Nonlinear Impact of Electrolyte Solutions on Protein Dynamics.

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 of decreasing fresh-water resources, have excess acidic amino acids. It has been suggested that conformational fluctuations - critical for protein function - decrease in the presence of a stronger hydrophobic effect, and that an acidic proteome would counteract this decrease. However, our understanding of the salt- and acidic amino acid dependency of enzymatic activity is limited. Here, using solution NMR relaxation and molecular dynamics simulations for in total 14 proteins, we show that salt concentration has a limited and moreover non-monotonic impact on protein dynamics. The results speak against the conformational-fluctuations model, instead indicating that maintaining protein dynamics to ensure protein function is not an evolutionary driving force behind the acidic proteome of halophilic proteins.

Cooperativity and ion pairing in magnesium sulfate aqueous solutions from the dilute regime to the solubility limit.

We report a terahertz absorption spectroscopy study of MgSO4 aqueous solutions in the concentration range 0.1 mol dm-3 to 2.4 mol dm-3. Accompanying classical MD simulations were carried out that use a polarizable force field parameterized to reproduce the solution thermodynamics. Contrary to prior reports, we find no evidence of contact ion pairs, even close to the solubility limit. Only solvent separated and different types of solvent shared ion pairs are found, being abundant even at the lowest concentration investigated here. The structure of the solution is concentration-dependent: the number of both types of ion pairs grows with increasing salt concentration. The combined theoretical and experimental analysis of the spectra in the frequency region 50-640 cm-1 suggests that the dynamics of water directly between two ions in solvent shared configuration is very strongly perturbed, via a cooperative, supra-additive, effect arising from the two ions. At high concentrations, the results support a scenario, where the perturbations in the water dynamics extend up to the third hydration layer via a cooperative, but additive, effect involving multiple ions. The SO42- and its hydration shell are much more strongly perturbed by the presence of the counterions than the first hydration shell of Mg2+. It is further shown that our simulations and observations are in agreement with thermodynamic properties of aqueous MgSO4 solutions derived by other methods.

Hydrophobic but Water-Friendly: Favorable Water-Perfluoromethyl Interactions Promote Hydration Shell Defects.

Although perfluorination is known to enhance hydrophobicity and change protein activity, its influence on hydration-shell structure and thermodynamics remains an open question. Here we address that question by combining experimental Raman multivariate curve resolution spectroscopy with theoretical classical simulations and quantum mechanical calculations. Perfluorination of the terminal methyl group of ethanol is found to enhance the disruption of its hydration-shell hydrogen bond network. Our results reveal that this disruption is not due to the associated volume change but rather to the electrostatic stabilization of the water dangling OH···F interaction. Thus, the hydration shell structure of fluorinated methyl groups results from a delicate balance of solute-water interactions that is intrinsically different from that associated with a methyl group.

Temperature-sensitive colloidal phase behavior induced by critical Casimir forces.

We report Monte Carlo simulations of phase behavior of colloidal suspensions with near-critical binary solvents using effective pair potentials from experiments. At off-critical solvent composition, the calculated phase diagram agrees well with measurements of the experimental system, indicating that many-body effects are limited. Close to the critical composition, however, agreement between experiment and simulation becomes poorer, signaling the increased importance of many-body effects. Both at and off the critical solvent concentration, the colloidal phase diagram is qualitatively similar to those of molecular systems and obeys the principle of corresponding states with one striking difference: it occurs in a narrow temperature interval of <1 °C below the solvent phase separation temperature.

Investigating the specificity of peptide adsorption on gold using molecular dynamics simulations.

We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold surfaces modeled with dispersive interactions. We examine the dependence of adsorption on both identity of the amino acids and mobility of the peptides. Within the limitations of the approach, results indicate that when the peptides are solvated, adsorption requires both configurational changes and local flexibility of individual amino acids. This is achieved when peptides consist mostly of random coils or when their secondary structural motifs (helices, sheets) are short and connected by flexible hinges. In the absence of solvent, only affinity for the surface is required: mobility is not important. In combination, these results suggest the barrier to adsorption presented by displacement of water molecules requires conformational sampling enabled through mobility.

Influence of glycosidic linkage neighbors on disaccharide conformation in vacuum.

Correct description of the free energy of conformation change of disaccharides is important in understanding a variety of biochemical processes and, ultimately, in the manufacture of better food and paper products. In this study, we determine the relative free energy of a series of 12 disaccharides in vacuum using replica exchange molecular dynamics (repMD) simulations. The chosen sugars and the novel application of this method allow the exploration of the role of glycosidic linkage neighbors in conformer stabilization. In line with expectations, we find that hydrogen bonding (and therefore energetically preferred conformations) are determined both by the nature of the glycosidic linkage (i.e., 1 --> 2, 1 --> 3, or 1 --> 4), the C1 epimer of the of the nonreducing monosaccharide, and by the configuration of carbon atoms once removed from the glycosidic linkage. Contrary to suggestions by prior authors for repMD more generally, we also demonstrate that repMD provides enhanced sampling, relative to conventional MD simulations of equivalent length, for disaccharides in vacuum at 300 K. (Zuckerman, D. M.; Lyman, E. J. Chem. Theory Comput. 2006, 2, 1200-1202.)

Disaccharide topology induces slowdown in local water dynamics.

Molecular level insight into water structure and structural dynamics near proteins, lipids, and nucleic acids is critical to the quantitative understanding of many biophysical processes. Unfortunately, understanding hydration and hydration dynamics around such large molecules is challenging because of the necessity of deconvoluting the effects of topography and chemical heterogeneity. Here we study, via classical all-atom simulation, the water structure and structural dynamics around two biologically relevant solutes large enough to have significant chemical and topological heterogeneity but small enough to be computationally tractable: the disaccharides kojibiose and trehalose. We find both molecules to be strongly amphiphilic (as quantified from normalized local density fluctuations) and to induce nonuniform local slowdown in water translational and rotational motions. Detailed analysis of the rotational slowdown shows that, while the rotational mechanism is similar to that previously identified in other aqueous systems by Laage, Hynes, and coworkers, two novel characteristics are observed: broadening of the transition state during hydrogen bond exchange (water rotation) and a subpopulation of water for which rotation is slowed because of hindered access of the new accepting water molecule to the transition state. Both characteristics are expected to be generic features of water rotation around larger biomolecules and, taken together, emphasize the difficulty in transferring insight into water rotation around small molecules to much larger amphiphilic solutes.