Ligand diffusion on protein surface observed in molecular dynamics simulation

Dmitry Nerukh, Noriaki Okimoto, Atsushi Suenaga, Makoto Taiji

    Research output: Contribution to journalArticlepeer-review


    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 languageEnglish
    Pages (from-to)3476–3479
    Number of pages4
    JournalJournal of Physical Chemistry Letters
    Issue number23
    Publication statusPublished - 6 Nov 2012


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


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