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

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

Cooperative binding of cucurbit[n]urils and β-cyclodextrin to heteroditopic imidazolium-based guests

Imidazolium-based guests containing two distinct binding epitopes are capable of binding beta-cyclodextrin and cucurbit[6/7]uril (CB) simultaneously to form heteroternary 1:1:1 inclusion complexes. In the final the hosts occupy binding sites disfavored in the binary complexes because of the chemically induced reorganization of the intermediate 1:1 aggregate. In addition, the reported guests are capable of binding two CBs to form either 1:2 or 1:1:1 ternary assemblies despite consisting of a single cationic moiety. Whereas the adamantane site binds CB solely via hydrophobic interactions, the CB unit at the butyl site is stabilized by a combination of hydrophobic and ion-dipole interactions.Internal Funding Agency of Tomas Bata University in Zlin [IGA/FT/2016/001]; Czech Science Foundation [16-05961S]; Ministry of Education, Youth and Sports of the Czech Republic under Project CEITEC [LQ1601]; CERIT Scientific Cloud under the program "Projects of Large Research, Development, and Innovations Infrastructures" [LM2015085

Adamantane-bearing benzylamines and benzylamides: Novel building blocks for supramolecular systems with finely tuned binding properties towards β-cyclodextrin

Novel building blocks for the synthesis of supramolecular components based on adamantane-bearing benzylamines were prepared. The binding properties of these amines and the corresponding acetamides towards β-cyclodextrin (β-CD) were studied using mass spectrometry, NMR spectrometry, isothermal titration calorimetry and semi-empirical calculations. It was found that all of the examined guests predominantly formed 1:1 inclusion complexes in an enthalpy-driven manner with association constants of the order of 10 2-103 M-1. Stronger binding to the β-CD cavity was observed for guests with a longer spacer between the adamantane and benzene moieties and/or a 1,4-disubstituted benzene ring. © 2013 Taylor & Francis Group, LLC