Modulation of the axial water hydrogen-bonding properties by chemical modification of the substrate in resting state, substrate-bound heme oxygenase from Neisseria meningitidis; coupling to the distal H-bond network via ordered water molecules

The hydrogen bonding of ligated water in ferric, high-spin, resting-state substrate complexes of heme oxygenase from Neisseria meningitidis has been systematically perturbed by variable electron-withdrawing substituents on the hemin periphery. The pattern of 1H NMR-detected dipolar shifts due to the paramagnetic anisotropy is strongly conserved among the four complexes, with the magnitude of dipolar shifts or anisotropy increasing in the order of substituent formyl < vinyl < methyl. The magnetic anisotropy is axial and oriented by the axial Fe-His23 bond, and while individual anisotropies have uncertainties of approximately 5%, the relative values of deltachi (and the zero-field splitting constant, D proportional, variant deltachi(ax)) are defined to 1%. The unique changes in the axial field strength implied by the variable zero-field splitting are in accord with expectations for the axial water serving as a stronger H-bond donor in the order of hemin substituents formyl > vinyl > methyl. These results establish the axial anisotropy (and D) as a sensitive probe of the H-bonding properties of a ligated water in resting-state, substrate complexes of heme oxygenase. Correction of observed labile proton chemical shifts for paramagnetic influences indicates that Gln49 and His53, some approximately 10 angstroms from the iron, sense the change in the ligated water H-bonding to the three nonligated ordered water molecules that link the two side chains to the iron ligand. The present results augur well for detecting and characterizing changes in distal water H-bonding upon mutagenesis of residues in the distal network of ordered water molecules and strong H-bonds.     

Hydration free energies and entropies for water in protein interiors

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein hydrogen bonds, and one which is more hydrophobic, forming only one water-protein hydrogen bond. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the nonpolar cavity is entropically favorable. For both proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increased length and weakened strength of protein-protein hydrogen bonds near the cavity.     

New model pair potential for water. Effect of inclusion of specific O⋯H interactions on the topology and dynamics of the hydrogen-bond network

Classical molecular dynamics was used to calculate the topologic and dynamic characteristics of H-bond networks in water, using various model potentials. The explicit inclusion of intermolecular interactions of oxygen and hydrogen atoms leads to a model involving additional stabilization of tetrahedrally coordinated molecules and, as a consequence, increased number of such molecules in the system. The H-bond lifetimes point to a strongly correlated molecular motion in the immediate environment.     

Confinement effects on water structure in membrane lyotropic phases

The change of the water structure in aqueous solutions of the tri-ethyleneglycol mono n-decyl ether (C(10)E(3)) was studied by micro Raman scattering. The results obtained on the O-H stretching band show that the behavior of the hydrogen bonding (H-bonds) water network can be used as a probe to follow the lamellar (L(α)) to sponge (L(3)) phase transition. In the lamellar phase, the stack of the surfactant molecules aggregated into a two-dimensional structure (membrane) acts as a soft confinement system for the H-bond water network of which the regular tetrahedral structure is perturbed. The change of the planar organization of the membranes to a highly disordered and infinite array of bilayers in the sponge phase amplifies the surface of contact between amphiphilic surfactant and water molecules which drives a strong disruption of the regular tetrahedral H-bonding water network.     

Stochastic dynamic simulation of a protein

The internal motions of a small protein, the bovine pancreatic trypsin inhibitor (BPTI) in solution, are investigated in the framework of the Langevin equation. In this approach, the effects of the solvent molecules are incorporated by suitably defining the friction and random forces. The friction coefficients are determined from a molecular dynamics simulation. The details of the rapid fluctuations of protein atoms obtained by stochastic and molecular dynamics simulation techniques are compared by calculating the generalized density of states obtained via an incoherent neutron scattering. Presently, our stochastic dynamics simulation is one order of magnitude faster than the molecular dynamics simulation with the explicit inclusion of the water molecules. Generalizations of the present stochastic dynamics approach for studying the large-scale motion in proteins are briefly outlined and the probability of a further speedup by an additional order of magnitude is discussed.     

Influence of electric field on the hydrogen bond network of methanol

The understanding of the structure of hydrogen (H) bonding liquids in electric (E) fields is important in the context of several areas of research, such as electrochemistry, surface science, and thermodynamics of electrolyte solutions. We had earlier presented a general thermodynamic framework for this purpose, and had shown that the application of E field enhances H-bond interactions among water molecules. The present investigation with methanol suggests a different result-the H-bond structure, as indicated by the average number of H bonds per molecule, goes through a maxima with increasing field strength. This result is explained based on the symmetry in the location of the H-bonding sites in the two types of molecules.     

Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules

Large-scale protein conformational motions on nanosecond-microsecond time scales are important for many biological processes, but remain largely unexplored because of methodological limitations. NMR relaxation methods can access these time scales if protein tumbling is prevented, but the isotropy required for high-resolution solution NMR is then lost. However, if the immobilized protein molecules are randomly oriented, the water 2H and 17O spins relax as in a solution of freely tumbling protein molecules, with the crucial difference that they now sample motions on all time scales up to approximately 100 micros. In particular, the exchange rates of internal water molecules can be determined directly from the 2H or 17O magnetic relaxation dispersion (MRD) profile. This possibility opens up a new window for characterizing the motions of individual internal water molecules as well as the large-scale protein conformational fluctuations that govern the exchange rates of structural water molecules. We introduce and validate this new NMR method by presenting and analyzing an extensive set of 2H and 17O MRD data from cross-linked gels of two model proteins: bovine pancreatic trypsin inhibitor and ubiquitin. We determine residence times and order parameters of four internal water molecules in these proteins and show that they are quantitatively consistent with the information available from crystallography and solution MRD. We also show how slow motions of side-chains bearing labile hydrogens can be monitored by the same approach. Proteins of any size can be studied at physiological hydration levels with this method.     

On the hydrogen bonding between water and ammonia molecules

The hydrogen bond N·HO between the water and ammonia molecules has been investigated ab initio using the SCF LCAO MO method. The minimal and extended basis sets of Slater type orbitals were used. It was found that the energy of the hydrogen bond is equal to 6.44 kcal/mole and the equilibrium separation of the oxygen and nitrogen atoms in the dimer is 5.72 au. At this intermolecular distance there is only one minimum in the potential energy curve for the motion of proton.     

Structure and dynamics of water confined in dimethyl sulfoxide.

We study the structure and dynamics of hydrogen-bonded complexes of H2O/D2O and dimethyl sulfoxide (DMSO) by infrared spectroscopy, NMR spectroscopy and ab initio calculations. We find that single water molecules occur in two configurations. For one half of the water monomers both OH/OD groups form strong hydrogen bonds to DMSO molecules, whereas for the other half only one of the two OH/OD groups is hydrogen-bonded to a solvent molecule. The H-bond strength between water and DMSO is in the order of that in bulk water. NMR deuteron relaxation rates and calculated deuteron quadrupole coupling constants yield rotational correlation times of water. The molecular reorientation of water monomers in DMSO is two-and-a-half times slower than in bulk water. This result can be explained by local structure behavior.     

How protein surfaces induce anomalous dynamics of hydration water

Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.     

Changes in water structure induced by the guanidinium cation and implications for protein denaturation

The effect of the guanidinium cation on the hydrogen bonding strength of water was analyzed using temperature-excursion Fourier transform infrared spectra of the OH stretching vibration in 5% H 2O/95% D 2O solutions containing a range of different guanidine-HCl and guanidine-HBr concentrations. Our findings indicate that the guanidinium cation causes the water H-bonds in solution to become more linear than those found in bulk water, and that it also inhibits the response of the H-bond network to increased temperature. Quantum chemical calculations also reveal that guanidinium affects both the charge distribution on water molecules directly H-bonded to it as well as the OH stretch frequency of H-bonds in which that water molecule is the donor. The implications of our findings to hydrophobic solvation and protein denaturation are discussed.     

Molecular dynamics of hydrogen bonds in protein-D2O: the solvent isotope effect

We suggest that the H-bond in proteins not only mirrors the motion of hydrogen in its own atomistic setting but also finds its origin in the collective environment of the hydrogen bond in a global lattice of surrounding H2O molecules. This water lattice is being perturbed in its optimal entropic configuration by the motion of the H-bond. Furthermore, bonding interaction with the lattice drop the H-bond energy from some 5 kcal/mol for the pure protein in the absence of H2O, to some 1.6 kcal/mol in the presence of the H2O medium. This low value here is determined in a computer experiment involving MD calculations and is a value close to the generally accepted value for biological systems. In accordance with these computer experiments under ambient conditions, the H-bond energy is seriously depressed, hence confirming the subtle effect of the H2O medium directly interacting with the H-bond and permitting a strong fluxional behavior. Furthermore, water produces a very large change in the entropy of activation due to the hydrogen bond breakage, which affects the rate by as much as 2 orders of magnitude. We also observe that there is an entire ensemble of H-bond structures, rather than a single transition state, all of which contribute to this H-bond. Here the model is tested by changing to D2O as the surrounding medium resulting in a substantial solvent isotope effect. This demonstrates the important influence of the environment on the individual hydrogen bond.     

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.     

Carbohydrate clustering in aqueous solutions and the dynamics of confined water

We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.     

Intramolecular Hydrogen Bonding Restricts Gd–Aqua-Ligand Dynamics

Aqua ligands can undergo rapid internal rotation about the M−O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H-bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H-bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H-bond, while alternative hypotheses that could explain the higher relaxivity were systematically ruled out. Intramolecular H-bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.     

Disruption of hydrogen bond structure of water near charged electrode surfaces

The understanding of the hydrogen (H) bonded structure of water near charged surfaces is highly relevant in the context of several important areas of research, including electrochemistry, biochemistry, and geology. Past simulation studies have not yielded conclusive answers; while some suggest breakage of H bonds near a charged surface, others argue that H-bonding interactions can stabilize the structure of surface water even in the presence of high electric (E) fields. Recent experiments, on the other hand, suggest a partial breakdown of H-bond structure near a charged electrode. In all these studies, however, the conclusions regarding H bonding were drawn based on the density profile of hydrogen/oxygen atoms near the interface. In the present paper, we investigate this problem using a new theory that explicitly accounts for the influence of E field on the H-bond network of water near the solid-liquid interface. We find that the average number of H bonds per molecule in bulk increases from approximately 3.8 at E<10(5) V/m to approximately 3.95 at E=2x10(9) V/m (suggesting enhancement in H-bond network), while that near the electrode surface decreases from approximately 2.8 to a saturation value of approximately 2.0 (suggesting weakening of H-bond network).     

A molecular dynamics simulation of the adsorption of water molecules surrounding an Au nanoparticle

This study uses molecular dynamics simulations performed in a parallel computing environment to investigate the adsorption of water molecules surrounding Au nanoparticles of various sizes. An observation of the oxygen and hydrogen atom distributions reveals that the adsorption of the water molecules creates two shell-like formations of water in close vicinity to the Au nanoparticle surface. These shell-like formations are found to be more pronounced around smaller Au nanoparticles. The rearrangement of water molecules in this region reduces the local hydrogen bond strength to below that which is observed in the bulk region. Finally, the simulation results indicate that the absolute value of the interaction energy between the water molecules and the Au nanoparticle is reduced when the water molecules surround a nanoparticle of larger diameter. This observation implies that a stronger adsorption effect exists between smaller Au nanoparticles and water molecules. Hence, the value of the adsorption constant increases for smaller Au nanoparticles.     

Internal dynamics of a globular protein under external force field

The inelastic neutron-scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low-frequency internal dynamics, < 200 cm^?1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron-derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.     

Cooperative interactions of hydrogen bonds in proton-transfer processes involving water molecules. Simulation of biochemical systems

Quantum-chemical calculations of molecular complexes simulating the proton channel of influenza A virus and the proton-transfer system of the active site of carboanhydrase enzyme were performed. These complexes comprise a proton-donor and a proton-acceptor groups bridged by a chain of water molecules. Calculations of the methylimidazole (H⁺)-H₂O-CH₃COO^? complex as a model of influenza M₂ virus revealed free translation motion of the water molecule between the donor and acceptor, as well as concerted proton transfer in both H bonds. The barrier for proton transfer is independent of the position of the bridging water molecule and varies linearly with the difference in the electrostatic potentials between the donor and acceptor. With elongation of the H-bond bridge between the donor and acceptor groups, the H-bond lengths and proton shifts in the chain links vary periodically. This process can be defined as an H-bond deformation wave (proton wave). It was shown that motion of one proton along the H bond is associated with vibrational motion of protons in other links, which results in wave propagation along the chain. The calculation results allowed the rate of the proton wave and the time of proton transfer from the donor to acceptor to be estimated.     

The topological and dynamic characteristics of H-bond networks in water according to computer simulation results

The classic molecular dynamics methods were employed to calculate the topological and dynamic characteristics of H-bond networks in water with the use of various model potentials. The explicit inclusion of specific intermolecular interactions between oxygen and hydrogen atoms additionally stabilized tetrahedrally coordinated molecules and, as a consequence, increased their number in the system. The lifetimes of H-bonds were found to characterize high correlation of movements of nearest environment molecules.