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Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

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Elucidating protein-ligand binding kinetics based on returning probability theory.

Kento Kasahara¹, Ren Masayama¹, Kazuya Okita¹

¹Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.

The Journal of Chemical Physics

|October 3, 2023

Summary

This summary is machine-generated.

The returning probability theory analyzes molecular binding using molecular dynamics simulations. This method clarifies that the FK506 binding protein binds methyl methylthiomethyl sulphoxide faster than 4-hydroxy-2-butanone due to thermodynamic stability.

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Area of Science:

Computational chemistry
Biophysics
Molecular dynamics simulations

Background:

The returning probability (RP) theory provides a framework for analyzing diffusion-influenced reactions.
Molecular dynamics (MD) simulations are crucial for studying complex binding processes.
Extending RP theory to atomistic detail requires a suitable reaction coordinate, like host-guest interaction energy.

Purpose of the Study:

To develop a novel methodology combining RP theory and energy representation theory for complex binding phenomena.
To enable systematic analysis of protein-ligand binding thermodynamics and kinetics.
To provide a versatile scheme for calculating equilibrium constants for arbitrary reactive states.

Main Methods:

Integration of returning probability (RP) theory with energy representation theory of solution.
Utilizing molecular dynamics (MD) simulations to compute thermodynamic and kinetic properties.
Applying the methodology to FK506 binding protein (FKBP) with small fragment molecules (BUT and DSS).

Main Results:

The developed method accurately estimates binding rate constants, consistent with long-timescale MD simulations.
The methodology was successfully applied to protein-ligand binding systems.
Decomposition of rate constants revealed thermodynamic contributions to binding kinetics.

Conclusions:

The proposed methodology offers a robust approach for studying complex binding phenomena.
Thermodynamic stability of the reactive state significantly influences binding kinetics.
FK506 binding protein exhibits faster binding with DSS compared to BUT due to enhanced thermodynamic stability.