Project description:Phase separation in aqueous solutions of macromolecules underlies the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phases. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. How do different solutes contribute to the driving forces for phase separation? To answer this question, we introduce a formalism we term energy dominance analysis. This approach rests on analysis of shapes of the dilute phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. The framework is based solely on conditions for phase equilibria in systems with arbitrary numbers of macromolecules and solution components. Its practical application relies on being able to measure dilute phase concentrations of the components of interest. The dominance framework is both theoretically facile and experimentally applicable. We present the formalism that underlies dominance analysis and establish its accuracy and flexibility by deploying it to analyze phase diagrams probed in simulations and in experiments.
Project description:Bacteria rely on ATP binding cassette (ABC) transporters for the import of various nutrients. Bacterial ABC importers utilize an extracellular solute binding protein (SBP) to bind the substrate with high affinity and specificity and deliver it to the membrane permease for transport. The essential metals iron, manganese, and zinc are bound and transported by the cluster A-I SBPs. Crystal structures exist for the metal-bound and metal-free forms of several cluster A-I SBPs that show relatively subtle conformational changes that accompany metal binding. Recent solution studies and molecular dynamics simulations indicate a more complex conformational landscape for the cluster A-I SBPs, suggesting that changes in protein dynamics upon metal binding may have an important role in recognition by the membrane permease and effective transport. Here, we investigate conformational states and dynamics in the cluster A-I SBP AztC fromParacoccus denitrificans, characterizing its unusual intrinsic fluorescence behavior and thermodynamics of zinc binding. These data suggest a dynamic equilibrium of at least two conformational states in the apo form and compensatory changes in the holo that provide for a significant entropic contribution to zinc binding. Correlation with available crystal structures suggests that the formation of a Trp-Phe π-stacking interaction in the metal-bound form may mediate the observed changes in fluorescence. The conformational dynamics identified here for AztC are likely applicable to other cluster A-I SBPs with relevance to their exploitation as potential antibiotic drug targets.
Project description:The origins of the hydrophobic effect are widely thought to lie in structural changes of the water molecules surrounding a nonpolar solute. The spatial distribution functions of the water molecules surrounding benzene and cyclohexane computed previously from molecular dynamics simulations show a high density first hydration shell surrounding both solutes. In addition, benzene showed a strong preference for hydrogen bonding with two water molecules, one to each face of the benzene ring. The position data alone, however, do not describe the majority of orientational changes in the water molecules in the first hydration shells surrounding these solutes. In this paper, we measure the changes in orientation of the water molecules with respect to the solute through spatial orientation functions as well as radial/angular distribution functions. These data show that the water molecules hydrogen bonded to benzene have a strong orientation preference, whereas those around cyclohexane show a weaker tendency. In addition, the water-water interactions within and between the first two hydration shells were measured as a function of distance and "best" hydrogen bonding angle. Water molecules within the first hydration shell have increased hydrogen bonding structure; water molecules interacting across shell 1 and shell 2 have reduced hydrogen bonding structure.
Project description:Bimolecular collision rate constants of a model solute are measured in water at T = 259-303 K, a range encompassing both normal and supercooled water. A stable, spherical nitroxide spin probe, perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl, is studied using electron paramagnetic resonance spectroscopy (EPR), taking advantage of the fact that the rotational correlation time, τ(R), the mean time between successive spin exchanges within a cage, τ(RE), and the long-time-averaged spin exchange rate constants, K(ex), of the same solute molecule may be measured independently. Thus, long- and short-time translational diffusion behavior may be inferred from K(ex) and τ(RE), respectively. In order to measure K(ex), the effects of dipole-dipole interactions (DD) on the EPR spectra must be separated, yielding as a bonus the DD broadening rate constants that are related to the dephasing rate constant due to DD, W(dd). We find that both K(ex) and W(dd) behave hydrodynamically; that is to say they vary monotonically with T/η or η/T, respectively, where η is the shear viscosity, as predicted by the Stokes-Einstein equation. The same is true of the self-diffusion of water. In contrast, τ(RE) does not follow hydrodynamic behavior, varying rather as a linear function of the density reaching a maximum at 276 ± 2 K near where water displays a maximum density.
Project description:Many important biological solutes possess not only polar and hydrogen bonding functionalities, but also weakly-hydrating, or hydrophobic, surfaces. Theories of the hydration of such surfaces predict that their solvent interactions will change from a wetting type interaction to a dewetting regime as a function of the solute size, with a gradual transition in behavior taking place around characteristic lengths of ∼1 nm. Aggregations of non-polar species over this size range will undergo a transition from being dominated by entropy to being dominated by enthalpy. These transitions can be understood in part in terms of the geometries required of the solvating water molecules. We report here a series of simulations in aqueous solution of organic molecules with planar faces of increasing size, ranging from cyclopropane to circumcircumcoronene, in order to explore the transition in behavior for such solutes as their size increases. For this series, the dewetting transition occurred gradually, converging asymptotically to a limiting separation value for first layer water molecules of around 3.3 Å, while the transition in hydrogen bonding orientational structure occurred between cyclopropane and cyclopentadene. Water immediately adjacent to the largest planar hydrophobic surfaces oriented in ways that resembled on average the structural organization of the basal planes of ice.
Project description:Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions-the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems.
Project description:Hydrophobicity is a phenomenon of great importance in biology, chemistry, and biochemistry. It is defined as the interaction between nonpolar molecules or groups in water and their low solubility. Hydrophobic interactions affect many processes in water, for example, complexation, surfactant aggregation, and coagulation. These interactions play a pivotal role in the formation and stability of proteins or biological membranes. In the present study, we assessed the effect of ionic strength, solute size, and shape on hydrophobic interactions between pairs of nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene, ethane, propane, butane, hexane, octane, and decane were simulated by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P and TIP4PEW water models were used. Potential of mean force (PMF) plots of these dimers were determined at four values of ionic strength, 0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact on hydrophobic interactions. The characteristic shape of PMFs with three extrema (contact minimum, solvent-separated minimum, and desolvation maximum) was observed for most of the compounds for hydrophobic interactions. Ionic strength affected hydrophobic interactions. We observed a tendency to deepen contact minima with an increase in ionic strength value in the case of spherical and spheroidal molecules. Additionally, two-dimensional distribution functions describing water density and average number of hydrogen bonds between water molecules were calculated in both water models for adamantane and hexane. It was observed that the density of water did not significantly change with the increase in ionic strength, but the average number of hydrogen bonds changed. The latter tendency strongly depends on the water model used for simulations.
Project description:Social interactions in classic cognitive games like the ultimatum game or the prisoner's dilemma typically lead to Nash equilibria when multiple competitive decision makers with perfect knowledge select optimal strategies. However, in evolutionary game theory it has been shown that Nash equilibria can also arise as attractors in dynamical systems that can describe, for example, the population dynamics of microorganisms. Similar to such evolutionary dynamics, we find that Nash equilibria arise naturally in motor interactions in which players vie for control and try to minimize effort. When confronted with sensorimotor interaction tasks that correspond to the classical prisoner's dilemma and the rope-pulling game, two-player motor interactions led predominantly to Nash solutions. In contrast, when a single player took both roles, playing the sensorimotor game bimanually, cooperative solutions were found. Our methodology opens up a new avenue for the study of human motor interactions within a game theoretic framework, suggesting that the coupling of motor systems can lead to game theoretic solutions.
Project description:Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affects hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size from subnanometer to a few nanometers. The interfaces are self-assembled monolayers with a range of chemistries, from hydrophilic to hydrophobic. We show that the driving force for assembly in the vicinity of a hydrophobic surface is weaker than that in bulk water and decreases with increasing temperature, in contrast to that in the bulk. We explain these distinct features in terms of an interplay between interfacial fluctuations and excluded volume effects--the physics encoded in Lum-Chandler-Weeks theory [Lum K, Chandler D, Weeks JD (1999) J Phys Chem B 103:4570-4577]. Our results suggest a catalytic role for hydrophobic interfaces in the unfolding of proteins, for example, in the interior of chaperonins and in amyloid formation.
Project description:Open Reading Frame 9b (Orf9b), an accessory protein of SARS-CoV and -2, is involved in innate immune suppression through its binding to the mitochondrial receptor Translocase of Outer Membrane 70 (Tom70). Previous structural studies of Orf9b in isolation revealed a β-sheet-rich homodimer, however, structures of Orf9b in complex with Tom70 revealed a monomeric helical fold. Here, we developed a biophysical model that quantifies how Orf9b switches between these conformations and binds to Tom70, a requirement for suppressing the type 1 interferon response. We used this model to characterize the effect of lipid binding and mutations in variants of concern to the Orf9b:Tom70 equilibrium. We found that the binding of a lipid to the Orf9b homodimer biases the Orf9b monomer:dimer equilibrium towards the dimer by reducing the dimer dissociation rate ~100-fold. We also found that mutations in variants of concern can alter different microscopic rate constants without significantly affecting binding to Tom70. Together our results highlight how perturbations to different steps in these coupled equilibria can affect the apparent affinity of Orf9b to Tom70, with potential downstream implications for interferon signaling in coronavirus infection.