Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36

Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.     

Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36

Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.     

Correlation between the dynamics of hydrogen bonds and the local density reorganization in the protein hydration layer

An atomistic molecular dynamics simulation of the protein villin headpiece subdomain or HP-36 has been carried out with explicit water to explore the microscopic inhomogeneity of local density reorganization of the hydration layers of the three alpha-helical segments of the protein. The density reorganization of the hydration layer of helix-3 is found to occur faster than that for the hydration layers of the other two helices. It is noticed that such inhomogeneous density reorganization at the surface of different secondary structures exhibits excellent correlation with the microscopic dynamics of hydrogen bonds between the protein residues and the hydration water. Further, it is observed that the reorientation of water molecules involved in the formation and breaking of protein-water or water-water hydrogen bonds plays an important role in determining the dynamics of local density of the hydration layer. The faster density reorganization of the hydration layer of helix-3 is also consistent with the functionality of HP-36, as helix-3 contains several active site residues.     

Thickness of the hydration layer of a protein from molecular dynamics simulation

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.     

Hydrogen bond breaking mechanism and water reorientational dynamics in the hydration layer of lysozyme

The mechanism and the rate of hydrogen bond-breaking in the hydration layer surrounding an aqueous protein are important ingredients required to understand the various aspects of protein dynamics, its function, and stability. Here, we use computer simulation and a time correlation function technique to understand these aspects in the hydration layer of lysozyme. Water molecules in the layer are found to exhibit three distinct bond-breaking mechanisms. A large angle orientational jump of the donor water molecule is common among all of them. In the most common ( approximately 80%) bond-breaking event in the layer, the new acceptor water molecule comes from the first coordination shell (initially within 3.5 A of the donor), and the old acceptor water molecule remains within the first coordination shell, even after the bond-breaking. This is in contrast to that in bulk water, in which both of the acceptor molecules involve the second coordination shell. Additionally, the motion of the incoming and the outgoing acceptor molecules involved is not diffusive in the hydration layer, in contrast to their observed diffusive motion in the bulk. The difference in rotational dynamics between the bulk and the hydration layer water molecules is clearly manifested in the calculated time-dependent angular van Hove self-correlation function ( G(theta, t)) which has a pronounced two-peak structure in the layer, and this can be traced to the constrained translational motion in the layer. The longevity of the surrounding hydrogen bond network is found to be significantly enhanced near a hydrophilic residue.     

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.     

Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer

The heterogeneous nature of a protein surface plays an essential role in its biological activity and molecular recognition, and this role is mediated at least partly through the surrounding water molecules. We have performed atomistic molecular dynamics simulations of an aqueous solution of HP-36 to investigate the correlation between the dynamics of the hydration layer water molecules and the lifetimes of protein-water hydrogen bonds. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the quasi-bound states in the surface and quantification of the dynamic equilibrium between quasi-bound and free water molecules in terms of time-dependent rate of interconversion. It is noticed that, irrespective of the structural heterogeneity of different segments of the protein, namely the three alpha-helices, the positively charged amino acid residues form longer-lived hydrogen bonds with water. The overall relaxation behavior of protein-water hydrogen bonds is found to differ significantly among the three helices of the protein. Study of water number density fluctuation reveals that the hydration layer of helix-3 is much less rigid, which can be correlated with faster structural relaxation of the hydrogen bonds between its residues and water. This also agrees excellently with faster translational and rotational motions of water near helix-3, and hence the lower rigidity of its hydration layer. The lower rigidity of the helix-3 hydration layer also correlates well with the biological activity of the protein, as several of the active-site residues of HP-36 are located in helix-3.     

Shear dynamics of hydration layers

Molecular dynamics (MD) simulations have been performed to investigate the shear dynamics of hydration layers of the thickness of D=0.61-2.44 nm confined between two mica surfaces. Emphases are placed on the external shear response and internal relaxation properties of aqueous films. For D=0.92-2.44 nm liquid phase, the shear responses are fluidic and similar to those observed in surface force balance experiments [U. Raviv and J. Klein, Science 297, 1540 (2002)]. However, for the bilayer ice (D=0.61 nm) [Y. S. Leng and P. T. Cummings, J. Chem. Phys. 124, 74711 (2006)] significant shear enhancement and shear thinning over a wide range of shear rates in MD regime are observed. The rotational relaxation time of water molecules in this bilayer ice is found to be as high as 0.017 ms (10(-5) s). Extrapolating the shear rate to the inverse of this longest relaxation time, we obtain a very high shear viscosity for the bilayer ice, which is also observed quite recently for D< or =0.6+/-0.3 nm hydration layers [H. Sakuma et al., Phys. Rev. Lett. 96, 46104 (2006)]. We further investigate the boundary slip of water molecules and hydrated K(+) ions and concluded that no-slip boundary condition should hold for aqueous salt solution under extreme confinement between hydrophilic mica surfaces, provided that the confined film is of Newtonian fluid.     

Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.     

Coupling between kinetics and rheological parameters in the flow-induced crystallization of thermoplastic polymers

Flow Induced Crystallization (FIC) is the common term to indicate the acceleration in polymer crystallization kinetics due to the action of flow. FIC is expected to be the result of the coupling between the intrinsic (quiescent) crystallization kinetics and the rheological response of the polymer. The choice of a suitable rheological model, therefore, is a crucial requirement for a successful FIC model. Recent work of our group^[1] has demonstrated that the Doi-Edwards rheological model (DE), based on the concept of chain reptation, can be easily incorporated into classical crystallization models to successful predict the enhancement in nucleation rate under the action of a steady shear flow. In this paper, the interaction between the rheological parameters of the DE model and the crystallization kinetics parameters is investigated in more details. In particular, the effect of the crystallization temperature, which acts on both the polymer relaxation time and the free energy jump between liquid and solid phase, is determined and discussed.     

Thermal signature of hydrophobic hydration dynamics

Hydrophobic hydration, the perturbation of the aqueous solvent near an apolar solute or interface, is a fundamental ingredient in many chemical and biological processes. Both bulk water and aqueous solutions of apolar solutes behave anomalously at low temperatures for reasons that are not fully understood. Here, we use (2)H NMR relaxation to characterize the rotational dynamics in hydrophobic hydration shells over a wide temperature range, extending down to 243 K. We examine four partly hydrophobic solutes: the peptides N-acetyl-glycine-N'-methylamide and N-acetyl-leucine-N'-methylamide, and the osmolytes trimethylamine N-oxide and tetramethylurea. For all four solutes, we find that water rotates with lower activation energy in the hydration shell than in bulk water below 255 +/- 2 K. At still lower temperatures, water rotation is predicted to be faster in the shell than in bulk. We rationalize this behavior in terms of the geometric constraints imposed by the solute. These findings reverse the classical "iceberg" view of hydrophobic hydration by indicating that hydrophobic hydration water is less ice-like than bulk water. Our results also challenge the "structural temperature" concept. The two investigated osmolytes have opposite effects on protein stability but have virtually the same effect on water dynamics, suggesting that they do not act indirectly via solvent perturbations. The NMR-derived picture of hydrophobic hydration dynamics differs substantially from views emerging from recent quasielastic neutron scattering and pump-probe infrared spectroscopy studies of the same solutes. We discuss the possible reasons for these discrepancies.     

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.     

Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.     

Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

Non-isothermal unfolding/denaturing kinetics of egg white protein

Egg protein is an important part of our food to get protein in our daily diet, and makes this protein more important to researchers to understand its kinetic behavior to understand the energy involved in the digestion of the egg protein. Hence, the present study explores the denaturing kinetics of the protein obtained from the hen??s egg white (EW) using high resolution calorimetric technique. Fresh EW was scanned for heating and cooling to see the thermodynamics from 10 to 100?°C at different heating ramp rates varying from 1 to 20?°C?min^?1. An endothermic peak was found on heating scan showing denaturing of protein which was found absent at the cooling indicating the absence of any residue after heating. The denature peak shifted towards higher temperature as ramp rate increases following Arrhenius behavior and shows an activated denaturing kinetics of the egg protein. This peak was also compared with the water to avoid water effects. Behavior of denaturing peak can be explained in terms of Arrhenius theory and further discussed to get the energy involved in digestion.     

Correlation between solvent-reorganization dynamics and the kinetics of metallotropy in polar media

The kinetics of metallotropy of the 3,6-di-tert-butyl-2-(triphenylstannyl)oxyphenoxyl radical has been studied by ESR. The correlation between chemical exchange time _ex, solvent polarity, and longitudinal relaxation time of the solvent corresponds to the model of a process controlled by molecular dynamics. A linear relation between _ex and correlation time _c for reorientation movements of the radical is found: _ex = · _c. The coefficient depends on the dielectric properties of the solvent.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 410–413, March, 1994.This work was supported by the Russian Foundation for Basic Research, project No. 93-03-4372.     

Hydrogen exchange and hydration dynamics in gelatin gels

Gelatin, derived from the collagen triple helix, is the most widely used functional biopolymer and a prototype for studies of physical gels. Gelatin gels have also served as models for soft biological tissue in efforts to elucidate the molecular basis of the magnetic relaxation phenomena that govern magnetic resonance image contrast. Yet, the microstructure, hydration, and magnetic relaxation behavior of gelatin gels are not well understood. To address these issues, we report here the water 2H and 17O magnetic relaxation dispersion (MRD) profiles from gelatin gels over wide ranges of resonance frequency and pH. For the global analysis of this extensive data set, we use a generalized relaxation theory that remains valid for arbitrarily slow molecular dynamics. The strong pH dependence in the 2H profiles can be rationalized quantitatively as the result of exchange with bulk water of labile hydrogens in gelatin side chains. The global analysis of the MRD data yields hydrogen-exchange rate constants, acid dissociation constants, and orientational order parameters in agreement with independent structural, thermodynamic, and kinetic data. The MRD analysis reveals a highly mobile hydration layer at the surface of the gelatin triple helix and a small number of trapped water molecules with residence times on the order of 10(-8) s, presumably associated with structural defects and branch points in the gel. The MRD data also indicate that approximately 20% of the gelatin residues belong to flexible polypeptide chains, rather than to rigid triple-helical segments. By identifying the molecular species and motions responsible for the 2H and 17O dispersion profiles, this study takes a significant step toward a quantitative understanding of water relaxation in aqueous gels and biological tissue.