Detailed Information on Publication Record
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.Basic information
Original name
The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations
Authors
VÍCHA, Jan (203 Czech Republic, belonging to the institution), Martin BABINSKÝ (703 Slovakia, belonging to the institution), Gabriel DEMO (703 Slovakia, belonging to the institution), Olga OTRUSINOVÁ (203 Czech Republic, belonging to the institution), Séverine JANSEN (250 France, belonging to the institution), Blanka PEKÁROVÁ (203 Czech Republic, belonging to the institution), Lukáš ŽÍDEK (203 Czech Republic, belonging to the institution) and Markéta MUNZAROVÁ (203 Czech Republic, guarantor, belonging to the institution)
Edition
Proteins: Structure, Function, and Bioinformatics, 2016, 0887-3585
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 2.289
RIV identification code
RIV/00216224:14310/16:00087872
Organization unit
Faculty of Science
UT WoS
000374688500011
Keywords in English
Arabidopsis thaliana; CKI1 histidine kinase; Mg2+ coordination; NMR chemical shift; 13C; 15N; molecular dynamics; density functional theory
Změněno: 14/4/2017 14:39, Ing. Andrea Mikešková
Abstract
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.
Links
| GAP305/11/0756, research and development project |
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