Ligand diffusion on protein surface observed in molecular dynamics simulation

Dmitry Nerukh; Noriaki Okimoto; Atsushi Suenaga; Makoto Taiji

doi:10.1021/jz301635h

Ligand diffusion on protein surface observed in molecular dynamics simulation

Dmitry Nerukh, Noriaki Okimoto, Atsushi Suenaga, Makoto Taiji

Research output: Contribution to journal › Article › peer-review

Abstract

The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein’s surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.

Original language	English
Pages (from-to)	3476–3479
Number of pages	4
Journal	Journal of Physical Chemistry Letters
Volume	3
Issue number	23
DOIs	https://doi.org/10.1021/jz301635h
Publication status	Published - 6 Nov 2012

Keywords

small ligand binding
protein ligand binding
binding rate
facilitated binding
surface diffusion
mycobacterium tuberculosis dihydrofolate reductase

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10.1021/jz301635h

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abstract = "The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein{\textquoteright}s surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.",

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AU - Nerukh, Dmitry

AU - Okimoto, Noriaki

AU - Suenaga, Atsushi

AU - Taiji, Makoto

PY - 2012/11/6

Y1 - 2012/11/6

N2 - The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein’s surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.

AB - The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein’s surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.

KW - small ligand binding

KW - protein ligand binding

KW - binding rate

KW - facilitated binding

KW - surface diffusion

KW - mycobacterium tuberculosis dihydrofolate reductase

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JO - Journal of Physical Chemistry Letters

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ER -

Ligand diffusion on protein surface observed in molecular dynamics simulation

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