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.
abstract: Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), 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 Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) 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 Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Vícha
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Babinský
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Demo
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.|Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Olga
authors.initials: O
authors.lastname: Otrusinová
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Séverine
authors.initials: S
authors.lastname: Jansen
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Blanka
authors.initials: B
authors.lastname: Pekárová
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.|Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
authors.forename: Lukáš
authors.initials: L
authors.lastname: Žídek
authors.affiliation: Faculty of Science, Department of Chemistry, Masaryk University, Kotlářská 2, Brno, 61137, Czech Republic.
authors.forename: Markéta L
authors.initials: ML
authors.lastname: Munzarová
mesh_terms: D029681:Arabidopsis Proteins / Q000737:chemistry*; D002247:Carbon Isotopes / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009587:Nitrogen Isotopes / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D000072417:Protein Domains; D011494:Protein Kinases / Q000737:chemistry*
chemical_list: D029681:Arabidopsis Proteins; D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D011494:Protein Kinases; C101990:CKI1 protein, Arabidopsis; D008274:Magnesium
keywords: 13C; 15N; Arabidopsis thaliana; CKI1 histidine kinase; Mg2+ coordination; NMR chemical shift; density functional theory; molecular dynamics