Water-tryptophan interactions: lone-pair-pi or O-H-pi?
Molecular dynamics simulations of beta-galactosidase suggest
that both modes can co-exist

J 2018

Water-tryptophan interactions: lone-pair-pi or O-H-pi? Molecular dynamics simulations of beta-galactosidase suggest that both modes can co-exist

DUREC, Matúš; Radek MAREK a Jiří KOZELKA

Základní údaje

Originální název

Water-tryptophan interactions: lone-pair-pi or O-H-pi? Molecular dynamics simulations of beta-galactosidase suggest that both modes can co-exist

Autoři

DUREC, Matúš; Radek MAREK a Jiří KOZELKA

Vydání

Chemistry - A European Journal, Weinheim, Wiley, 2018, 0947-6539

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

DOI: 10.1002/chem.201705364

Impakt faktor

Impact factor: 5.160

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/18:00100777

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

water; tryptophane; interaction; molecular dynamics

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 10. 2020 08:36, prof. RNDr. Radek Marek, Ph.D.

Anotace

V originále

In proteins, the indole side-chain of tryptophan can interact with water molecules either in-plane, forming H-bonds, or out-of-plane, with the water molecule contacting the aromatic pi-face. The latter interaction can be either of the lone-pair---pi (lp---pi) type or correspond to the O-H---pi binding mode, an ambiguity that X-ray structures usually do not resolve. Here we report molecular dynamics (MD) simulations of a solvated beta-galactosidase monomer which illustrate how a water molecule located at the pi-face of an indole side-chain of tryptophan can adapt to the position of proximate residues and "select" its binding mode. In one such site, the water molecule is predicted to rapidly oscillate between the O-H---pi and lp---pi binding modes, gaining thus entropic advantage. Our MD simulations provide support for the role of lp---pi interactions in the stabilization of protein structures.

Návaznosti

ED3.2.00/08.0144, projekt VaV

Název: CERIT Scientific Cloud

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

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Přiložené soubory

CEJ18_24_5849.pdf

Požádat o autorskou verzi souboru

Citovat

DUREC, Matúš; Radek MAREK a Jiří KOZELKA. Water-tryptophan interactions: lone-pair-pi or O-H-pi? Molecular dynamics simulations of beta-galactosidase suggest that both modes can co-exist. Chemistry - A European Journal. Weinheim: Wiley, 2018, roč. 24, č. 22, s. 5849-5859. ISSN 0947-6539. Dostupné z: https://doi.org/10.1002/chem.201705364.

@article{1402057,
   author = {Durec, Matúš and Marek, Radek and Kozelka, Jiří},
   article_location = {Weinheim},
   article_number = {22},
   doi = {https://doi.org/10.1002/chem.201705364},
   keywords = {water; tryptophane; interaction; molecular dynamics},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Water-tryptophan interactions: lone-pair-pi or O-H-pi? Molecular dynamics simulations of beta-galactosidase suggest that both modes can co-exist},
   url = {http://dx.doi.org/10.1002/chem.201705364},
   volume = {24},
   year = {2018}
}

TY  - JOUR
ID  - 1402057
AU  - Durec, Matúš - Marek, Radek - Kozelka, Jiří
PY  - 2018
TI  - Water-tryptophan interactions: lone-pair-pi or O-H-pi? Molecular dynamics simulations of beta-galactosidase suggest that both modes can co-exist
JF  - Chemistry - A European Journal
VL  - 24
IS  - 22
SP  - 5849-5859
EP  - 5849-5859
PB  - Wiley
SN  - 09476539
KW  - water
KW  - tryptophane
KW  - interaction
KW  - molecular dynamics
UR  - http://dx.doi.org/10.1002/chem.201705364
L2  - http://dx.doi.org/10.1002/chem.201705364
N2  - In proteins, the indole side-chain of tryptophan can interact with water molecules either in-plane, forming H-bonds, or out-of-plane, with the water molecule contacting the aromatic pi-face. The latter interaction can be either of the lone-pair---pi (lp---pi) type or correspond to the O-H---pi binding mode, an ambiguity that X-ray structures usually do not resolve. Here we report molecular dynamics (MD) simulations of a solvated beta-galactosidase monomer which illustrate how a water molecule located at the pi-face of an indole side-chain of tryptophan can adapt to the position of proximate residues and "select" its binding mode. In one such site, the water molecule is predicted to rapidly oscillate between the O-H---pi and lp---pi binding modes, gaining thus entropic advantage. Our MD simulations provide support for the role of lp---pi interactions in the stabilization of protein structures.
ER  -

DUREC, Matúš; Radek MAREK a Jiří KOZELKA. Water-tryptophan interactions: lone-pair-pi or O-H-pi? Molecular dynamics simulations of beta-galactosidase suggest that both modes can co-exist. \textit{Chemistry - A European Journal}. Weinheim: Wiley, 2018, roč.~24, č.~22, s.~5849-5859. ISSN~0947-6539. Dostupné z: https://doi.org/10.1002/chem.201705364.

Přehled o publikaci