Informace o publikaci

Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants

Autoři

ŠPAČKOVÁ Naděžda TROŠANOVÁ Zuzana SEBESTA F. JANSEN Séverine BURDA J.V. SRB Pavel ZACHRDLA Milan ŽÍDEK Lukáš KOZELKA Jiří

Rok publikování 2018
Druh Článek v odborném periodiku
Časopis / Zdroj Physical Chemistry Chemical Physics
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www https://pubs.rsc.org/en/Content/ArticleLanding/2018/CP/C7CP08623G#!divAbstract
Doi http://dx.doi.org/10.1039/c7cp08623g
Klíčová slova NUCLEAR-MAGNETIC-RESONANCE; MOLECULAR-DYNAMICS; CRYSTAL-STRUCTURES; PROTON-EXCHANGE; DNA COMPLEX; CLEANEX-PM; SIMULATIONS; CONSTRAINTS; RESTRAINTS; PARAMETERS
Popis Water molecules can interact with aromatic moieties using either their O-H bonds or their lone-pairs of electrons. In proteins, water-pi interactions have been reported to occur with tryptophan and histidine residues, and dynamic exchange between O-H center dot center dot center dot pi hydrogen bonding and lone-pair center dot center dot center dot pi interactions was suggested to take place, based on ab initio calculations. Here we used classical and QM/MM molecular dynamics simulations, complemented with an NMR study, to examine a specific water-indole interaction observed in the engrailed homeodomain and in its mutants. Our simulations indicate that the binding mode between water and indole can adapt to the potential created by the surrounding amino acids (and by the residues at the DNA surface in protein-DNA complexes), and support the model of dynamic switching between the O-H center dot center dot center dot pi hydrogen bonding and lone-pair center dot center dot center dot pi binding modes.
Související projekty: