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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F18%3A00101218" target="_blank" >RIV/00216224:14310/18:00101218 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61388963:_____/18:00490468 RIV/00216208:11320/18:10384676

Výsledek na webu

<a href="http://dx.doi.org/10.1039/c7cp08623g" target="_blank" >http://dx.doi.org/10.1039/c7cp08623g</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1039/c7cp08623g" target="_blank" >10.1039/c7cp08623g</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2018

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Physical Chemistry Chemical Physics

ISSN

1463-9076

e-ISSN

—

Svazek periodika

20

Číslo periodika v rámci svazku

18

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

14

Strana od-do

12664-12677

Kód UT WoS článku

000431825300034

EID výsledku v databázi Scopus

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