scholarly journals Water density fluctuations relevant to hydrophobic hydration are unaltered by attractions

2015 ◽  
Vol 142 (2) ◽  
pp. 024502 ◽  
Author(s):  
Richard C. Remsing ◽  
Amish J. Patel
Keyword(s):  
Hydrophobic Hydration ◽  
Density Fluctuations ◽  
Water Density

scholarly journals Understanding Hydrophobic Effects: Insights from Water Density Fluctuations

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Nicholas B. Rego ◽  
Amish J. Patel
Keyword(s):  
Materials Science ◽  
Hydrophobic Interactions ◽  
Hydrophobic Hydration ◽  
Surface Hydrophobicity ◽  
Bulk Water ◽  
Density Fluctuations ◽  
Annual Review ◽  
Publication Date ◽  
Water Density ◽  
Hydrophobic Effects

The aversion of hydrophobic solutes for water drives diverse interactions and assemblies across materials science, biology, and beyond. Here, we review the theoretical, computational, and experimental developments that underpin a contemporary understanding of hydrophobic effects. We discuss how an understanding of density fluctuations in bulk water can shed light on the fundamental differences in the hydration of molecular and macroscopic solutes; these differences, in turn, explain why hydrophobic interactions become stronger upon increasing temperature. We also illustrate the sensitive dependence of surface hydrophobicity on the chemical and topographical patterns the surface displays, which makes the use of approximate approaches for estimating hydrophobicity particularly challenging. Importantly, the hydrophobicity of complex surfaces, such as those of proteins, which display nanoscale heterogeneity, can nevertheless be characterized using interfacial water density fluctuations; such a characterization also informs protein regions that mediate their interactions. Finally, we build upon an understanding of hydrophobic hydration and the ability to characterize hydrophobicity to inform the context-dependent thermodynamic forces that drive hydrophobic interactions and the desolvation barriers that impede them. Expected final online publication date for the Annual Review of Condensed Matter Physics, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Pathways to dewetting in hydrophobic confinement

2015 ◽  
Vol 112 (27) ◽  
pp. 8181-8186 ◽  
Author(s):  
Richard C. Remsing ◽  
Erte Xi ◽  
Srivathsan Vembanur ◽  
Sumit Sharma ◽  
Pablo G. Debenedetti ◽  
...  
Keyword(s):  
Density Fluctuations ◽  
Sampling Techniques ◽  
Water Density ◽  
Hydrophobic Surfaces ◽  
Macroscopic Theory ◽  
Advanced Sampling ◽  
Gaussian Statistics ◽  
Kinetics Of ◽  
Peculiar Nature ◽  
Kinetic Barriers

Liquid water can become metastable with respect to its vapor in hydrophobic confinement. The resulting dewetting transitions are often impeded by large kinetic barriers. According to macroscopic theory, such barriers arise from the free energy required to nucleate a critical vapor tube that spans the region between two hydrophobic surfaces—tubes with smaller radii collapse, whereas larger ones grow to dry the entire confined region. Using extensive molecular simulations of water between two nanoscopic hydrophobic surfaces, in conjunction with advanced sampling techniques, here we show that for intersurface separations that thermodynamically favor dewetting, the barrier to dewetting does not correspond to the formation of a (classical) critical vapor tube. Instead, it corresponds to an abrupt transition from an isolated cavity adjacent to one of the confining surfaces to a gap-spanning vapor tube that is already larger than the critical vapor tube anticipated by macroscopic theory. Correspondingly, the barrier to dewetting is also smaller than the classical expectation. We show that the peculiar nature of water density fluctuations adjacent to extended hydrophobic surfaces—namely, the enhanced likelihood of observing low-density fluctuations relative to Gaussian statistics—facilitates this nonclassical behavior. By stabilizing isolated cavities relative to vapor tubes, enhanced water density fluctuations thus stabilize novel pathways, which circumvent the classical barriers and offer diminished resistance to dewetting. Our results thus suggest a key role for fluctuations in speeding up the kinetics of numerous phenomena ranging from Cassie–Wenzel transitions on superhydrophobic surfaces, to hydrophobically driven biomolecular folding and assembly.

scholarly journals Dynamical control by water at a molecular level in protein dimer association and dissociation

2020 ◽  
Vol 117 (5) ◽  
pp. 2302-2308 ◽  
Author(s):  
Puja Banerjee ◽  
Biman Bagchi
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Large Scale ◽  
Hydrophobic Hydration ◽  
Active Role ◽  
Separation Distance ◽  
Density Fluctuations ◽  
Dynamics Simulation ◽  
Free Energy Surface ◽  
Protein Dissociation

Water, often termed as the “lubricant of life,” is expected to play an active role in navigating protein dissociation–association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1–2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance RMM from ∼4 to ∼2 nm, orientation of monomers and hydrophobic hydration in the monomers. A quasistable, solvent-shared, protein monomer pair (SSPMP) forms at around 2 nm during association process which is a local free-energy minimum having ∼50–60% of native contacts. Simulations starting with arrangements sampled from the transition state (TS) of the dimer dissociation reveal that the final outcome depends on relative orientation of the backbone in the “hotspot” region.

scholarly journals Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

2017 ◽  
Vol 114 (51) ◽  
pp. 13345-13350 ◽  
Author(s):  
Erte Xi ◽  
Vasudevan Venkateshwaran ◽  
Lijuan Li ◽  
Nicholas Rego ◽  
Amish J. Patel ◽  
...  
Keyword(s):  
Self Assembly ◽  
Driving Forces ◽  
Hydrophobic Interactions ◽  
Density Fluctuations ◽  
Hydroxyl Groups ◽  
Water Density ◽  
Hydration Shells ◽  
Protein Mutants ◽  
Assembled Monolayers ◽  
Water Adhesion

Hydrophobic interactions drive many important biomolecular self-assembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute–water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.

scholarly journals Pressure effects on collective density fluctuations in water and protein solutions

2017 ◽  
Vol 114 (43) ◽  
pp. 11410-11415 ◽  
Author(s):  
Daniela Russo ◽  
Alessio Laloni ◽  
Alessandra Filabozzi ◽  
Matthias Heyden
Keyword(s):  
High Frequency ◽  
Brillouin Scattering ◽  
Bulk Water ◽  
Density Fluctuations ◽  
Pressure Effects ◽  
Protein Solutions ◽  
Protein Hydration ◽  
Water Density ◽  
Dynamics Simulations ◽  
Induced Changes

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces.

scholarly journals On the role of water density fluctuations in the inhibition of a proton channel

2016 ◽  
Vol 113 (52) ◽  
pp. E8359-E8368 ◽  
Author(s):  
Eleonora Gianti ◽  
Lucie Delemotte ◽  
Michael L. Klein ◽  
Vincenzo Carnevale
Keyword(s):  
Water Distribution ◽  
Binding Free Energy ◽  
Salt Bridge ◽  
Binding Pocket ◽  
Density Fluctuations ◽  
Proton Channel ◽  
General Strategy ◽  
Water Density ◽  
Pore Waters ◽  
Computational Docking

Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel’s most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.

scholarly journals Sparse sampling of water density fluctuations near liquid-vapor coexistence

2018 ◽  
Vol 44 (13-14) ◽  
pp. 1124-1135 ◽  
Author(s):  
Erte Xi ◽  
Sean M. Marks ◽  
Suruchi Fialoke ◽  
Amish J. Patel
Keyword(s):  
Sparse Sampling ◽  
Density Fluctuations ◽  
Water Density ◽  
Liquid Vapor

scholarly journals On Water Density Fluctuations with Helices of Hydrogen Bonds

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Alexander Shimkevich ◽  
Inessa Shimkevich
Keyword(s):  
Hydrogen Bonds ◽  
Liquid Water ◽  
Condensed Matter ◽  
Matter Density ◽  
Density Fluctuations ◽  
Point Of View ◽  
Spectral Series ◽  
Adaptive Model ◽  
Water Density ◽  
The One

An adaptive model is developed here for the liquid water density fluctuations as momentary dense clusters with helices of hydrogen bonds and nondense tetrahedral clusters of ice. This model can be useful for explanation of liquid water structural anomalies including the high quantity of hydrogen bonds with quasitetrahedral orientation in the nonordered liquid water. The topology of such clusters is essentially differed from the one of the crystalline ice. From this and only this point of view, the liquid water can be considered as a two-structural fluid by dynamic forming the two topological kinds of clusters as a consequence of condensed-matter density fluctuations. Another feature of the dense-water-part clusters is helical ordering of protons which can realize coherent vibrations. A spectral series of such vibrations is determined as a function of the number of molecules into the helical cluster.

scholarly journals Sparse Sampling of Water Density Fluctuations in Interfacial Environments

2016 ◽  
Vol 12 (2) ◽  
pp. 706-713 ◽  
Author(s):  
Erte Xi ◽  
Richard C. Remsing ◽  
Amish J. Patel
Keyword(s):  
Sparse Sampling ◽  
Density Fluctuations ◽  
Water Density
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