| ŠPAČKOVÁ, Naděžda, Zuzana TROŠANOVÁ, F. SEBESTA, Séverine JANSEN, J.V. BURDA, Pavel SRB, Milan ZACHRDLA, Lukáš ŽÍDEK and Jiří KOZELKA. Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Physical Chemistry Chemical Physics. CAMBRIDGE: Royal Society of Chemistry, 2018, vol. 20, No 18, p. 12664-12677. ISSN 1463-9076. Available from: https://dx.doi.org/10.1039/c7cp08623g. |
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@article{1443202,
author = {Špačková, Naděžda and Trošanová, Zuzana and Sebesta, F. and Jansen, Séverine and Burda, J.V. and Srb, Pavel and Zachrdla, Milan and Žídek, Lukáš and Kozelka, Jiří},
article_location = {CAMBRIDGE},
article_number = {18},
doi = {http://dx.doi.org/10.1039/c7cp08623g},
keywords = {NUCLEAR-MAGNETIC-RESONANCE; MOLECULAR-DYNAMICS; CRYSTAL-STRUCTURES; PROTON-EXCHANGE; DNA COMPLEX; CLEANEX-PM; SIMULATIONS; CONSTRAINTS; RESTRAINTS; PARAMETERS},
language = {eng},
issn = {1463-9076},
journal = {Physical Chemistry Chemical Physics},
title = {Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants},
url = {https://pubs.rsc.org/en/Content/ArticleLanding/2018/CP/C7CP08623G#!divAbstract},
volume = {20},
year = {2018}
}
TY - JOUR
ID - 1443202
AU - Špačková, Naděžda - Trošanová, Zuzana - Sebesta, F. - Jansen, Séverine - Burda, J.V. - Srb, Pavel - Zachrdla, Milan - Žídek, Lukáš - Kozelka, Jiří
PY - 2018
TI - Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants
JF - Physical Chemistry Chemical Physics
VL - 20
IS - 18
SP - 12664-12677
EP - 12664-12677
PB - Royal Society of Chemistry
SN - 14639076
KW - NUCLEAR-MAGNETIC-RESONANCE
KW - MOLECULAR-DYNAMICS
KW - CRYSTAL-STRUCTURES
KW - PROTON-EXCHANGE
KW - DNA COMPLEX
KW - CLEANEX-PM
KW - SIMULATIONS
KW - CONSTRAINTS
KW - RESTRAINTS
KW - PARAMETERS
UR - https://pubs.rsc.org/en/Content/ArticleLanding/2018/CP/C7CP08623G#!divAbstract
N2 - 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.
ER -
ŠPAČKOVÁ, Naděžda, Zuzana TROŠANOVÁ, F. SEBESTA, Séverine JANSEN, J.V. BURDA, Pavel SRB, Milan ZACHRDLA, Lukáš ŽÍDEK and Jiří KOZELKA. Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. \textit{Physical Chemistry Chemical Physics}. CAMBRIDGE: Royal Society of Chemistry, 2018, vol.~20, No~18, p.~12664-12677. ISSN~1463-9076. Available from: https://dx.doi.org/10.1039/c7cp08623g.
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