Descripción: Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis, J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2 -water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. © 2009 American Institute of Physics.

Descripción: Molecular dynamics simulations have been carried out to investigate the structure and dynamics of liquid methanol confined in 3.3 nm diameter cylindrical silica pores. Three cavities differing in the characteristics of the functional groups at their walls have been examined: (i) smooth hydrophobic pores in which dispersive forces prevail, (ii) hydrophilic cavities with surfaces covered by polar silanol groups, and (iii) a much more rugged pore in which 60% of the previous interfacial hydroxyl groups were replaced by the bulkier trimethylsilyl ones. Confinement promotes a considerable structure at the vicinity of the pore walls which is enhanced in the case of hydroxylated surfaces. Moreover, in the presence of the trimethylsilyl groups, the propagation of this interface-induced spatial ordering extends down to the central region of the pore. Concerning the dynamical modes, we observed an overall slowdown in both the translational and rotational motions. An analysis of these mobilities from a local perspective shows that the largest retardations operate at the vicinity of the interfaces. The gross features of the rotational dynamics were analyzed in terms of contributions arising from bulk and surface states. Compared to the bulk dynamical behavior, the characteristic timescales associated with the rotational motions show the most dramatic increments. A dynamical analysis of hydrogen bond formation and breaking processes is also included. © 2010 American Institute of Physics.

Descripción: In this work we studied the effect of NaCl on the thermodynamic and dynamic properties of supercooled water, for salt concentrations between 0.19 and 1.33mol kg-1, using molecular dynamic simulations for TIP5PE water model and ion parameters specially designed to be used in combination with this potential. We studied the isobaric heat capacity (Cp) temperature dependence and observed a maximum in Cp, occurring at Tm, that moves to lower temperature values with increasing salt concentration. Many characteristic changes were observed at scaled temperature TTm ∼ 0.96, namely a minimum in the density of the system, a reduction of the slope of the number of hydrogen bonds vs. temperature, and a crossover from Vogel-Tamman-Fulcher to Arrhenius dynamics. Finally, at low temperatures we observed that water dynamics become heterogeneous with an apparently common relationship between the fraction of immobile molecules and T/Tm for all studied systems. © 2011 American Institute of Physics.

Descripción: Pineal hormone melatonin (N-acetyl-5-methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca2+ concentration via activation of its G-protein-coupled membrane receptors, or through a direct interaction with calmodulin (CaM). The present work studies the direct interaction of melatonin with intact calcium-saturated CaM both experimentally, by fluorescence and nuclear magnetic resonance spectroscopies, and theoretically, by molecular dynamics simulations. The analysis of the experimental data shows that the interaction is calcium-dependent. The affinity, as obtained from monitoring 15N and 1H chemical shift changes for a melatonin titration, is weak (in the millimolar range) and comparable for the N- and C-terminal domains. Partial replacement of diamagnetic Ca2+ by paramagnetic Tb3+ allowed the measurement of interdomain NMR pseudocontact shifts and residual dipolar couplings, indicating that each domain movement in the complex is not correlated with the other one. Molecular dynamics simulations allow us to follow the dynamics of melatonin in the binding pocket of CaM. Overall, this study provides an example of how a combination of experimental and theoretical approaches can shed light on a weakly interacting system of biological and pharmacological significance.

Descripción: Molecular dynamics simulations of water in cylindrical hydrophilic pores with diameters of 1.5 and 3 nm were performed to explore the phase behavior and the nucleation dynamics of the confined fluid as a function of the percentage of volume filled f. The interactions of water with the pore wall were considered to be identical to the interactions between water molecules. At low water contents, all the water is adsorbed to the surface of the pore. A second phase consisting of a liquid plug appears at the onset filling for capillary condensation, fonset =27% and 34% for the narrow and wide pores, respectively. In agreement with experimental results for silica pores, the liquid phase appears close to the equilibrium filling feq in the 1.5 nm pore and under conditions of strong surface supersaturations for the 3 nm pore. After condensation, two phases, a liquid plug and a surface-adsorbed phase, coexist in equilibrium. Under conditions of phase coexistence, the water surface density Tcoex was found to be independent of the water content and the diameter of the pore. The value of Tcoex found in the simulations (∼3 nm-2) is in good agreement with experimental results for silica pores, suggesting that the interactions of water with silica and with itself are comparable. The surface-adsorbed phase at coexistence is a sparse monolayer with a structure dominated by small water clusters. We characterize the density and structure of the liquid and surface phases, the nucleation mechanism of the water plug, and the effect of surface hydrophilicity on the two-phase equilibrium and hysteresis. The results are discussed in light of experiments and previous simulations. © 2010 American Institute of Physics.

Descripción: An information theory description of finite systems explicitly evolving in time is presented. We impose a MaxEnt variational principle on the Shannon entropy at a given time while the constraints are set at a former time. The resulting density matrix contains explicit time odd components in the form of collective flows. As a specific application we consider the dynamics of the expansion in connection with heavy ion experiments. Lattice gas and classical molecular dynamics simulations are shown. © 2007 American Institute of Physics.

Descripción: Dimethyl sulfoxide (DMSO) has been known to enhance cell membrane permeability of drugs or DNA. Molecular dynamics (MD) simulations with single-component lipid bilayers predicted the existence of three regimes of action of DMSO: membrane loosening, pore formation and bilayer collapse. We show here that these modes of action are also reproduced in the presence of cholesterol in the bilayer, and we provide a description at the atomic detail of the DMSO-mediated process of pore formation in cholesterol-containing lipid membranes. We also successfully explore the applicability of DMSO to promote plasma membrane permeability to water, calcium ions (Ca2+) and Yo-Pro-1 iodide (Yo-Pro-1) in living cell membranes. The experimental results on cells in culture can be easily explained according to the three expected regimes: in the presence of low doses of DMSO, the membrane of the cells exhibits undulations but no permeability increase can be detected, while at intermediate DMSO concentrations cells are permeabilized to water and calcium but not to larger molecules as Yo-Pro-1. These two behaviors can be associated to the MD-predicted consequences of the effects of the DMSO at low and intermediate DMSO concentrations. At larger DMSO concentrations, permeabilization is larger, as even Yo-Pro-1 can enter the cells as predicted by the DMSO-induced membrane-destructuring effects described in the MD simulations. © 2012 de Ménorval et al.

Descripción: Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Descripción: We present 3D, gasdynamic simulations of jet/cloud collisions, with the purpose of modelling the HH 270/110 system. From the models, we obtain predictions of Hα and H2 1-0 s(1) emission line maps, which qualitatively reproduce some of the main features of the corresponding observations of HH 110. We find that the model that better reproduces the observed structures corresponds to a jet that was deflected at the surface of the cloud ∼ 1000 yr ago, but is now boring a tunnel directly into the cloud. This model removes the apparent contradiction between the jet/cloud collision model and the lack of detection of molecular emission in the crossing region of the HH 270 and HH 110 axes.

Descripción: We present results from molecular dynamics simulations performed on reverse micelles immersed in cyclohexane. Three different inner polar phases are considered: water (W), formamide (FM), and an equimolar mixture of the two solvents. In all cases, the surfactant was sodium bis(2-ethylhexyl) sulfosuccinate (usually known as AOT). The initial radii of the micelles were R∼15 Å, while the corresponding polar solvent-to-surfactant molar ratios were intermediate between w0 =4.3 for FM and w0 =7 for W. The resulting overall shapes of the micelles resemble distorted ellipsoids, with average eccentricities of the order of ∼0.75. Moreover, the pattern of the surfactant layer separating the inner pool from the non-polar phase looks highly irregular, with a roughness characterized by length scales comparable to the micelle radii. Solvent dipole orientation polarization along radial directions exhibit steady growths as one moves from central positions toward head group locations. Local density correlations within the micelles indicate preferential solvation of sodium ionic species by water, in contrast to the behavior found in bulk equimolar mixtures. Still, a sizable fraction of ∼90% of Na+ remains associated with the head groups. Compared to bulk results, the translational and rotational modes of the confined solvents exhibit important retardations, most notably those operated in rotational motions where the characteristic time scales may be up to 50 times larger. Modifications of the intramolecular connectivity expressed in terms of the average number of hydrogen bonds and their lifetimes are also discussed. © 2008 American Institute of Physics.

Descripción: Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function. © 2012 Roman et al.

Descripción: Papillomaviruses are small DNA tumor viruses that infect mammalian hosts, with consequences from benign to cancerous lesions. The Early protein 2 is the master regulator for the virus life cycle, participating in gene transcription, DNA replication, and viral episome migration. All of these functions rely on primary target recognition by its dimeric DNA-binding domain. In this work, we performed molecular dynamics simulations in order to gain insights into the structural dynamics of the DNA-binding domains of two prototypic strains, human papillomavirus strain 16 and the bovine papillomavirus strain 1. The simulations underline different dynamic features in the two proteins. The human papillomavirus strain 16 domain displays a higher flexibility of the β2-β3 connecting loop in comparison with the bovine papillomavirus strain 1 domain, with a consequent effect on the DNA-binding helices, and thus on the modulation of DNA recognition. A compact β-barrel is found in human papillomavirus strain 16, whereas the bovine papillomavirus strain 1 protein is characterized by a loose β-barrel with a large number of cavities filled by water, which provides great flexibility. The rigidity of the human papillomavirus strain 16 β-barrel prevents protein deformation, and, as a consequence, deformable spacers are the preferred targets in complex formation. In contrast, in bovine papillomavirus strain 1, a more deformable β-barrel confers greater adaptability to the protein, allowing the binding of less flexible DNA regions. The flexibility data are confirmed by the experimental NMR S2 values, which are reproduced well by calculation. This feature may provide the protein with an ability to discriminate between spacer sequences. Clearly, the deformability required for the formation of the Early protein 2 C-terminal DNA-binding domain-DNA complexes of various types is based not only on the rigidity of the base sequences in the DNA spacers, but also on the intrinsic deformability properties of each domain. © 2007 The Authors.

Descripción: The Antarctic icefish Chaenocephalus aceratus lacks the globins common to most vertebrates, hemoglobin and myoglobin, but has retained neuroglobin in the brain. This conserved globin has been cloned, over-expressed and purified. To highlight similarities and differences, the structural features of the neuroglobin of this colourless-blooded fish were compared with those of the well characterised human neuroglobin as well as with the neuroglobin from the retina of the red blooded, hemoglobin and myoglobin-containing, closely related Antarctic notothenioid Dissostichus mawsoni. A detailed structural and functional analysis of the two Antarctic fish neuroglobins was carried out by UV-visible and Resonance Raman spectroscopies, molecular dynamics simulations and laser-flash photolysis. Similar to the human protein, Antarctic fish neuroglobins can reversibly bind oxygen and CO in the Fe 2+ form, and show six-coordination by distal His in the absence of exogenous ligands. A very large and structured internal cavity, with discrete docking sites, was identified in the modelled three-dimensional structures of the Antarctic neuroglobins. Estimate of the free-energy barriers from laser-flash photolysis and Implicit Ligand Sampling showed that the cavities are accessible from the solvent in both proteins. Comparison of structural and functional properties suggests that the two Antarctic fish neuroglobins most likely preserved and possibly improved the function recently proposed for human neuroglobin in ligand multichemistry. Despite subtle differences, the adaptation of Antarctic fish neuroglobins does not seem to parallel the dramatic adaptation of the oxygen carrying globins, hemoglobin and myoglobin, in the same organisms. © 2012 Giordano et al.

Descripción: We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m 50 water molecules and n 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ∼ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain. © 2012 American Institute of Physics.

Descripción: The truncated hemoglobin N, HbN, of Mycobacterium tuberculosis is endowed with a potent nitric oxide dioxygenase (NOD) activity that allows it to relieve nitrosative stress and enhance in vivo survival of its host. Despite its small size, the protein matrix of HbN hosts a two-branched tunnel, consisting of orthogonal short and long channels, that connects the heme active site to the protein surface. A novel dual-path mechanism has been suggested to drive migration of O 2 and NO to the distal heme cavity. While oxygen migrates mainly by the short path, a ligand-induced conformational change regulates opening of the long tunnel branch for NO, via a phenylalanine (PheE15) residue that acts as a gate. Site-directed mutagenesis and molecular simulations have been used to examine the gating role played by PheE15 in modulating the NOD function of HbN. Mutants carrying replacement of PheE15 with alanine, isoleucine, tyrosine and tryptophan have similar O 2 /CO association kinetics, but display significant reduction in their NOD function. Molecular simulations substantiated that mutation at the PheE15 gate confers significant changes in the long tunnel, and therefore may affect the migration of ligands. These results support the pivotal role of PheE15 gate in modulating the diffusion of NO via the long tunnel branch in the oxygenated protein, and hence the NOD function of HbN. © 2012 Oliveira et al.

Descripción: Vertical excitation and electron detachment energies associated with the optical absorption of iodide ions dissolved in supercritical ammonia at 420 K have been calculated in two limiting scenarios: as a solvated free I- ion and forming a K+ I- contact ion pair (CIP). The evolution of the transition energies as a result of the gradual building up of the solvation structure was studied for each absorbing species as the solvent's density increased, i.e., changing the N H3 supercritical thermodynamic state. In both cases, if the solvent density is sufficiently high, photon absorption produces a spatially extended electron charge beyond the volume occupied by the solvated solute core; this excited state resembles a typical charge-transfer-to-solvent (CTTS) state. A combination of classical molecular dynamics simulations followed by quantum mechanical calculations for the ground, first-excited, and electron-detached electronic states have been carried out for the system consisting of one donor species (free I- ion or K+ I- CIP) surrounded by ammonia molecules. Vertical excitation and electron detachment energies were obtained by averaging 100 randomly chosen microconfigurations along the molecular dynamics trajectory computed for each thermodynamic condition (fluid density). Short- and long-range contributions of the solvent-donor interaction upon the CTTS states of I- and K+ I- were identified by performing additional electronic structure calculations where only the solvent interaction due to the first neighbor molecules was taken into account. These computations, together with previous experimental evidence that we collected for the system, have been used to analyze the solvent effects on the CTTS transition. In this paper we have established the following: (i) the CTTS electron of free I- ion or K+ I- CIP presents similar features, and it gradually localizes in close proximity of the iodine parent atom when the ammonia density is increased; (ii) for the free I- ion, the short-range solvent interaction contributes to the stabilization of the ground state more than it does for the CTTS excited state, which is evidenced experimentally as a blueshift in the maximum absorption of the CTTS transition when the density is increased; (iii) this effect is less noticeable for the K+ I- ion pair, because in this case a tight solvation structure, formed by four N H3 molecules wedged between the ions, appears at very low density and is very little affected by changes in the density; (iv) the long-range contribution to the solvent stabilization can be neglected for the K+ I- CIP, since the main features of its electronic transition can be explained on the basis of the vicinity of the cation; (v) however, the long-range solvent field contribution is essential for the free I- ion to become an efficient CTTS donor upon photoexcitation, and this establishes a difference in the CTTS behavior of I- in bulk and in clusters. © 2007 American Institute of Physics.

Descripción: A highly sulfated 3-linked β-arabinan (Ab1) with arabinose in the pyranose form was obtained from green seaweed Codium vermilara (Bryopsidales). It comprised major amounts of units sulfated on C-2 and C-4 and constitutes the first polysaccharide of this type isolated in the pure form and fully characterized. Ab1 showed anticoagulant activity by global coagulation tests. Less sulfated arabinans obtained from the same seaweed have less or no activity. Ab1 exerts its activity through direct and indirect (antithrombin- and heparin cofactor II-mediated) inhibition of thrombin. Direct thrombin inhibition was studied in detail. By native PAGE, it was possible to detect formation of a complex between Ab1 and human thrombin (HT). Ab1 binding to HT was measured by fluorescence spectroscopy. CD spectra of the Ab1 complex suggested that ligand binding induced a small conformational change on HT. Ab1-thrombin interactions were studied by molecular dynamic simulations using the persulfated octasaccharide as model compound. Most carbohydrate-protein contacts would occur by interaction of sulfate groups with basic amino acid residues on the surface of the enzyme, more than 60% of them being performed by the exosite 2-composing residues. In these interactions, the sulfate groups on C-2 were shown to interact more intensely with the thrombin structure. In contrast, the disulfated oligosaccharide does not promote major conformational modifications at the catalytic site when complexed to exosite 1. These results show that this novel pyranosic sulfated arabinan Ab1 exerts its anticoagulant activity by a mechanism different from those found previously for other sulfated polysaccharides and glycosaminoglycans. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.