Lewis-inspired representation of dissociable water in clusters and Grotthuss chains

Proton transfer to and from water is critical to the function of water in many settings. However, it has been challenging to model. Here, we present proof-of-principle for an efficient yet robust model based on Lewis-inspired submolecular particles with interactions that deviate from Coulombic at short distances to take quantum effects into account. This “LEWIS” model provides excellent correspondence with experimental structures for water molecules and water clusters in their neutral, protonated and deprotonated forms; reasonable values for the proton affinities of water and hydroxide; a good value for the strength of the hydrogen bond in the water dimer; the correct order of magnitude for the stretch and bend force constants of water; and the expected time course for Grotthuss transport in water chains.     

Differential scanning calorimetry study of the hydrophobic hydration of the elastin-based polypentapeptide, poly(VPGVG), from deficiency to excess of water

The polypentapeptide of elastin, poly(VPGVG), has become an interesting model polypeptide in understanding the mechanism of protein folding and assembly. Due to its simple amino acid composition and the predominance of apolar side chains, this polymer shows strong hydrophobic-hydration phenomena. This paper explores, by calorimetric methods, the nature and structure of the clathrate-like arrangements that take place, surrounding the apolar side chains of the polymer. The performance of these methods, especially differential scanning calorimetry, has a well-gained reputation. In this work, the development of the clathrate-like structures around this model polymer has been followed from water deficiency to water-excess states. Two main conclusions have been obtained from the data obtained. First, there is an upper limit of about 170 water molecules per pentamer as the number of water molecules required to form all the possible clathrate-like structures. Second, these structures exist as an inhomogeneous population with energies spreading in a significantly broad range, which is likely related to differences in geometrical parameters (bond lengths and angles) of the clathrate structure.Copyright 2000 John Wiley & Sons, Inc.     

Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture

A combined and sequential use of quantum mechanical (QM) calculations and classical molecular dynamics (MD) simulations was made to investigate the σ and π types of hydrogen bond (HB) in benzene-water and pyrrole-water as clusters and as their liquid mixture, respectively. This paper aims at analyzing similarities and differences of these HBs resulted from QM and MD on an equal footing. Based on the optimized geometry at ωb97xD/aug-cc-pVTZ level of theory, the nature and property of σ and π types of HBs are unveiled by means of atoms in molecules (AIM), natural bond orbital (NBO) and energy decomposition analysis (EDA). In light of the above findings, MD simulation with OPLS-AA and SPC model was applied to study the liquid mixture at different temperatures. The MD results further characterize the behavior and structural properties of σ and π types HBs, which are somewhat different but reasonable for the clusters by QM. Finally, we provide a reasonable explanation for the different solubility between benzene/water and pyrrole/water.

Macromolecular naloxone: a novel long-acting polymer-bound drug.

A widely applicable, prolonged-action drug delivery system has been developed using naloxone, a pure narcotic antagonist, as a model. The drug is attached to an inert, water soluble polymer by reversible covalent bonds, whose slow cleavage releases active drug. Naloxone, attached to a hydrazine-substituted polysaccharide by a hydrazone bond, antagonizes morphine analgesia more than 25 times longer than free naloxone.     

Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters

BackgroundThe availability of high-resolution X-ray structures has shown that proteins contain numerous water molecules, but their role is still not fully understood. Protonated and deprotonated water species are often involved in biochemical reactions. However protons are exceedingly difficult to detect directly because they are electron-poor species.MethodsThe oxygen‑oxygen distance of the crystallographic water molecules was analyzed in a large high-resolution data set. Moreover, a detailed analysis was carried out on the protein-bound water in the available structures of carbonic anhydrase II and cytochrome c oxidase, chosen as protein models in which protonated and deprotonated water species play a significant role.ResultsThe analysis shows an excess of water-water distances below the expected value for hydrogen bond. In the cavities and on the surface of the considered model proteins, clusters of water molecules are found, whose structure suggests the presence of chemical species deriving from self-ionization of water.ConclusionsThe presence of a small maximum below the hydrogen bond threshold in the oxygen‑oxygen distance distribution of crystallographic water molecules, along with the location of many of these water clusters, suggest the presence of Zundel-like structures in, or near, the proteins. Particularly significant is the presence of such structures in protein regions which have been identified as proton antennae or channels.General significanceThis work shows the possibilities, still unexplored, offered by this type of analysis in detecting in structures obtained by X-ray diffraction the presence of aqueous protons or hydroxide ions, which are chemical species as important as elusive.     

Adsorption Behavior of Polydisperse Polymeric Systems

Adsorption behavior of polydisperse polymers at interfaces is studied by the Monte Carlo simulation method based on a lattice model. Effects of temperature and adsorption energies on the polymer density profile, cluster distributions and adsorption layer thickness are evaluated in two different polydisperse systems. It is found that adsorption properties are greatly different in these two systems. In normal distribution polydisperse systems, polymers are more sensitive to the excluded volume effects while in average distribution polymers are more inclined to adsorb on adsorbing interfaces. As higher temperature and lower attraction constrain the polymer adsorption, more clusters are found under these conditions. When temperature approaches the critical temperature of monodisperse systems, stable and large clusters exist in these two polydisperse systems. These results suggest that micro phase transition may exist in polydisperse systems. Polydisperse systems take little change of phase transition temperatures but altered the clusters morphology to some extent. The adsorption layer thickness changes are more sensitive to both temperature and polymer–interface interactions in average distribution systems when the whole polymer concentration increases slightly. This work also suggests significant differences between the polydisperse and the monodisperse systems in adsorption behavior. Therefore, quantitative system errors may exist when the monodisperse system models are used in simulation to evaluate polymer adsorption properties.     

Stability of molecular adhesion mediated by confined polymer repellers and ligand-receptor bonds

Experiments have shown that stable adhesion of a variety of animal cells on substrates prepared with precisely controlled ligand distribution can be formed only if the ligand spacing is below 58 nm. To explain this phenomenon, here we propose a confined polymer model to study the stability of molecular adhesion mediated by polymer repellers and ligand-receptor bonds. In this model, both repellers and binders are treated as wormlike chains confined in a nanoslit, and the stability of adhesion is considered as a competition between attractive interactions of ligand-receptor binding and repulsive forces due to the size mismatch between repellers and binders. The force on each ligand-receptor bond is calculated from the confined polymer model, and the classic model of Bell is used to describe the association/dissociation reactions of ligand-receptor bonds. The calculated equilibrium bond distribution shows that there exists a critical ligand density for stable adhesion, corresponding to a critical ligand spacing which agrees not only qualitatively but also quantitatively with the experimental observation. In the case of stable adhesion, the model predicts an equilibrium separation between adhesion surfaces below 60% of the contour length of the ligand-receptor bonds.     

Molecular modeling study of sulfonated SIBS triblock copolymers

An important class of thermoplastic elastomers involves polystyrene and polyisobutylene blocks (SIBS). Sulfonated SIBS Triblock Copolymers (S-SIBS) are of particular interest because of potential applications for fuel cell and textile applications, where breathable, protective clothing is required. We have used multiscale modeling to gain an understanding of the static and dynamic properties of these polymer systems at detailed atomistic levels. Quantum chemistry tools were used to elucidate the bonding of water molecules and sulfonate groups. In addition, molecular dynamics was applied to calculate the polymer density at various levels of sulfonation. The structures of polymer with hydronium ions and also water were studied and the mechanism of water self-diffusion was proposed. It was found that with increase of water content the hydronium ions move further away from sulfonate groups. The self-diffusion coefficients of water were found to reproduce well experimental trends. Two different distributions of sulfonate groups were studied: one blocky and another perfectly dispersed. In the case of the blocky architecture, the water clusters are connected at a lower sulfonation level, leading to increased water diffusion coefficients as compared to the dispersed architecture.     

Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta

Molecular dynamics simulations reveal that the hydrophobic cavity in human cytokine Interleukin-1beta is hydrated and can dynamically accommodate between one and four water molecules. These waters have residence times > 500 ps and can give rise to detectable NOEs, in agreement with NMR observations of Ernst et al. (Science 1995; 267:1813-1817). The waters also display high positional disorder within the cavity, which explains why they have not been resolved crystallographically. The average distribution of water molecules over time within the cavity matches well the low resolution electron density extracted by Yu et al. (Proc Natl Acad Sci 1999; 96:103-108). The water molecules hydrate the hydrophobic cavity preferentially as complex clusters. These clusters result from a combination of hydrogen bonds between the waters and stabilizing interactions between the waters and aromatic rings forming the cavity. Free energy estimates suggest that it takes 4-waters to hydrate the cavity in a thermodynamically stable manner leading to a gain in free energy of transfer from bulk of approximately approximately 3.6 kcal/mol. This arises from the existence of the water clusters in multiple hydrogen bonded states. In addition, the waters are found to migrate either individually or as clusters out of the cavity through several pathways. The upper limit for one-dimensional diffusion of the waters within the protein matrix is 4 A/ps (relative to 6 A/ps for bulk). Simulations reveal pathways in addition to those identified crystallographically, with motions controlled by the rotations of sidechains. We find that only when the hydrophobic cavity is hydrated, do correlated motions couple distant sites with the sites that make contact with the receptor and this data partly offers an explanation of experimental mutagenesis data. Simulations, together with recent observations based on mutagenesis by Heidary et al. (J Mol Biol 2005; 353:1187-1198) that hydrogen bond networks couple motions across long distances in interleukin-1beta, lead us to hypothesize that the hydration of the cavity (conserved across mammals) can thermodynamically enhance hydrogen bond networks to enable coupling across long distances by acting as a plug and this in turn enables a kinetic control of the rate of transmission of signals.     

A stochastic model of leukocyte rolling.

Selectin-mediated leukocyte rolling under flow is an important process in leukocyte recruitment during inflammation. The rolling motion of individual cells has been observed to fluctuate randomly both in vivo and in vitro. This paper presents a stochastic model of the micromechanics of cell rolling and provides an analytical method of treating experimental data. For a homogeneous cell population, the velocity distribution is obtained in an analytical form, which is in good agreement with experimentally determined velocity histograms obtained previously. For a heterogeneous cell population, the model provides a simple, analytical method of separating the contributions of temporal fluctuations and population heterogeneity to the variance of measured rolling velocities. The model also links the mean and variance of rolling velocities to the molecular events underlying the observed cellular motion, allowing characterization of the distribution and release rate of the clusters of molecular bonds that tether the cell to substratum. Applying the model to the analysis of data obtained for neutrophils rolling on an E-selectin-coated surface at a wall shear stress of 1.2 dyn/cm2 yields estimations of the average distance between bond clusters (approximately micron) and the average time duration of a bond cluster resisting the applied fluid force (approximately 0.5 s).     

Refinement of the 7 Fe ferredoxin from Azotobacter vinelandii at 1.9 A resolution

The recently redetermined structure of the 7 Fe ferredoxin from Azotobacter vinelandii has been refined against a new 1.9 A data set. The crystallographic R-factor is 0.215 for all 9586 observed reflections 8.0 to 1.9 A. The model contains 106 amino acid residues, two Fe-S clusters and 21 water molecules. The root-mean-square deviations from ideality of bonds and angles are 0.014 A and 3.3 degrees, respectively. The refinement confirms the presence of two free cysteines: the thiol of C11 is in association with the side-chain of K100; the thiol of C24 is 3.35 A from inorganic sulfur of the [4 Fe-4 S] cluster. The refinement confirms a [3 Fe-4 S] model for the 3 Fe cluster. The two Fe-S clusters have similar bond distances and angles. The structure of the protein for residues 1 to 57 superposes within 0.85 A on residues 1 to 53 of the 8 Fe ferredoxin structure for main-chain N, CA and C atoms, if residues 9, 10, 29 and 30 of 7 Fe ferredoxin are omitted. These residues are part of two loops in contact with residues of the extended C-terminal chain of 7 Fe ferredoxin.     

The structure of percolated polymer systems: a computer simulation study

We studied the percolation process in a system consisting of long flexible polymer chains and solvent molecules. The polymer chains were approximated by linear sequences of beads on a two-dimensional triangular lattice. The system was athermal and the excluded volume was the only potential. The properties of the model system across the entire range of polymer concentrations were determined by Monte Carlo simulations employing a cooperative motion algorithm (CMA). The scaling behavior and the structure of the percolation clusters are presented and discussed.     

A comparative theoretical study for the methanol dehydrogenation to CO over Pt3 and PtAu2 clusters

The density functional theory (DFT) calculations are carried out to study the mechanism details and the ensemble effect of methanol dehydrogenation over Pt(3) and PtAu(2) clusters, which present the smallest models of pure Pt clusters and bimetallic PtAu clusters. The energy diagrams are drawn out along both the initial O-H and C-H bond scission pathways via the four sequential dehydrogenation processes, respectively, i.e., CH(3)OH → CH(2)OH → CH(2)O → CHO → CO and CH(3)OH → CH(3)O → CH(2)O → CHO → CO, respectively. It is revealed that the reaction kinetics over PtAu(2) is significantly different from that over Pt(3). For the Pt(3)-mediated reaction, the C-H bond scission pathway, where an ensemble composed of two Pt atoms is required to complete methanol dehydrogenation, is energetically more favorable than the O-H bond scission pathway, and the maximum barrier along this pathway is calculated to be 12.99 kcal mol(-1). In contrast, PtAu(2) cluster facilitates the reaction starting from the O-H bond scission, where the Pt atom acts as the active center throughout each elementary step of methanol dehydrogenation, and the initial O-H bond scission with a barrier of 21.42 kcal mol(-1) is the bottom-neck step of methanol decomposition. Importantly, it is shown that the complete dehydrogenation product of methanol, CO, can more easily dissociate from PtAu(2) cluster than from Pt(3) cluster. The calculated results over the model clusters provide assistance to some extent for understanding the improved catalytic activity of bimetal PtAu catalysts toward methanol oxidation in comparison with pure Pt catalysts.     

Dual fluorescent HPMA copolymers for passive tumor targeting with pH-sensitive drug release: synthesis and characterization of distribution and tumor accumulation in mice by noninvasive multispectral optical imaging

Preclinical in vivo characterization of new polymeric drug conjugate candidates is crucial for understanding the effects of certain chemical modifications on distribution and elimination of these carrier systems, which is the basis for rational drug design. In our study we synthesized dual fluorescent HPMA copolymers of different architectures and molecular weights, containing one fluorescent dye coupled via a stable hydrazide bond functioning as the carrier label and the other one modeling the drug bound to a carrier via a pH-sensitive hydrolytically cleavable hydrazone bond. Thus, it was possible to track the in vivo fate, namely distribution, elimination and tumor accumulation, of the polymer drug carrier and a cleavable model drug simultaneously and noninvasively in nude mice using multispectral optical imaging. We confirmed our in vivo results by more detailed ex vivo characterization (imaging and microscopy) of autopsied organs and tumors. There was no significant difference in relative biodistribution in the body between the 30 KDa linear and 200 KDa star-like polymer, but the star-like polymer circulated much longer. We observed a moderate accumulation of the polymeric carriers in the tumors. The accumulation of the pH-sensitive releasable model drug was even higher compared to the polymer accumulation. Additionally, we were able to follow the long-term in vivo fate and to prove a time-dependent tumor accumulation of HPMA copolymers over several days.     

Solution structure of a pentasaccharide representing the repeating unit of the O-antigen polysaccharide from Escherichia coli O142: NMR spectroscopy and molecular simulation studies

Conformational studies have been performed of a pentasaccharide derived from the O-polysaccharide from Escherichia coli O142. The polymer was selectively degraded by anhydrous hydrogen fluoride and reduced to yield an oligosaccharide model of its repeating unit, which in the branching region consists of four aminosugars. A comparison of (1)H and (13)C chemical shifts between the pentasaccharide and the polymer showed only minor differences, except where the cleavage had taken place, indicating that the oligomer is a good model of the repeating unit. Langevin dynamics and molecular dynamics simulations with explicit water molecules were carried out to sample the conformational space of the pentasaccharide. For the glycosidic linkages between the hexopyranoside residues, small but significant changes were observed between the simulation techniques. One-dimensional (1D) (1)H,(1)H double pulsed field gradient spin echo (DPFGSE) transverse rotating-frame Overhauser effect spectroscopy (T-ROESY) experiments were performed, and homonuclear cross-relaxation rates were obtained. Subsequently, a comparison of interproton distances from NMR experiment and the two simulation approaches showed that in all cases the use of explicit water in the simulations resulted in better agreement. Hydrogen-bond analysis of the trajectories from the molecular dynamics simulation revealed interresidue interactions to be important as a cluster of different hydrogen bonds and as a distinct highly populated hydrogen bond. NMR data are consistent with the presence of hydrogen bonding within the model of the repeating unit.     

Molecular complexity favors the evolution of ribopolymers

We have explored the stability of selected ribo oligomers in water and have determined the physical-chemical conditions in which the key 3'-phosphoester bond is more stable when embedded in the polymer than when present in the monomer. In these conditions, the spontaneous formation and the survival of ribo polymers are potentially favored. A narrow pH range was identified in which complex sequences resist degradation markedly more than monotonous ones, thus potentially favoring the evolution of sequence-based genetic information. Given that the founding property of a polymer is to maintain its polymeric form and its sequence information, these findings support the view that the evolution of pregenetic molecular information occurred based on intrinsic properties of nucleic polymers.     

Barrier height of free energy on confined polymer translocation through a short nano-channel

The translocation of a confined polymer chain through a nano-channel has been simulated by using two-dimensional bond fluctuation model (BFM) with Monte Carlo dynamics. It is found that the trapping time for the polymer chain to overcome the free energy barrier during the translocation, tautrap, depends exponentially on the chain length N and the channel length M, respectively. The results suggest that the barrier height of free energy depends linearly on N and M, which is different from that predicted for the Gaussian chain.     

The properties of liquid water in electric and magnetic fields

A new model of liquid water is proposed, which involves the liquid-crystalline phase, namely, the presence of linearly ordered chains of water molecules and large clusters of these molecules. The presence of linearly ordered chains and clusters in liquid water makes itself evident after the exposure of water to low-frequency electromagnetic radiation. The kinetics of the linearly ordered chains is described by nonlinear excitations (solitons). A hydrodynamic equation describing the behavior of this model system was derived. On the basis of the model, the dimensions of clusters were determined (approximately 600 A). The calculated values of dielectric permeability in the range of low frequencies appeared to be close to their experimentally obtained values. A tenfold increase in the stationary value of dielectric permeability compared with the known value of the dielectric constant in the frequency range of 10(4)-10(6) Hz was predicted. The frequency dependence of dielectric permeability in this range was studied.     

The role of water in cell architecture

The role of water in biochemical and cellular events is ignored by most workers. However, much recent research has pointed to the importance of physical processes of the cell, which focus attention on such straight forward, elementary questions as position and relationship in space of cell components. In this communication these questions are examined in terms of a new model of water structure. A radically new feature of this model is that water clusters have long-term rather than flickering existence and are as large as the macromolecular components of the cell. These properties allow the clusters and other components to pack together spacially so giving rise to integrated, large-scale, subcellular structures. The intimate participation of water in these structures would explain the fragility of the cytoplasmic organization.     

Strength of a weak bond connecting flexible polymer chains

Bond dissociation under steadily rising force occurs most frequently at a time governed by the rate of loading (Evans and Ritchie, 1997 Biophys. J. 72:1541-1555). Multiplied by the loading rate, the breakage time specifies the force for most frequent failure (called bond strength) that obeys the same dependence on loading rate. The spectrum of bond strength versus log(loading rate) provides an image of the energy landscape traversed in the course of unbonding. However, when a weak bond is connected to very compliant elements like long polymers, the load applied to the bond does not rise steadily under constant pulling speed. Because of nonsteady loading, the most frequent breakage force can differ significantly from that of a bond loaded at constant rate through stiff linkages. Using generic models for wormlike and freely jointed chains, we have analyzed the kinetic process of failure for a bond loaded by pulling the polymer linkages at constant speed. We find that when linked by either type of polymer chain, a bond is likely to fail at lower force under steady separation than through stiff linkages. Quite unexpectedly, a discontinuous jump can occur in bond strength at slow separation speed in the case of long polymer linkages. We demonstrate that the predictions of strength versus log(loading rate) can rationalize conflicting results obtained recently for unfolding Ig domains along muscle titin with different force techniques.