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.

Základní údaje

Originální název

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

Autoři

ŠPAČKOVÁ, Naděžda (203 Česká republika, domácí), Zuzana TROŠANOVÁ (703 Slovensko, domácí), F. SEBESTA (203 Česká republika), Séverine JANSEN (250 Francie, domácí), J.V. BURDA (203 Česká republika), Pavel SRB (203 Česká republika, domácí), Milan ZACHRDLA (203 Česká republika, domácí), Lukáš ŽÍDEK (203 Česká republika, domácí) a Jiří KOZELKA (250 Francie, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.567

Kód RIV

RIV/00216224:14310/18:00101218

Organizační jednotka

Přírodovědecká fakulta

DOI

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

UT WoS

000431825300034

Klíčová slova anglicky

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

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 23. 4. 2024 12:32, Mgr. Michal Petr

Anotace

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.

Návaznosti

GA14-14654S, projekt VaV

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

Investor: Grantová agentura ČR, Towards the physical basis of lone-pair-pi interactions. Do lone-pair-pi interactions stabilize the structure of the Engrailed homeodomain?

LM2010005, projekt VaV

Název: Velká infrastruktura CESNET (Akronym: VI CESNET)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Velká infrastruktura CESNET

LM2015043, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

Citovat

ŠPAČKOVÁ, Naděžda, Zuzana TROŠANOVÁ, F. SEBESTA, Séverine JANSEN, J.V. BURDA, Pavel SRB, Milan ZACHRDLA, Lukáš ŽÍDEK a 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, roč. 20, č. 18, s. 12664-12677. ISSN 1463-9076. Dostupné z: 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 a 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, roč.~20, č.~18, s.~12664-12677. ISSN~1463-9076. Dostupné z: https://dx.doi.org/10.1039/c7cp08623g.

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