The influence of Mg2+ coordination on 13C and 15N chemical
shifts in CKI1RD protein domain from experiment and molecular
dynamics/density functional theory calculations

J 2016

The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations

VÍCHA, Jan, Martin BABINSKÝ, Gabriel DEMO, Olga OTRUSINOVÁ, Séverine JANSEN et. al.

Základní údaje

Originální název

The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations

Autoři

VÍCHA, Jan (203 Česká republika, domácí), Martin BABINSKÝ (703 Slovensko, domácí), Gabriel DEMO (703 Slovensko, domácí), Olga OTRUSINOVÁ (203 Česká republika, domácí), Séverine JANSEN (250 Francie, domácí), Blanka PEKÁROVÁ (203 Česká republika, domácí), Lukáš ŽÍDEK (203 Česká republika, domácí) a Markéta MUNZAROVÁ (203 Česká republika, garant, domácí)

Vydání

Proteins: Structure, Function, and Bioinformatics, 2016, 0887-3585

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.289

Kód RIV

RIV/00216224:14310/16:00087872

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1002/prot.25019

UT WoS

000374688500011

Klíčová slova anglicky

Arabidopsis thaliana; CKI1 histidine kinase; Mg2+ coordination; NMR chemical shift; 13C; 15N; molecular dynamics; density functional theory

Štítky

AKR, rivok

Změněno: 14. 4. 2017 14:39, Ing. Andrea Mikešková

Anotace

V originále

Sequence dependence of 13C and 15N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD, and its complexed form, CKI1RD.Mg2+, was studied by means of MD/DFT calculations. MD simulations of a 20–ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 A environment of Mg2+, a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg2+ binding was described better by the 15 A as compared to the 10 A model. Thirteen chemical shifts were analyzed in terms of the effect of Mg2+ insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg2+ binding. The strongest individual effects were found for 15N of D70, S74, and V68, where the electrostatics dominated; for 13C_beta of D69 and 15N of K76, where the influences were equal, and for 13C_alpha of F72 and 13C_beta of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.

Návaznosti

GAP305/11/0756, projekt VaV

Název: Strukturní princip specificity přenosu signálu v rostlinách: síť interakcí příjímačové domény histidinkinas u Arabidospis (Akronym: HKRD-AHP)

Investor: Grantová agentura ČR, Strukturní princip specificity přenosu signálu v rostlinách: síť interakcí příjímačové domény histidinkinas u Arabidospis

Citovat

VÍCHA, Jan, Martin BABINSKÝ, Gabriel DEMO, Olga OTRUSINOVÁ, Séverine JANSEN, Blanka PEKÁROVÁ, Lukáš ŽÍDEK a Markéta MUNZAROVÁ. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. Proteins: Structure, Function, and Bioinformatics. 2016, roč. 84, č. 5, s. 686-699. ISSN 0887-3585. Dostupné z: https://dx.doi.org/10.1002/prot.25019.

@article{1341586,
   author = {Vícha, Jan and Babinský, Martin and Demo, Gabriel and Otrusinová, Olga and Jansen, Séverine and Pekárová, Blanka and Žídek, Lukáš and Munzarová, Markéta},
   article_number = {5},
   doi = {http://dx.doi.org/10.1002/prot.25019},
   keywords = {Arabidopsis thaliana; CKI1 histidine kinase; Mg2+ coordination; NMR chemical shift; 13C; 15N; molecular dynamics; density functional theory},
   language = {eng},
   issn = {0887-3585},
   journal = {Proteins: Structure, Function, and Bioinformatics},
   title = {The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations},
   volume = {84},
   year = {2016}
}

TY  - JOUR
ID  - 1341586
AU  - Vícha, Jan - Babinský, Martin - Demo, Gabriel - Otrusinová, Olga - Jansen, Séverine - Pekárová, Blanka - Žídek, Lukáš - Munzarová, Markéta
PY  - 2016
TI  - The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations
JF  - Proteins: Structure, Function, and Bioinformatics
VL  - 84
IS  - 5
SP  - 686-699
EP  - 686-699
SN  - 08873585
KW  - Arabidopsis thaliana
KW  - CKI1 histidine kinase
KW  - Mg2+ coordination
KW  - NMR chemical shift
KW  - 13C
KW  - 15N
KW  - molecular dynamics
KW  - density functional theory
N2  - Sequence dependence of 13C and 15N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD, and its complexed form, CKI1RD.Mg2+, was studied by means of MD/DFT calculations. MD simulations of a 20–ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 A environment of Mg2+, a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg2+ binding was described better by the 15 A as compared to the 10 A model. Thirteen chemical shifts were analyzed in terms of the effect of Mg2+ insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg2+ binding. The strongest individual effects were found for 15N of D70, S74, and V68, where the electrostatics dominated; for 13C_beta of D69 and 15N of K76, where the influences were equal, and for 13C_alpha of F72 and 13C_beta of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.
ER  -

VÍCHA, Jan, Martin BABINSKÝ, Gabriel DEMO, Olga OTRUSINOVÁ, Séverine JANSEN, Blanka PEKÁROVÁ, Lukáš ŽÍDEK a Markéta MUNZAROVÁ. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. \textit{Proteins: Structure, Function, and Bioinformatics}. 2016, roč.~84, č.~5, s.~686-699. ISSN~0887-3585. Dostupné z: https://dx.doi.org/10.1002/prot.25019.

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