like structure, with slower dynamics. Results show that pairwise entropies of local hydration layers, calculated from regional radial distribution functions, scale logarithmically with local hydration dynamics. Thus, the Rosenfeld relationship describes the heterogeneous structure-dynamics of the hydration layer around the enzyme CALB. These findings raise the question of whether this may be a general principle for understanding the structure-dynamics of biomolecular solvation.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study.

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.

Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average.

Since the pioneering works of Pethig, Grant, and Wüthrich on a protein hydration layer, many studies have been devoted to find out if there are any "general and universal" characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform an atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at average properties but the distribution of relaxation times. We present results of calculations of distributions of residence times and rotational relaxation times for four different protein-water systems and compare them with the same quantities in the bulk. The distributions in the hydration layer are unusually broad and log-normal in nature due to the simultaneous presence of peptide backbones that form weak hydrogen bonds, hydrophobic amino acid side chains that form no hydrogen bond, and charged polar groups that form a strong hydrogen bond with the surrounding water molecules. The broad distribution is responsible for the non-exponential dielectric response and also agrees with large specific heat of the hydration water. Our calculations reveal that while the average time constant is just about 2-3 times larger than that of bulk water, it provides a poor representation of the real behaviour. In particular, the average leads to the erroneous conclusion that water in the hydration layer is bulk-like. However, the observed and calculated lower value of static dielectric constant of hydration layer remained difficult to reconcile with the broad distribution observed in dynamical properties. We offer a plausible explanation of these unique properties.

Probing the Surface Hydration of Nonfouling Zwitterionic and PEG Materials in Contact with Proteins.

Zwitterionic polymers and poly(ethylene glycol) (PEG) have been reported as promising nonfouling materials, and strong surface hydration has been proposed as a significant contributor to the nonfouling mechanism. Better understanding of the similarity and difference between these two types of materials in terms of hydration and protein interaction will benefit the design of new and effective nonfouling materials. In this study, sum frequency generation (SFG) vibrational spectroscopy was applied for in situ and real-time assessment of the surface hydration of the sulfobetaine methacrylate (SBMA) and oligo(ethylene glycol) methacrylate (OEGMA) polymer brushes, denoted as pSBMA and pOEGMA, in contact with proteins. Whereas a majority of strongly hydrogen-bonded water was observed at both pSBMA and pOEGMA surfaces, upon contact with proteins, the surface hydration of pSBMA remained unaffected, but the water ordering at the pOEGMA surface was disturbed. The effects of free sulfobetaine, free PEG chains with two different molecular weights, and PEG coated gold nanoparticles on the surface hydration of proteins were investigated. The results indicated that free sulfobetaine could strengthen the protein hydration layer, but free PEG chains greatly disrupt the protein hydration layer and likely directly interact with the protein molecules. In contrast to free PEG, the PEG chains anchored on the nanoparticles behave similarly to the pOEGMA surface and could induce strong hydrogen bonding of the water molecules at the protein surfaces.

16. Controlling cryoprotectant toxicity and chilling injury

Cryoprotectant toxicity and chilling injury are the central problems blocking the full deployment of vitrification, including its use for organ cryopreservation. Controlling these sources of injury is handicapped by the fact that little information is available about the nature of either cryoprotectant toxicity or chilling injury. To date, toxicity has been controlled by following 14 largely empirical rules of toxicity suppression in vitrification, but recently both theory and empirical experiment have begun to point the way to a coming ability to transcend cryoprotectant toxicity and with it, chilling injury as well. One interpretation of a recent gene expression profiling experiment on rat liver slices is that cryoprotectant toxicity in advanced vitrification solutions is related to protein denaturation. This is consistent with independent evidence that toxicity is correlated with stronger water hydrogen bonding by the permeating cryoprotectants in such solutions, which might destabilize the protein hydration layer and thus induce denaturation. Individual cryoprotectants apparently injure cells by specific mechanisms that don’t include denaturation, but when individual agents are diluted and combined to form vitrification solutions of high total concentration, injury may be primarily non-specific and mediated by denaturation linked to reduced water availability. Although worrisome at first, cells have evolved many ways of coping with protein denaturation, which may be augmented to achieve a therapeutic effect. In addition, chilling injury of vitrifiable liver slices was found to mimic cryoprotectant toxicity based on additional gene expression profiling, suggesting that chilling injury during vitrification may arise from the superimposition of cold denaturation on pre-existing protein destabilization by cryoprotectants. This implies that reducing cryoprotectant toxicity will also reduce chilling injury, but other interventions for chilling injury may also be helpful, including interventions that have been aimed at preventing membrane lipid phase transitions in other systems. Interestingly, those interventions include using antifreeze proteins to stabilize the cell membrane, which raises the question of whether other ice-active agents that might be more practically incorporated into vitrification solutions would have similar protective effects in addition to their intended role of interfering with ice formation. Another factor in controlling chilling injury has been tonicity adjustment. It has been reported that setting the nominal osmolality of non-penetrating species in a vitrification solution to 1.2–1.5 times isotonic minimizes chilling injury in rabbit renal cortical slices at all temperatures from −20 °C to −80 °C, below which chilling injury no longer increases. While helpful, this intervention places constraints on the amount of impermeant that can be used in vitrification solutions for the kidney. The mechanism of this effect is unknown, although it has been speculated that hypertonicity prevents injury otherwise caused by thermal contraction of cell membranes.

Hydrophobic hydration driven self-assembly of curcumin in water: similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces.

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of β-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer.

Water in biological and chemical processes: from structure and dynamics to function

Part I. Bulk Water: 1. Uniqueness of water 2. Anomalies of water 3. Dynamics of water: molecular motions and hydrogen bond breaking kinetics 4. Inherent structures of liquid water 5. pH of water Part II. Water in Biology: Dynamical View and Function: 6. Biological water 7. Explicit role of water in biological functions 8. Hydration of proteins 9. Can we understand protein hydration layer: lessons from computer simulations 10. Water in and around DNA and RNA 11. Role of water in protein-DNA interaction 12. Water surrounding lipid bilayers 13. Water in Darwin's world Part III. Water in Complex Chemical Systems: 14. Hydrophilic effects 15. Hydrophobic effects 16. Aqueous binary mixtures: amphiphilic effect 17. Water in and around micelles, reverse micelles and microemulsions 18. Water in carbon nanotubes Part IV. Bulk Water: Advanced Topics: 19. Entropy of water 20. Freezing of water into ice 21. Supercritical water 22. Microscopic approaches to understand water anomalies.

Three Stages of Lysozyme Thermal Stabilization by High and Medium Charge Density Anions

Addition of high and medium charge density anions (phosphate, sulfate, and chloride) to lysozyme in pure water demonstrates three stages for stabilization of the protein structure. The first two stages have a minor impact on lysozyme stability and are probably associated with direct interaction of the ions with charged and partial charges on the protein's surface. There is a clear transition between the second and third stages; in the case of sodium chloride, disodium sulfate and disodium hydrogen phosphate this is at 550, 210, and 120 mM, respectively. Stabilization of lysozyme can be explained by the free energy required to hydrate the protein as it unfolds. At low ion concentrations, the protein's hydration layer is at equilibrium with the bulk water. After the transition, bulk water is depleted and the protein is competing for water with the ions. With competition for water between the protein and the ions at higher salt concentrations, the free energy required to hydrate the interior of the protein rises and it is this that stabilizes the protein structure.

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (∼ 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Nanoscale Confinement Effects on the Fast Motions of the Backbone and Side Chains of Ubiquitin

The prevailing model for solvent dependence of protein motions, the solvent slaving model, predicts that protein motions should be dramatically dependent on the dynamics of the solvent. We have previously measured the dynamics of water near the surface of ubiquitin when encapsulated in reverse micelles. In order to directly investigate the relationship between protein and solvent motions, we have measured the backbone and side chain ps-ns motions of ubiquitin under various reverse micelle encapsulation conditions using nuclear spin relaxation methods. Confinement of the protein in the aqueous core of the reverse micelle produces a strong, general damping of the fast backbone motions of the protein. In distinct contrast, the side chain methyl motions are only slightly affected by encapsulation in reverse micelles. No strong correlations between the protein motional character and the dynamics of the protein's hydration layer were observed, suggesting that the dynamics of water molecules near the protein surface have minimal consequences for fast dynamic motions of proteins. Supported by NSF grant MCB 0842814, NIH GM102477, and NIH postdoctoral fellowship GM087099 to N.V.N.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these "slow" water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.