PubMed Health⌕ Search

Biomedical subjects

Thomas M Truskett

Publications and source records attributed to Thomas M Truskett.

18 recordsLinked to original sources
PubMed2007

Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water.

We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer-water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, DeltaG = gamma(T)DeltaA, where the surface tension, gamma, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000) Proc Natl Acad Sci USA 97:] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer-water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor-liquid interface.

Hydrophobic and Hydrophilic Interactions↗
PubMed2006

Excess-entropy-based anomalies for a waterlike fluid.

Many thermodynamic and dynamic properties of water display unusual behavior at low enough temperatures. In a recent study, Yan et al. [Phys. Rev. Lett. 95, 130604 (2005)] identified a spherically symmetric two-scale potential that displays many of the same anomalous properties as water. More specifically, for select parametrizations of the potential, one finds that the regions where isothermal compression anomalously (i) decreases the fluid's structural order, (ii) increases its translational self-diffusivity, and (iii) increases its entropy form nested domes in the temperature-density plane. These property relationships are similar to those found for more realistic models of water. In this work, the authors provide evidence that suggests that the anomalous regions specified above can all be linked through knowledge of the excess entropy. Specifically, the authors show how entropy scaling relationships developed by Rosenfeld [Phys. Rev. A 15, 2545 (1977)] can be used to describe the region of diffusivity anomalies and to predict the state conditions for which anomalous viscosity and thermal conductivity behavior might be found.

Journal Article↗
PubMed2006

Analytical model for studying how environmental factors influence protein conformational stability in solution.

We introduce an analytical modeling strategy for probing the conformational stability of globular proteins in aqueous solution. In this approach, the intrinsic (i.e., infinite dilution) thermodynamic stability and coarse structural properties of the proteins, as well as the effective protein-protein interactions, derive from a heteropolymer collapse theory that incorporates predicted temperature- and pressure-dependent hydrophobic interactions. Protein concentration effects are estimated by integrating this information into a molecular thermodynamic model, which is an ad hoc generalization of the exact equilibrium theory of a one-dimensional binary mixture of square-well particles that interconvert through an isomerization (i.e., folding) reaction. The end result is an analytical multiscale modeling approach which, although still schematic, can predict that folded proteins exhibit a closed-loop region of stability in the pressure-temperature plane and that protein concentration has a nonmonotonic effect on protein stability, results consistent with qualitative trends observed in both experiments of protein solutions and simulations of coarse-grained protein models.

Computer Simulation↗
PubMed2006

Using available volume to predict fluid diffusivity in random media.

We propose a simple equation for predicting self-diffusivity of fluids embedded in random matrices of identical, but dynamically frozen, particles (i.e., quenched-annealed systems). The only nontrivial input is the volume available to mobile particles, which also can be predicted for two common matrix types that reflect equilibrium and nonequilibrium fluid structures. The proposed equation can account for the large differences in mobility exhibited by quenched-annealed systems with indistinguishable static pair correlations, illustrating the key role that available volume plays in transport.

Journal Article↗
PubMed2006

Quantitative link between single-particle dynamics and static structure of supercooled liquids.

We present evidence via molecular simulation that the supercooled fluid states of SPC/E water as well as the "repulsive" and "attractive" supercooled fluid states of a recently introduced model for colloids with short-ranged attractions are characterized by the same functional relationship between self-diffusivity and the pair correlation function. We discuss how this simple relationship connects to an earlier finding that the temperature dependency of a supercooled fluid's single-particle dynamics tracks that of its excess entropy (relative to ideal gas). The generality of this observed structure-property relationship is supported by its ability to successfully describe the nontrivial behaviors of these very different types of model systems.

Chemistry, Physical↗
PubMed2006

Transport in amorphous solid water films: implications for self-diffusivity.

Thermal desorption spectroscopy is employed to examine transport mechanisms in structured, nanoscale films consisting of labeled amorphous solid water (ASW, H(2)(18)O, H(2)(16)O) and organic spacer layers (CCl(4), CHCl(3)) prior to ASW crystallization (T approximately 150-160 K). Self-transport is studied as a function of both the ASW layer and the organic spacer layer film thickness, and the effectiveness of these spacer layers as a bulk diffusion "barrier" is also investigated. Isothermal desorption measurements of structured films are combined with gas uptake measurements (CClF(2)H) to investigate water self-transport and changes in ASW film morphology during crystallization and annealing. CCl(4) desorption is employed as a means to investigate the effects of ASW film thickness and heating schedule on vapor-phase transport. Combined, these results demonstrate that the interlayer mixing observed near T approximately 150-160 K is inconsistent with a mechanism involving diffusion through a dense phase; rather, we propose that intermixing occurs via vapor-phase transport through an interconnected network of cracks/fractures created within the ASW film during crystallization. Consequently, the self-diffusivity of ASW prior to crystallization (T approximately 150-160 K) is significantly smaller than that expected for a "fragile" liquid, indicating that water undergoes either a glass transition or a fragile-to-strong transition at a temperature above 160 K.

Journal Article↗
PubMed2006

Heteropolymer collapse theory for protein folding in the pressure-temperature plane.

We revisit a heteropolymer collapse theory originally introduced to explore how the balance between hydrophobic interactions and configurational entropy determines the thermal stability of globular proteins at ambient pressure. We generalize the theory by introducing a basic statistical mechanical treatment for how pressure impacts the solvent-mediated interactions between hydrophobic amino-acid residues. In particular, we estimate the strength of the hydrophobic interactions using a molecular thermodynamic model for the interfacial free energy between liquid water and a curved hydrophobic solute. The model, which also reproduces many of the distinctive thermodynamic properties of aqueous solutions in bulk and interfacial environments, predicts that the water-solute interfacial free energy is significantly reduced by the application of high hydrostatic pressures. This allows water to penetrate into folded heteropolymers at high pressure and break apart their hydrophobic cores, a scenario suggested earlier by information theory calculations. As a result, folded heteropolymers are predicted to display the kind of closed region of stability in the pressure-temperature plane exhibited by native proteins. We compare predictions of the collapse theory with experimental data for several proteins.

Amino Acids↗
PubMed2006

Evidence that amorphous water below 160 K is not a fragile liquid.

We have examined transport mechanisms in amorphous solid water (ASW) by studying thermal desorption of layered nanoscale films of CCl4 and labeled ASW. The interlayer mixing observed near T approximately 150-160 K is inconsistent with a mechanism involving diffusion through a dense phase. Instead, intermixing occurs via vapor-phase transport through an interconnected porous network created within the film during crystallization. As a consequence, the self-diffusivity of ASW is significantly smaller than previously thought, indicating that water undergoes either a glass transition or a fragile-to-strong transition at a temperature above 160 K.

Letter↗
PubMed2006

Model for the free-volume distributions of equilibrium fluids.

We introduce and test via molecular simulation a simple model for predicting the manner in which interparticle interactions and thermodynamic conditions impact the single-particle free-volume distributions of equilibrium fluids. The model suggests a scaling relationship for the density-dependent behavior of the hard-sphere system. It also predicts how the second virial coefficients of fluids with short-range attractions affect their free-volume distributions.

Journal Article↗
PubMed2006

Thermodynamics predicts how confinement modifies the dynamics of the equilibrium hard-sphere fluid.

We study how confining the equilibrium hard-sphere fluid to restrictive one- and two-dimensional channels with smooth interacting walls modifies its structure, dynamics, and entropy using molecular dynamics and transition-matrix Monte Carlo simulations. Although confinement strongly affects local structuring, the relationships between self-diffusivity, excess entropy, and average fluid density are, to an excellent approximation, independent of channel width or particle-wall interactions. Thus, thermodynamics can be used to predict how confinement impacts dynamics.

Biological Transport↗
PubMed2006

Free volumes and the anomalous self-diffusivity of attractive colloids.

Free volume theories for the dynamics of dense fluids commonly assume (i) that diffusivity increases with average free volume per particle and (ii) that the size distribution of free volumes can be approximated by that of an equivalent hard-sphere reference system. We use molecular simulations to demonstrate that these assumptions break down when one considers concentrated suspensions of particles with short-range attractions. In these systems, self-diffusivity shows nonmonotonic dependencies on both average free volume and the strength of the interparticle attraction. Moreover, when interparticle attractions are strong, the shape of the free volume distribution is qualitatively different than that of the corresponding hard-sphere reference fluid. We propose a conceptual revision to the traditional free volume perspective that takes into account both the size distribution and the persistence time of the free volumes, and we demonstrate that it can qualitatively capture the disparate behaviors of a model fluid with short-range attractions and its hard-sphere reference fluid.

Algorithms↗
PubMed2005

Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior.

We use highly efficient transition-matrix Monte Carlo simulations to determine equilibrium unfolding curves and fluid phase boundaries for solutions of coarse-grained globular proteins. The model we analyze derives the intrinsic stability of the native state and protein-protein interactions from basic information about protein sequence using heteropolymer collapse theory. It predicts that solutions of low hydrophobicity proteins generally exhibit a single liquid phase near their midpoint temperatures for unfolding, while solutions of proteins with high sequence hydrophobicity display the type of temperature-inverted, liquid-liquid transition associated with aggregation processes of proteins and other amphiphilic molecules. The phase transition occurring in solutions of the most hydrophobic protein we study extends below the unfolding curve, creating an immiscibility gap between a dilute, mostly native phase and a concentrated, mostly denatured phase. The results are qualitatively consistent with the solution behavior of hemoglobin (HbA) and its sickle variant (HbS), and they suggest that a liquid-liquid transition resulting in significant protein denaturation should generally be expected on the phase diagram of high-hydrophobicity protein solutions. The concentration fluctuations associated with this transition could be a driving force for the nonnative aggregation that can occur below the midpoint temperature.

Computer Simulation↗
PubMed2005

Coarse-grained strategy for modeling protein stability in concentrated solutions.

We present a coarse-grained approach for modeling the thermodynamic stability of single-domain globular proteins in concentrated aqueous solutions. Our treatment derives effective protein-protein interactions from basic structural and energetic characteristics of the native and denatured states. These characteristics, along with the intrinsic (i.e., infinite dilution) thermodynamics of folding, are calculated from elementary sequence information using a heteropolymer collapse theory. We integrate this information into Reactive Canonical Monte Carlo simulations to investigate the connections between protein sequence hydrophobicity, protein-protein interactions, protein concentration, and the thermodynamic stability of the native state. The model predicts that sequence hydrophobicity can affect how protein concentration impacts native-state stability in solution. In particular, low hydrophobicity proteins are primarily stabilized by increases in protein concentration, whereas high hydrophobicity proteins exhibit richer nonmonotonic behavior. These trends appear qualitatively consistent with the available experimental data. Although factors such as pH, salt concentration, and protein charge are also important for protein stability, our analysis suggests that some of the nontrivial experimental trends may be driven by a competition between destabilizing hydrophobic protein-protein attractions and entropic crowding effects.

Binding Sites↗
PubMed2005

Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover.

Small and large hydrophobic solutes exhibit remarkably different hydration thermodynamics. Small solutes are accommodated in water with minor perturbations to water structure, and their hydration is captured accurately by theories that describe density fluctuations in pure water. In contrast, hydration of large solutes is accompanied by dewetting of their surfaces and requires a macroscopic thermodynamic description. A unified theoretical description of these lengthscale dependencies was presented by Lum, Chandler, and Weeks [(1999) J. Phys. Chem. B 103, 4570-4577]. Here, we use molecular simulations to study lengthscale-dependent hydrophobic hydration under various thermodynamic conditions. We show that the hydration of small and large solutes displays disparate dependencies on thermodynamic variables, including pressure, temperature, and additive concentration. Understanding these dependencies allows manipulation of the small-to-large crossover lengthscale, which is nanoscopic under ambient conditions. Specifically, applying hydrostatic tension or adding ethanol decreases the crossover length to molecular sizes, making it accessible to atomistic simulations. With detailed temperature-dependent studies, we further demonstrate that hydration thermodynamics changes gradually from entropic to enthalpic near the crossover. The nanoscopic lengthscale of the crossover and its sensitivity to thermodynamic variables imply that quantitative modeling of biomolecular self-assembly in aqueous solutions requires elements of both molecular and macroscopic hydration physics. We also show that the small-to-large crossover is directly related to the Egelstaff-Widom lengthscale, the product of surface tension and isothermal compressibility, which is another fundamental lengthscale in liquids.

Biophysical Phenomena↗
PubMed2005

Modeling water, the hydrophobic effect, and ion solvation.

Water plays a central role in the structures and properties of biomolecules--proteins, nucleic acids, and membranes--and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global properties-water's thermodynamics, phase diagram, and solvation properties, for example-and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water.

Biophysics↗
PubMed2003

A simple analytical model of water.

Water is an unusual liquid. It expands upon freezing, has minima in its volume, heat capacity, and isothermal compressibility with temperature, and shows signs of a first-order phase transition when supercooled. These anomalies disappear at high pressures. We review a recent analytical theory that predicts water's thermal properties and the main features of its phase diagram, including multiple crystalline phases and a fluid-fluid transition in the supercooled liquid. It also predicts a fragile-to-strong crossover in supercooled water's temperature-dependent relaxation processes. The theory is based on a simplified model for how triplets of waters interact via hydrogen bonds, steric repulsions, and dispersion attractions. It is designed to give simple insights into the microscopic origins of water's properties.

Hydrogen Bonding↗