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A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
As a common view the hydrophobic association between molecular-scale binding partners is supposed to be dominantly driven by entropy. Recent calorimetric experiments and computer simulations heavily challenge this established paradigm by…
We investigate the impact of water fluctuations on the key-lock association kinetics of a hydrophobic ligand (key) binding to a hydrophobic pocket (lock) by means of a minimalistic stochastic model system. It describes the collective…
A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form…
We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…
Using explicit-water molecular dynamics (MD) simulations of a generic pocket-ligand model we investigate how chemical and shape anisotropy of small ligands influences the affinities, kinetic rates and pathways for their association to…
The interactions of a hydrophilic surface with water can significantly influence the characteristics of the liquid water interface. In this manuscript, we explore this influence by studying the molecular structure of liquid water at a…
We study the dynamics of water confined between hydrophobic flat surfaces at low temperature. At different pressures, we observe different behaviors that we understand in terms of the hydrogen bonds dynamics. At high pressure, the formation…
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…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but…
Experimental data bases are typically very large and high dimensional. To learn from them requires to recognize important features (a pattern), often present at scales different to that of the recorded data. Following the experience…
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple…
Rich quantum effects emerge when several quantum systems are indistinguishable from the point of view of the bath they interact with. In particular, delocalised excitations corresponding to coherent superposition of excited states appear…
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…