Inferring Pathways of Oxidative Folding from Prefolding Free Energy Landscapes of Disulfide-Rich Toxins
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Engineering topics
Patel, Lara A.
Publications and source records attributed to Patel, Lara A..
NaCl aggregation in water at elevated temperatures and pressures: Comparison of classical force fields
The properties of water vary dramatically with temperature and density. This can be exploited to control its effectiveness as a solvent. Thus, supercritical water is of keen interest as solvent in many extraction processes. The low solubility of salts in lower density supercritical water has even been suggested as a means of desalination. The high temperatures and pressures required to reach supercritical conditions can present experimental challenges during collection of required physical property and phase equilibria data, especially in salt-containing systems. Molecular simulations have the potential to be a valuable tool for examining the behavior of solvated ions at these high temperatures and pressures. However, the accuracy of classical force fields under these conditions is unclear. We have, therefore, undertaken a parametric study of NaCl in water, comparing several salt and water models at 200 bar–600 bar and 450 K–750 K for a range of salt concentrations. We report a comparison of structural properties including ion aggregation, hydrogen bonding, density, and static dielectric constants. All of the force fields qualitatively reproduce the trends in the liquid phase density. An increase in ion aggregation with decreasing density holds true for all of the force fields. The propensity to aggregate is primarily determined by the salt force field rather than the water force field. This coincides with a decrease in the water static dielectric constant and reduced charge screening. While a decrease in the static dielectric constant with increasing NaCl concentration is consistent across all model combinations, the salt force fields that exhibit more ionic aggregation yield a slightly smaller dielectric decrement.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The RIT1 C-terminus associates with lipid bilayers via charge complementarity
RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. For this study, we used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.
59 BASIC BIOLOGICAL SCIENCES↗
Thermodynamics, dynamics, and structure of supercritical water at extreme conditions
Molecular dynamics (MD) simulations to understand the thermodynamic, dynamic, and structural changes in supercritical water across the Frenkel line and the melting line have been performed. The two-phase thermodynamic model [J. Phys. Chem. B(2010), 114(24), 8191-8198] and the velocity autocorrelation functions are used to locate the Frenkel line and to calculate the thermodynamic and dynamic properties. The Frenkel lines obtained from the two-phase thermodynamic model and the velocity autocorrelation criterion do not agree with each other. Structural characteristics and the translational diffusion dynamics of water suggest that this inconsistency could arise from the two oscillatory modes in water, which are associated with the bending of hydrogen bonds and intermolecular collisions inside the first coordination shell. Finally, the overall results lead us to conclude that the universality of the Frenkel line as a dynamic crossover line from rigid to nonrigid fluids is preserved in water.
74 ATOMIC AND MOLECULAR PHYSICS↗
Electrical conductivity, ion pairing, and ion self-diffusion in aqueous NaCl solutions at elevated temperatures and pressures
We have performed classical molecular dynamics (MD) simulations of aqueous sodium chloride (NaCl) solutions from 298 to 674 K at 200 bars to understand the influence of ion pairing and ion self-diffusion on electrical conductivity in high-temperature/high-pressure salt solutions. Conductivity data obtained from the MD simulation highlight an apparent anomaly, namely, a conductivity maximum as temperature increases along an isobar, which has been also observed in experimental studies. By examining both velocity autocorrelation and cross-correlation terms of the Green-Kubo integral, we quantitatively demonstrate that the conductivity anomaly arises mainly from a competition between the single-ion self-diffusion and the contact ion pair formation. The velocity autocorrelation function in conjunction with structural analysis suggests that diffusive motion of ions is suppressed at high temperatures due to the persistence of an inner hydration shell. Here, the contribution of velocity cross-correlation functions between oppositely charged ions becomes significant at the onset of the conductivity decrease. Structural analysis based on Voronoi tessellation and pair correlation functions indicates that the fraction of contact ion pairs increases as temperature increases. Spatial decomposition of the electrical conductivity also indicates that the formation of contact ion pairs significantly decreases the electrical conductivity compared to Nernst-Einstein conductivity, but the contribution of distant opposite charges cannot be ignored except at the highest temperature due to unscreened long-range interactions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗