The three-dimensional structure of Arabidopsis thaliana O-methyltransferase predicted by homology-based modelling.

O-methylation of flavonoid compounds is an important enzymatic reaction since it not only reduces the chemical reactivity of their phenolic hydroxyl groups but also increases their lipophilicity and, hence, their intracellular compartmentation. Several genes encoding flavonoid O-methyltransferases (OMTs) have been isolated and characterized both at the molecular and biochemical levels. In contrast with mammalian enzymes, plant OMTs exhibit narrow substrate specificities as well as position-specific activities, so that the homology comparison, derived using programs such as BLAST can not provide sufficient information on the enzyme function or its substrate preference. In order to study these characteristics, therefore, another approach, homology-based modelling is being carried out. We report here the determination of the 3-D structure of Arabidopsis thaliana O-methyltransferase, AtOMT1 as well as its dynamics when complexed with its substrate. The predicted structure obtained by homology-based modelling is conserved during molecular dynamics simulations. AtOMT1 exhibits a structure similar to that of caffeic acid O-methyltransferase, COMT when the latter was used as a template. Whereas COMT includes 20 alpha-helices and nine beta-sheets, AtOMT1 has 16 and 9, respectively. Although the homology between both proteins is higher than 77% and all amino acids surrounding the active sites, except one residue, are similar in their primary sequences, the two proteins exhibit different substrate preferences. The differences in substrate specificity may be explained on the basis of the predicted structures of the protein and its complex with the substrate. In addition, docking the substrate into the active site of the protein allowed the study of the structural change of the active site on the dihedral angle distribution of the residues surrounding the active site.

Chiral recognition based on enantioselective interactions of propranolol enantiomers with cyclosophoraoses isolated from Rhizobium meliloti.

Cyclosophoraoses isolated from Rhizobium meliloti, as an NMR chiral shift agent, were used to discriminate propranolol enantiomers. Continuous variation plot made from the complex of cyclosophoraoses with propranolol showed that the diastereomeric complex had predominantly 1:1 stoichiometry through UV spectroscopic analysis. The chiral recognition of propranolol enantiomers by cyclosophoraoses was investigated through the determination of binding constant based on the (13)C NMR chemical shift changes. The averaged K(obs) values from the plots were 55.7 M(-1) for (R)-(+)-propranolol and 36.6 M(-1) for (S)-(-)-propranolol, respectively. Enantioselectivity (alpha = K(R+)/K(S(-)) of 1.52 was then obtained. Computational calculation also revealed that (R)-(+) propranolol was more tightly bound with cyclosophoraose than (S)-(-)-propranolol due to the enhanced van der Waals interaction.

Dynamics of fullerene coalescence.

Fullerene coalescence experimentally found in fullerene-embedded single-wall nanotubes under electron-beam irradiation or heat treatment is simulated by minimizing the classical action for many atom systems. The dynamical trajectory for forming a (5,5) C120 nanocapsule from two C60 fullerene molecules consists of thermal motions around potential basins and ten successive Stone-Wales-type bond rotations after the initial cage-opening process for which energy cost is about 8 eV. Dynamical paths for forming large-diameter nanocapsules with (10,0), (6,6), and (12,0) chiral indexes have more bond rotations than 25 with the transition barriers in a range of 10-12 eV.

Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A).

The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.