The influence of Mg2 coordination on C-13 and N-15 chemical shifts in CKI1(RD) 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%2F70883521%3A28610%2F16%3A43875261" target="_blank" >RIV/70883521:28610/16:43875261 - isvavai.cz</a>

Výsledek na webu

<a href="http://onlinelibrary.wiley.com/doi/10.1002/prot.25019/abstract;jsessionid=9470182C85F2F0FA6260CD61782AF325.f03t02" target="_blank" >http://onlinelibrary.wiley.com/doi/10.1002/prot.25019/abstract;jsessionid=9470182C85F2F0FA6260CD61782AF325.f03t02</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 C-13 and N-15 chemical shifts in CKI1(RD) protein domain from experiment and molecular dynamics/density functional theory calculations

Popis výsledku v původním jazyce

Sequence dependence of13C and15N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana,CKI1RD, and its complexed form, CKI1RD.Mg21, was studied by means of MD/DFT calculations. MD simulations of a 20-nsproduction r un length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and itssequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/inte-r ior position. Using models covering a 10 and a 15 Aoenvironment of Mg21, a semi-quantitative agreement has beenobtained between experiment and theory for the V672I73 sequence. The influence of Mg21binding was described better bythe 15 Aoas compared to the 10 Aomodel. Thirteen chemical shifts were analyzed in terms of the effect of Mg21insertionand geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg21binding. Thestrongest individual effects were found for15N of D70, S74, and V68, where the electrostatics dominated; for13Cb of D69and15N of K76, where the influences were equal, and for13Ca of F72 and13Cb of K76, where the geometry adjustmentdominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination hasbeen observed.

Název v anglickém jazyce

The influence of Mg2 coordination on C-13 and N-15 chemical shifts in CKI1(RD) protein domain from experiment and molecular dynamics/density functional theory calculations

Popis výsledku anglicky

Sequence dependence of13C and15N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana,CKI1RD, and its complexed form, CKI1RD.Mg21, was studied by means of MD/DFT calculations. MD simulations of a 20-nsproduction r un length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and itssequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/inte-r ior position. Using models covering a 10 and a 15 Aoenvironment of Mg21, a semi-quantitative agreement has beenobtained between experiment and theory for the V672I73 sequence. The influence of Mg21binding was described better bythe 15 Aoas compared to the 10 Aomodel. Thirteen chemical shifts were analyzed in terms of the effect of Mg21insertionand geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg21binding. Thestrongest individual effects were found for15N of D70, S74, and V68, where the electrostatics dominated; for13Cb of D69and15N of K76, where the influences were equal, and for13Ca of F72 and13Cb of K76, where the geometry adjustmentdominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination hasbeen observed.

Druh

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

CEP obor

CE - Biochemie

OECD FORD obor

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Projekt

—

Návaznosti

V - Vyzkumna aktivita podporovana z jinych verejnych zdroju

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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