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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F16%3A00087872" target="_blank" >RIV/00216224:14310/16:00087872 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1002/prot.25019" target="_blank" >http://dx.doi.org/10.1002/prot.25019</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/prot.25019" target="_blank" >10.1002/prot.25019</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

<a href="/cs/project/GAP305%2F11%2F0756" target="_blank" >GAP305/11/0756: Strukturní princip specificity přenosu signálu v rostlinách: síť interakcí příjímačové domény histidinkinas u Arabidospis</a><br>

Návaznosti

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

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

Proteins: Structure, Function, and Bioinformatics

ISSN

0887-3585

e-ISSN

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Svazek periodika

84

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

686-699

Kód UT WoS článku

000374688500011

EID výsledku v databázi Scopus

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