Dataset Information

How hydrophobic drying forces impact the kinetics of molecular recognition.

ABSTRACT: 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 states with lifetimes in each state that are long enough for the extraction of a separable potential of mean force and wet-to-dry transitions. We present a diffusive surface hopping model that is represented by a 2D Markovian master equation. One dimension is the standard reaction coordinate, the ligand-pocket separation, and the other is the solvent state in the region between ligand and binding pocket which specifies whether it is wet or dry. In our model, the ligand diffuses on a dynamic free-energy surface which undergoes kinetic transitions between the wet and dry states. The model yields good agreement with results from explicit solvent molecular dynamics simulation and an improved description of the kinetics of hydrophobic assembly. Furthermore, it is consistent with a "non-Markovian Brownian theory" for the ligand-pocket separation coordinate alone.

SUBMITTER: Mondal J

PROVIDER: S-EPMC3746852 | biostudies-other | 2013 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

How hydrophobic drying forces impact the kinetics of molecular recognition.

Mondal Jagannath J Morrone Joseph A JA Berne B J BJ

Proceedings of the National Academy of Sciences of the United States of America 20130730 33

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 states with lifetimes in each state that are long enough for the extraction of a separable potential of mean force and wet-to-dry transitions. We present a diffusive surface hopping model that is represented by a 2D Markovian master equation. One dimension ...[more]

PMID: 23901110

Similar Datasets

Project description:A new sanitation technology has been proposed in which a laminated hydrophobic membrane contains and enhances drying of fecal sludge in a toilet, with particular focus on application to urban regions of low-income countries. The proposed technology uses a laminated hydrophobic membrane liner as an integral component of container-based sanitation systems. The focus of this study is to quantitatively evaluate the laminate's clogging after repeated use, which will affect replacement interval and might limit the laminate's application in container-based toilets. The membrane of the laminated hydrophobic membrane used in this process is hydrophobic and only allows vapor transport. Drying of water vapor using the laminated hydrophobic membrane occurs due to moderate temperature or humidity gradients, while other constituents such as aqueous dissolved solutes of fecal sludge are retained. Controlled laboratory experiments evaluated repeated use of a laminated hydrophobic membrane for fecal sludge drying, with mild brushing/rinsing of the laminate between each application. Drying occurred at a constant rate as long as the fecal sludge moisture content exceeded 11.6 (g/g), below which water activity <1. Over five drying cycles, at a significance level of ??=?0.05 the dimensionless drying rate in the constant-rate period was not reduced. While scanning electron microscopy and energy dispersive X-ray analyses of used laminated hydrophobic membrane showed deposition of fecal sludge on the inner fabric of the laminate, particulate accumulation was never sufficient to alter the fecal sludge drying rate. Experiments with only water indicated that the fecal sludge increased the effective diffusion length through the laminate by 10-30%. These data demonstrate that clogging of the laminated hydrophobic membrane is minor over five cycles of fecal sludge drying with mild rinsing between cycles, indicating that use of the laminate may be feasible in many field applications.

Dataset Information

How hydrophobic drying forces impact the kinetics of molecular recognition.

Publications

How hydrophobic drying forces impact the kinetics of molecular recognition.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets