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

J 2018

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

ŠPAČKOVÁ, Naděžda, Zuzana TROŠANOVÁ, F. SEBESTA, Séverine JANSEN, J.V. BURDA et. al.

Basic information

Original name

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

Authors

ŠPAČKOVÁ, Naděžda (203 Czech Republic, belonging to the institution), Zuzana TROŠANOVÁ (703 Slovakia, belonging to the institution), F. SEBESTA (203 Czech Republic), Séverine JANSEN (250 France, belonging to the institution), J.V. BURDA (203 Czech Republic), Pavel SRB (203 Czech Republic, belonging to the institution), Milan ZACHRDLA (203 Czech Republic, belonging to the institution), Lukáš ŽÍDEK (203 Czech Republic, belonging to the institution) and Jiří KOZELKA (250 France, guarantor, belonging to the institution)

Edition

Physical Chemistry Chemical Physics, CAMBRIDGE, Royal Society of Chemistry, 2018, 1463-9076

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.567

RIV identification code

RIV/00216224:14310/18:00101218

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1039/c7cp08623g

UT WoS

000431825300034

Keywords in English

NUCLEAR-MAGNETIC-RESONANCE; MOLECULAR-DYNAMICS; CRYSTAL-STRUCTURES; PROTON-EXCHANGE; DNA COMPLEX; CLEANEX-PM; SIMULATIONS; CONSTRAINTS; RESTRAINTS; PARAMETERS

Abstract

V originále

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.

Links

GA14-14654S, research and development project

Name: Studium fyzikální podstaty interakcí lone-pair-pi v biomolekulárních systémech. Role interakcí lone-pair-pi při stabilizaci proteinu Engrailed (Acronym: Lone-pair-pi interactions)

Investor: Czech Science Foundation

LM2010005, research and development project

Name: Velká infrastruktura CESNET (Acronym: VI CESNET)

Investor: Ministry of Education, Youth and Sports of the CR

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

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.

@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.

Detailed Information on Publication Record