# Solvent fluctuations induce non-Markovian kinetics in hydrophobic pocket-ligand binding

Source: [Solvent fluctuations induce non-Markovian kinetics in hydrophobic pocket-ligand binding](<https://www.sota2.com/research/paper/68fa32e71e209131ce88bc7f>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-27T03:38:49.449Z

Authors: R. Gregor Wei{\\ss}, Piotr Setny, Joachim Dzubiella

Published: 2016-02-04T09:59:07.000Z

## Abstract

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 hydration behavior of the pocket by bimodal fluctuations of a water-pocket interface that dynamically couples to the diffusive motion of the approaching ligand via the hydrophobic interaction. This leads to a set of overdamped Langevin equations in 2D-coordinate-space, that is Markovian in each dimension. Numerical simulations demonstrate locally increased friction of the ligand, decelerated binding kinetics, and local non-Markovian (memory) effects in the ligand's reaction coordinate as found previously in explicit-water molecular dynamics studies of model hydrophobic pocket-ligand binding \[1,2\]. Our minimalistic model elucidates the origin of effectively enhanced friction in the process that can be traced back to long-time decays in the force-autocorrelation function induced by the effective, spatially fluctuating pocket-ligand interaction. Furthermore, we construct a generalized 1D-Langevin description including a spatially local memory function that enables further interpretation and a semi-analytical quantification of the results of the coupled 2D-system.

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1602.01611>)

[PDF](<https://arxiv.org/pdf/1602.01611.pdf>)