Family 18 chitinases catalyze the hydrolysis of β-1,4-glycosidic bonds in chitin. The mechanism has been proposed to involve the formation of an oxazolinium ion intermediate via an unusual substrate-assisted mechanism, in which the substrate itself acts as an intramolecular nucleophile (instead of an enzyme residue). Here, we have modeled the first step of the chitin hydrolysis catalyzed by Serratia marcescens chitinase B for the first time using a combined quantum mechanics/molecular mechanics approach. The calculated reaction barriers based on multiple snapshots are 15.8-19.8 kcal mol(-1) [B3LYP/6-31+G(d)//AM1-CHARMM22], in good agreement with the activation free energy of 16.1 kcal mol(-1) derived from experiment. The enzyme significantly stabilizes the oxazolinium intermediate. Two stable conformations ((4)C(1)-chair and B(3,O)-boat) of the oxazolinium ion intermediate in subsite -1 were unexpectedly observed. The transition state structure has significant oxacarbenium ion-like character. The glycosyl residue in subsite -1 was found to follow a complex conformational pathway during the reaction ((1,4)B → [(4)H(5)/(4)E](++) → (4)C(1) ↔ B(3,O)), indicating complex conformational behavior in glycoside hydrolases that utilize a substrate-assisted catalytic mechanism. The D142N mutant is found to follow the same wild-type-like mechanism: the calculated barriers for reaction in this mutant (16.0-21.1 kcal mol(-1)) are higher than in the wild type, in agreement with the experiment. Asp142 is found to be important in transition state and intermediate stabilization.

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Molecular and crystal structures of a series of model compounds of poly(m-phenylene isophthalamide) have been analyzed by the X-ray diffraction method and the various types of 3-D hydrogen bond network structures have been clarified. The twisting angles between benzene and amide groups are in the range of 25−40°, which is common to all of the analyzed model compounds and the parent polymer itself and could be reproduced well by the energy calculation with the nonbonded interatomic interactions between the benzene and amide groups taken into consideration. The molecular conformation, the packing mode of molecules, and the intermolecular hydrogen bond network structure were found to have good correlation with each other and could be classified systematically into several groups. This classification should be important for the energetic interpretation of the formation mechanism of the 3-D hydrogen bond network structure.

To clarify the factors that govern the complicated three-dimensional hydrogen-bond network structure of poly(m-phenylene isophthalamide) and its model compounds, the packing energy calculations were performed with computer simulation software (Polymorph Predictor) and the important energy terms were extracted successfully. The crystal structures were predicted with and without the various types of interaction terms being taken into consideration and were compared with the X-ray-analyzed structures. Initially, the conformation analysis was made for a single molecule. However, the structure with the lowest energy did not always correspond to the actually observed structure. This finding suggested the importance of intermolecular, as well as intramolecular, interactions. By performing the lattice-energy calculations with and without various types of intermolecular interactions being taken into consideration, and by comparing the results with the observed structures, it has been found that the van der Waals interaction was a primarily important factor in the prediction of the molecular packing structures; however, the electrostatic (and hydrogen-bond) interaction could not be ignored at all. In other words, a good and sensitive balance between these interaction terms was quite important for obtaining a successful reproduction of the observed molecular packing structures of the model compounds.

Crystal structures have been predicted by using a software Polymorph Predictor and compared with those analyzed by X-ray method for a series of low-molecular-weight aromatic amide compounds as models of poly(m-phenylene isophthalamide) and poly(p-phenylene terephthalamide). For most of the compounds investigated here, the predicted crystal structure of the lowest or the next lowest packing energy has been found to be in good agreement with the X-ray analyzed structure. However, the energy difference was not very large between these energetically most plausible structures and the other less stable candidates, indicating a difficulty of unique prediction of 3D molecular packing structure and a possibility of existence of various types of crystal modification.

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Tyrosinase is a key enzyme in melanogenesis. Generally, mushroom tyrosinase from A. bisporus had been used as a model in skin-whitening agent tests employed in the cosmetic industry. The recently obtained crystal structure of bacterial tyrosinase from B. megaterium has high similarity (33.5%) to the human enzyme and thus it was used as a template for constructing of the human model. Binding of tyrosinase to a series of its inhibitors was simulated by automated docking calculations. Docking and MD simulation results suggested that N81, N260, H263, and M280 are involved in the binding of inhibitors to mushroom tyrosinase. E195 and H208 are important residues in bacterial tyrosinase, while E230, S245, N249, H252, V262, and S265 bind to inhibitors and are important in forming pi interaction in human tyrosinase.