Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability

To isolate the effects of the inclusion of polarizability in the force field model on the structure and dynamics of the solvating water in differing electrostatic environments of proteins, we present the results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in water with force fields that explicitly include polarization for both the protein and the water. We use three model potentials for water and two model potentials for the protein. Two of the water models and one of the protein models are polarizable. A total of six systems were simulated representing all combinations of these polarizable and nonpolarizable protein and water force fields. We find that all six systems behave in a similar manner in regions of the protein that are weakly electrostatic (either hydrophobic or weakly hydrophilic). However, in the vicinity of regions of the protein with relatively strong electrostatic fields (near positively or negatively charged residues), we observe that the water structure and dynamics are dependent on both the model of the protein and the model of the water. We find that a large part of the dynamical dependence can be described by small changes in the local environments of each region that limit the local density of non-hydrogen-bonded waters, precisely the water molecules that facilitate the dynamical relaxation of the water-water hydrogen bonds. We introduce a simple method for rescaling for this effect. When this is done, we are able to effectively isolate the influence of polarizability on the dynamics. We find that the solvating water's relaxation is most affected when both the protein and the water models are polarizable. However, when only one model (or neither) is polarizable, the relaxation is similar regardless of the models used.     

The bovine basic pancreatic trypsin inhibitor (Kunitz inhibitor): a milestone protein

The pancreatic Kunitz inhibitor, also known as aprotinin, bovine basic pancreatic trypsin inhibitor (BPTI), and trypsin-kallikrein inhibitor, is one of the most extensively studied globular proteins. It has proved to be a particularly attractive and powerful tool for studying protein conformation as well as molecular bases of protein/protein interaction(s) and (macro)molecular recognition. BPTI has a relatively broad specificity, inhibiting trypsin- as well as chymotrypsin- and elastase-like serine (pro)enzymes endowed with very different primary specificity. BPTI reacts rapidly with serine proteases to form stable complexes, but the enzyme: inhibitor complex formation may involve several intermediates corresponding to discrete reaction steps. Moreover, BPTI inhibits the nitric oxide synthase type-I and -II action and impairs K+ transport by Ca2+-activated K+ channels. Clinically, the use of BPTI in selected surgical interventions, such as cardiopulmonary surgery and orthotopic liver transplantation, is advised, as it significantly reduces hemorrhagic complications and thus blood-transfusion requirements. Here, the structural, inhibition, and bio-medical aspects of BPTI are reported.     

Hydroiodic acid attachment kinetics as a chemical probe of gaseous protein ion structure: Bovine pancreatic trypsin inhibitor

The kinetics of attachment of hydroiodic acid (HI) to the (M + 6H)6+ ions of native and reduced forms of bovine pancreatic trypsin inhibitor (BPTI) in the quadrupole ion trap environment are reported. Distinctly nonlinear (pseudo first-order) reaction kinetics are observed for reaction of the native ions, indicating two or more noninterconverting structures in the parent ion population. The reduced form, on the other hand, shows very nearly linear reaction kinetics. Both forms of the parent ion attach a maximum of five molecules of hydroiodic acid. This number is expected based on the amino acid composition of the protein. There is a total of 11 strongly basic sites in the protein (i.e., six arginines, four lysines, and one N-terminus). An ion with protons occupying six of the basic sites has five available for hydroiodic acid attachment. The kinetics of successive attachment of HI to the native and reduced forms of BPTI also differ, particularly for the addition of the fourth and fifth HI molecules. A very simple kinetic model describes the behavior of the reduced form reasonably well, suggesting that all of the neutral basic sites in the reduced BPTI ions have roughly equal reactivity. However, the behavior of the native ion is not well-described by this simple model. The results are discussed within the context of differences in the three-dimensional structures of the ions that result from the presence or absence of the three disulfide linkages found in native BPTI. The HI reaction kinetics appears to have potential as a chemical probe of protein ion three-dimensional structure in the gas phase. Hydroiodic acid attachment chemistry is significantly different from other chemistries used to probe three-dimensional structure and hence, promises to yield complementary information.     

Specific ion effects: Interaction between nanoparticles in electrolyte solutions

Dependence of colloidal interactions on salt identity, observed frequently in experiments, can be accounted for once ion specific non-electrostatic forces are included in the theory. Ability to predict the effect of added salt on the phase diagram of colloid dispersions is essential for the design of processes involving nanocolloids. The Ornstein–Zernike equation with hypernetted chain closure approximation provides a viable first estimate for the potential of mean force between ionized nanoparticles like alumina aggregates in aqueous electrolytes subject to dispersion interactions with hydrated simple ions. Calculated potentials of mean force enable the prediction of osmotic second virial coefficients and phase diagrams showing a dramatic dependence on ion type. The choice of salt therefore provides an efficient, non-intrusive way to tune the phase behavior of nanoparticle dispersions.     

Sodium diffusion through amorphous silica surfaces: a molecular dynamics study

We have studied the diffusion inside the silica network of sodium atoms initially located outside the surfaces of an amorphous silica film. We have focused our attention on structural and dynamical quantities, and we have found that the local environment of the sodium atoms is close to the local environment of the sodium atoms inside bulk sodo-silicate glasses obtained by quench. This is in agreement with recent experimental results.     

Ligand-to-metal charge-transfer dynamics in a blue copper protein plastocyanin: a molecular dynamics study

Equilibrium and nonequilibrium dynamics of a blue copper protein plastocyanin in an oxidized state are studied by molecular dynamics (MD) simulation. Potential energy functions of the lowest seven electronic states, including ligand-to-metal charge-transfer (LMCT) and copper d --> d excited states, were taken from our previous work (Ando, K. J. Phys. Chem. B 2004, 108, 3940), which employed ab initio molecular orbital and density functional calculations on the active-site model. The equilibrium MD simulations in the ground state indicate that ligand motions coupled to transition from the ground state to the LMCT state are mostly represented by stretching and bending vibrations of the Cu-S(Cys) distance, Ndelta(His)-Cu-Ndelta(His) angle, and S(Cys)-Cu-[Ndelta(His)]2 trigonal pyramid structure. The nonequilibrium dynamics on the LMCT potential exhibit rapid decays in which surface crossings to the d --> d and the first excited states occur in 70-80 fs. The crossing dynamics mostly correlate with cleavage of the Cu-S(Cys) bond and the associated response in the Ndelta(His)-Cu-Ndelta(His) moiety. The average dynamics of the vertical energy gap coordinates exhibit an overdamped decay with a recurrence oscillation in 500 fs, which shows clear coherence surviving after the ensemble averaging. This oscillation stems mostly from the recoiling motion of the Ndelta(His)-Cu-Ndelta(His) part. The dynamics of the energy gaps after this coherent oscillation are randomized such that the ensemble average yields flat profiles along time, although each single trajectory exhibits fluctuations with amplitudes large enough to reach surface crossings. These indicate that the relaxation from the LMCT state first occurs via ballistic and coherent potential crossings in 70-80 and 500 fs, followed by thermally activated random transitions.     

Specific ion effects in aqueous eletrolyte solutions confined within graphene sheets at the nanometric scale

The underlying mechanisms of specific ion effects on structure and dynamics of aqueous solutions have been long debated. On the other hand, the role of polarization at hydrophobic interfaces when aqueous electrolytes are present is of great importance, as it has been observed at the air-vapor interface. In this work, we have explored influence of ionic species on microscopical properties of aqueous sodium halide solutions constrained inside a double layer graphene channel, as a model for a realistic hydrophobic interface. Our systems have been simulated by molecular dynamics techniques, explicitly including polarization in water molecules and ions. Water and ionic density profiles showed the tendency of ionic species to occupy the whole space available, in good agreement with spectroscopic experimental data. The exception to this general behavior was fluoride, which preferred to stay away from interfaces. Two main regions were defined: interfaces and the central part of the slab, the bulklike region. Ionic hydration numbers at interfaces were lower than those at the bulklike area by about one to two units. We have also analyzed water-ion orientations and polarization distributions and obtained a marked dependence on ionic concentration. Residence time of anions suffered important fluctuations and tended to be largest at interfaces. Large variations of the static permittivity between interfacial and bulklike regions were observed. Ionic diffusion was found to be between 10(-5) and 10(-6) cm(2) s(-1) and showed to be mainly dependent on the concentration, whereas the type of anion considered and the polarizability had significantly less relevance. Conductivities were found to be dependent on ionic concentrations and the polarizabilities of anions, as well as on the spatial direction considered.     

Hydration of Y3+ ion: a Car-Parrinello molecular dynamics study

The solvation shell structure of Y3+ and the dynamics of the hydrated ion in an aqueous solution of 0.8 M YCl3 are studied in two conditions with and without an excess proton by using first principles molecular dynamics method. We find that the first solvation shell around Y3+ contains eight water molecules forming a square antiprism as expected from x-ray absorption near edge structure in both the conditions we examined. A detailed analysis relying upon localized orbitals reveals that the complexation of water molecules with yttrium cation leads to a substantial amount of charge redistribution particularly on the oxygen atoms, giving rise to the chemical shifts of approximately -20 ppm in 17O nuclear magnetic resonance relative to the computed nuclear shieldings of the bulk water.     

Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations

Binding energies of ion triplets formed in ionic liquids by Li⁺ with two anions have been studied using quantum‐chemical calculations with implicit and explicit solvent supplemented by molecular dynamics (MD) simulations. Explicit solvent approach confirms variation of solute‐ionic liquid interactions at distances up to 2 nm, resulting from structure of solvation shells induced by electric field of the solute. Binding energies computed in explicit solvent and from the polarizable continuum model approach differ largely, even in sign, but relative values generally agree between these two models. Stabilities of ion triplets obtained in quantum‐chemical calculations for some systems disagree with MD results; the discrepancy is attributed to the difference between static optimized geometries used in quantum chemical modeling and dynamic structures of triplets in MD simulations. © 2015 Wiley Periodicals, Inc.     

Principal active species of horseradish peroxidase, compound I: a hybrid quantum mechanical/molecular mechanical study

The active species, Compound I, of horseradish peroxidase (HRP) has been investigated by quantum mechanical/molecular mechanical (QM/MM) calculations using 10 different QM regions. In accord with experimental data, the lowest doublet and quartet states are found to be virtually degenerate, with two unpaired electrons on the FeO moiety and one localized on the porphyrin in an a(2u)-dominant orbital with a minor, but nonnegligible, a(1u) component. The proximal ligand appears to be imidazole rather than imidazolate. The hydrogen-bonding network around the FeO moiety (i.e., Arg38 and His42) has significant influence on the axial bonds and the spin density distribution in the FeO moiety. Including this network in the QM region was found to be essential for reproducing the experimental M?ssbauer parameters. The protein environment shapes most of the subtle features of Compound I of HRP.     

Blocking of the nicotinic acetylcholine receptor ion channel by chlorpromazine, a noncompetitive inhibitor: A molecular dynamics simulation study

A large series of pharmacological agents, distinct from the typical competitive antagonists, block in a noncompetitive manner the permeability response of the nicotinic acetylcholine receptor (nAChR) to the neurotransmitter acetylcholine. Taking the neuroleptic chlorpromazine (CPZ) as an example of such agents, the blocking mechanism of noncompetitive inhibitors to the ion channel pore of the nAChR has been explored at the atomic level using both conventional and steered molecular dynamics (MD) simulations. Repeated steered MD simulations have permitted calculation of the free energy (approximately 36 kJ/mol) of CPZ binding and identification of the optimal site in the region of the serine and leucine rings, at approximately 4 A from the pore entrance. Coulomb and the Lennard-Jones interactions between CPZ and the ion channel as well as the conformational fluctuations of CPZ were examined to assess the contribution of each to the binding of CPZ to the nAChR. The MD simulations disclose a dynamic interaction of CPZ binding to the nAChR ionic channel. The cationic ammonium head of CPZ forms strong hydrogen bonds with Glu262 (alpha), Asp268 (beta), Glu272 (beta), Ser276 (beta), Glu280 (delta), Gln271 (gamma), Glu275 (gamma), and Asn279 (gamma) nAChR residues. Finally, the conventional MD simulation of CPZ at its identified binding site demonstrates that the binding of CPZ not only blocks ion transport through the channel but also markedly inhibits the conformational transitions of the channel, necessary for nAChR to carry out its biological function.     

Specific ion effects in solutions of globular proteins: comparison between analytical models and simulation

Monte Carlo simulations have been performed for ion distributions outside a single globular macroion and for a pair of macroions, in different salt solutions. The model that we use includes both electrostatic and van der Waals interactions between ions and between ions and macroions. Simulation results are compared with the predictions of the Ornstein-Zernike equation with the hypernetted chain closure approximation and the nonlinear Poisson-Boltzmann equation, both augmented by pertinent van der Waals terms. Ion distributions from analytical approximations are generally very close to the simulation results. This demonstrates that properties that are related to ion distributions in the double layer outside a single interface can to a good approximation be obtained from the Poisson-Boltzmann equation. We also present simulation and integral equation results for the mean force between two globular macroions (with properties corresponding to those of hen-egg-white lysozyme protein at pH 4.3) in different salt solutions. The mean force and potential of mean force between the macroions become more attractive upon increasing the polarizability of the counterions (anions), in qualitative agreement with experiments. We finally show that the deduced second virial coefficients agree quite well with experimental results.     

Gas-phase binding of non-covalent protein complexes between bovine pancreatic trypsin inhibitor and its target enzymes studied by electrospray ionization tandem mass spectrometry

The potential of electrospray ionization (ESI) mass spectrometry (MS) to detect non-covalent protein complexes has been demonstrated repeatedly. However, questions about correlation of the solution and gas-phase structures of these complexes still produce vigorous scientific discussion. Here, we demonstrate the evaluation of the gas-phase binding of non-covalent protein complexes formed between bovine pancreatic trypsin inhibitor (BPTI) and its target enzymes over a wide range of dissociation constants. Non-covalent protein complexes were detected by ESI-MS. The abundance of the complex ions in the mass spectra is less than expected from the values of the dissociation constants of the complexes in solution. Collisionally activated dissociation (CAD) tandem mass spectrometry (MS/MS) and a collision model for ion activation were used to evaluate the binding of non-covalent complexes in the gas phase. The internal energy required to induce dissociation was calculated for three collision gases (Ne, Ar, Kr) over a wide range of collision gas pressures and energies using an electrospray ionization source. The order of binding energies of the gas-phase ions for non-covalent protein complexes formed by the ESI source and assessed using CAD-MS/MS appears to differ from that of the solution complexes. The implication is that solution structure of these complexes was not preserved in the gas phase.     

Structure and dynamics of 1,2-dimethoxyethane and 1,2-dimethoxypropane in aqueous and non-aqueous solutions: a molecular dynamics study

Herein, we report a comparative modelling study of 1,2-dimethoxyethane (DME) and 1,2-dimethoxypropane (DMP) at 298 K and 318 K in the liquid state, water mixtures, and at infinite dilution condition in water, methanol, carbon tetrachloride, and n-heptane. Both DME and DMP are united-atom models compatible with GROMOS∕OPLS force fields. Calculated thermodynamic and structural properties of the pure DME and DMP liquids resulted in excellent agreement with the experimental data. In aqueous solutions, densities, diffusion coefficients, and concentration dependent conformers of DME, were in agreement with experimental data. The calculated free energy of solvation (ΔG(hyd)) at 298 K is equal to -22.1 ± 0.8 kJ mol(-1) in good agreement with the experimental value of 20.2 kJ mol(-1). In addition, the free energy of solvation of DME in non-aqueous solvents follows the trend methanol ≈ water < carbon tetrachloride < n-heptane, consistently with the dielectric constant of the solvents. On contrary, the presence of an extra methyl group on chiral carbon makes DMP less soluble than DME in water (ΔG(hyd) = -16.0 ± 1.1 kJ mol(-1)) but more soluble in non-polar solvents as n-heptane. Finally, for the DMP the chiral discrimination of the two enantiomers was calculated as solvation free energy difference of one DMP isomer in the solution of the other. The obtained value of ΔΔG(RS) = -3.7 ± 1.4 kJ mol(-1) indicates a net chiral discrimination of the two enantiomers.     

Structural studies of the interactions of normal and abnormal human plasmins with bovine basic pancreatic trypsin inhibitor

Catalytic activity of human plasmin is inhibited by bovine basic pancreatic trypsin inhibitor (BPTI, also known as aprotinin). In spite of increased interest in the function of BPTI as an inhibitor of plasmin, the 3-D structure of the plasmin-BPTI complex has not yet been determined. Therefore, in the present paper, the structure of the plasmin-BPTI complex was constructed by the homology modeling method, which provided information about the high affinity of plasmin for BPTI. Moreover, normal mode analyses of free plasmin, free BPTI and the plasmin-BPTI complex were carried out to investigate the changes in dynamics following complex formation. After study of the plasmin-BPTI interaction, we also investigated the binding of BPTI with abnormal plasmin, theoretically and experimentally. The result showing that BPTI binds to abnormal plasmin in the same way as it does to normal plasmin supports the previous finding that the difference between normal and abnormal plasmins is very small and that the abnormality is localized to the catalytic site.     

Polypeptide friction and adhesion on hydrophobic and hydrophilic surfaces: a molecular dynamics case study

Using all-atomistic MD simulations including explicit water, the mobility and adhesion of a mildly hydrophobic single polypeptide chain adsorbed on hydrophobic and hydrophilic diamond surfaces is investigated by application of lateral and vertical pulling forces. Forced motion on the hydrophilic surface exhibits stick-slip due to breaking and reformation of hydrogen bonds; in contrast, on the hydrophobic surface, the motion is smooth. By carefully tuning the driving force magnitude, the linear-response regime is reached on a hydrophobic surface and equilibrium values for mobility and adhesive strength are obtained. On the hydrophilic surface, on the other hand, slow hydrogen-bond kinetics prevents equilibration and only upper bounds for adhesion force and mobility can be estimated. Whereas the desorption force is rather comparable on the two surfaces and differs at most by a factor of 2, the mobility on the hydrophilic surface is at least 30-fold reduced compared to the hydrophobic one. A simple model based on a single particle diffusing in a corrugated potential landscape suggests that cooperativity is rather limited and that the small mobility on a hydrophilic surface can be rationalized in terms of incoherently moving monomers. The experimentally well-known peptide mobility in bulk water is quantitatively reproduced in our simulations, which serves as a sensitive test on our methodology employed.