We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold surfaces modeled with dispersive interactions. examine the dependence both identity amino acids mobility peptides. Within limitations approach, results indicate that when are solvated, requires configurational changes local flexibility individual acids. This is achieved consist mostly random coils or their secondary structural motifs (helices, sheets) short connected...

We report the real-time measurement of ultrafast reorientational motion water molecules at water-air interface, using femtosecond time- and polarization-resolved vibrational sum-frequency spectroscopy. Vibrational excitation dangling OH bonds along a specific polarization axis induces transient anisotropy that decays due to reorientation vibrationally excited groups. The interfacial is shown occur on subpicosecond time scales, several times faster than in bulk, which can be attributed lower...

Shearing of short, dimeric coiled coils proceeds<italic>via</italic>three competing timescale-dependent mechanisms: progressive helix uncoiling, uncoiling-assisted sliding and dissociation.

We investigate the role of dynamics on adsorption peptides to gold surfaces using all-atom molecular simulations in explicit solvent. choose six homopolypeptides [Ala10, Ser10, Thr10, Arg10, Lys10, and Gln10], for which experimental surface coverages are not correlated with amino acid level affinities gold, idea that dynamic properties may also play a role. To assess we determine both conformational movement flexibility peptide within given conformation. Low indicates stability conformation...

A hybrid approach using <italic>ab initio</italic> simulations and experimental data yielding reliable, internally consistent parameters for ion–water anion–cation interactions.

We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation reorientation subpopulations OH groups belonging molecules at air/water interface 300 K: those that donate a hydrogen bond (called "bonded") do not "free"). Free interfacial reorient in distinct regimes: fast regime from 0 1 ps slow thereafter. Qualitatively similar behavior was reported by others for free near extended hydrophobic surfaces. In contrast, net...

We report Monte Carlo simulations of phase behavior colloidal suspensions with near-critical binary solvents using effective pair potentials from experiments. At off-critical solvent composition, the calculated diagram agrees well measurements experimental system, indicating that many-body effects are limited. Close to critical however, agreement between experiment and simulation becomes poorer, signaling increased importance effects. Both at off concentration, is qualitatively similar those...

Molecular level insight into water structure and structural dynamics near proteins, lipids, nucleic acids is critical to the quantitative understanding of many biophysical processes. Unfortunately, hydration around such large molecules challenging because necessity deconvoluting effects topography chemical heterogeneity. Here we study, via classical all-atom simulation, two biologically relevant solutes enough have significant topological heterogeneity but small be computationally tractable:...

The question "Can ions exert supra-additive effects on water dynamics?" has had several opposing answers from both simulation and experiment. We address this ongoing controversy by investigating reorientation in aqueous solutions of two salts with large (magnesium sulfate) small (cesium chloride) dynamics using molecular simulations classical, polarizable models. salt models are reparameterized to reproduce properties dilute concentrated solutions. demonstrate that rotation MgSO4 is...

The hydration free energy of fluorinated amino acids is calculated with molecular simulations and explained an analytical model.

We report coarse-grained, implicit-solvent simulations of aqueous solutions bile salts. The parameters in our model were optimized to reproduce some the experimentally known behavior dihydroxy salts at "physiological" temperature and counterion concentration. find that micelle formation trihydroxy is only weakly cooperative sense there barely a free energy barrier stabilizes these micelles against disassembly. Bile molecules are found pack many different orientations pure micelles. Both...

Although perfluorination is known to enhance hydrophobicity and change protein activity, its influence on hydration-shell structure thermodynamics remains an open question. Here we address that question by combining experimental Raman multivariate curve resolution spectroscopy with theoretical classical simulations quantum mechanical calculations. Perfluorination of the terminal methyl group ethanol found disruption hydrogen bond network. Our results reveal this not due associated volume but...

We investigate the reorientation dynamics of water at 300 K in solutions magnesium sulfate and cesium chloride from classical atomistic molecular simulations using "simple model with four sites negative Drude polarizability" (SWM4-NDP) accompanying ion models; for SO4(2-), we derive SWM4-NDP-compatible parameters. Results indicate that pairs ions have a cooperative effect on rotation but do not support based experiment whereby cooperativity increases number very slow molecules well beyond...

A combined THz and simulation study on MgSO₄ find no contact ion pairs in highly concentrated solutions.

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Biomolecular processes involve hydrated ions, and thus molecular simulations of such require accurate force-field parameters for these ions. In the best force-fields, both ion-water anion-cation interactions are explicitly parametrized. First, ion Lennard-Jones optimized to reproduce, example, single solvation free energies; then ion-pair adjusted match experimental activity or derivatives. Here, we apply this approach derive concentrated NaCl, KCl, MgCl2, CaCl2 salt solutions, be used with...

We examine the mechanism of formation micelles dihydroxy bile salts using a coarse-grained, implicit solvent model and Langevin dynamics simulations. find that salt primarily form via addition removal monomers, similarly to surfactants with typical head–tail molecular structures, not two-stage – involving oligomers their subsequent aggregation larger originally proposed for salts. The free energy barrier single monomers from is ≈2kBT, much less than what has been observed surfactants. Such...

Proteins of halophilic organisms, which accumulate molar concentrations KCl in their cytoplasm, have a much higher content acidic amino acids than proteins mesophilic organisms. It has been proposed that this excess is necessary to maintain hydrated an environment with low water activity, either via direct interactions between and the carboxylate groups or cooperative cations. Our simulation study five counterparts does not support possibility. The simulations use AMBER ff14SB force field...

The cytoplasmic proteins of some halophilic organisms remain stable and functional at multimolar concentrations KCl, i.e., under conditions that most mesophilic cannot withstand. Their stability arises from their unusual amino acid composition. dramatic difference between is the former are rich in acidic acids. It has been proposed one evolutionary driving forces for this occurrence synergistic interactions multiple acids surface protein, potassium cations solution, water. We investigate...

Abstract Halophilic organisms have adapted to multi‐molar salt concentrations, their cytoplasmic proteins functioning despite stronger attraction between hydrophobic groups. These proteins, of interest in biotechnology because decreasing fresh‐water resources, excess acidic amino acids. It has been suggested that conformational fluctuations – critical for protein function decrease the presence a effect, and an proteome would counteract this decrease. However, our understanding salt‐ acid...

Correct description of the free energy conformation change disaccharides is important in understanding a variety biochemical processes and, ultimately, manufacture better food and paper products. In this study, we determine relative series 12 vacuum using replica exchange molecular dynamics (repMD) simulations. The chosen sugars novel application method allow exploration role glycosidic linkage neighbors conformer stabilization. line with expectations, find that hydrogen bonding (and...

Air/water interfaces are both ubiquitous in the environment and technology a useful model for hydrophobic solvation more generally. Previous experimental computational studies have highlighted that molecular level markers of such an extended surface broken hydrogen bonds and, as result, OH groups not bond donors: free OH. Understanding time-averaged structure structural dynamics these thus plays critical role developing quantitative, understanding solvation. Here we show, by combining...

Trimeric coiled coils under shear are stronger and tougher than dimers; trimers deform by helix unfolding whereas dimers sliding.

SAHs under tension unfold residue-by-residue even at near-equilibrium pull speeds; this mechanical response is reproduced by the Sticky Chain Model, which helps to quantify average 1-D free energy landscape of amino acids.