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The influence of Mg2+coordination on13C and15N chemical shifts in CKI1RDprotein domain from experiment and molecular dynamics/density functional theory calculations

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dc.title The influence of Mg2+coordination on13C and15N chemical shifts in CKI1RDprotein domain from experiment and molecular dynamics/density functional theory calculations en
dc.contributor.author Vícha, Jan
dc.contributor.author Babinský, Martin
dc.contributor.author Demo, Gabriel
dc.contributor.author Otrusinová, Olga
dc.contributor.author Jansen, Séverine
dc.contributor.author Pekárová, Blanka
dc.contributor.author Žídek, Lukáš
dc.contributor.author Munzarová, Markéta
dc.relation.ispartof Proteins: Structure, Function and Bioinformatics
dc.identifier.issn 0887-3585 Scopus Sources, Sherpa/RoMEO, JCR
dc.date.issued 2016
utb.relation.volume 84
utb.relation.issue 5
dc.citation.spage 686
dc.citation.epage 699
dc.type article
dc.language.iso en
dc.publisher John Wiley and Sons Inc.
dc.identifier.doi 10.1002/prot.25019
dc.relation.uri http://onlinelibrary.wiley.com/doi/10.1002/prot.25019/abstract
dc.subject 13C en
dc.subject 15N en
dc.subject Arabidopsis thaliana en
dc.subject CKI1 histidine kinase en
dc.subject Density functional theory en
dc.subject Mg2+coordination en
dc.subject Molecular dynamics en
dc.subject NMR chemical shift en
dc.description.abstract Sequence dependence of13C and15N 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 Å 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 Å as compared to the 10 Å 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 for15N of D70, S74, and V68, where the electrostatics dominated; for13Cβ of D69 and15N of K76, where the influences were equal, and for13Cα of F72 and13Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed. © 2016 Wiley Periodicals, Inc. en
utb.faculty University Institute
dc.identifier.uri http://hdl.handle.net/10563/1006579
utb.identifier.rivid RIV/70883521:28610/16:43875261!RIV17-MSM-28610___
utb.identifier.obdid 43875996
utb.identifier.scopus 2-s2.0-84960398212
utb.source j-scopus
dc.date.accessioned 2016-09-21T13:12:21Z
dc.date.available 2016-09-21T13:12:21Z
utb.ou Centre of Polymer Systems
utb.contributor.internalauthor Vícha, Jan
utb.fulltext.affiliation Jan Vícha 1, Martin Babinský 1, Gabriel Demo 1, Olga Otrusinová 1,2, Séverine Jansen 1, Blanka Pekárová 1, Lukáš Žídek 1,2, Markéta L. Munzarová 3* 1 Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 62500, Czech Republic 2 Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno 62500, Czech Republic 3 Faculty of Science, Department of Chemistry, Masaryk University, Kotlarska 2, Brno 61137, Czech Republic * Correspondence to: Marketa L. Munzarova, Faculty of Science, Department of Chemistry, Masaryk University, Kotlarska 2, Brno 61137, Czech Republic. E-mail: marketa@chemi.muni.cz
utb.fulltext.dates Received 10 December 2015 Revised 29 January 2016 Accepted 10 February 2016 Published online 15 February 2016
utb.fulltext.ou Centre of Polymer Systems
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