Thermal unfolding of the histidine-containing phosphocarrier protein (HPr) was investigated by computation. Molecular dynamics simulations of HPr were performed in aqueous solution for 200 ps at 300 K and for 1 ns at 373 K. The initial structure remained stable during the simulation at 300 K ; however, two major structural changes as the unfolding intermediates were observed during the simulation at 373 K.
An exhaustive conformational search of typical pyrethroids shown in Figure 1 was carried out by a systematic search algorithm enhanced by PVM. A unique common structure between these compounds was obtained as their bioactive conformation from the result of the search. The result is summarized in Table 2. Structure similarity between these compounds was studied by several similarity measures introduced here One of the measures, Tanimoto coefficient derived from the distance matrix, discriminated two subtypes of pyrethroids suggested by the QSAR study, as summarized in Table 4.
A molecular graphics program 'Modrast-P' was extended in its function which generates a Virtual Reality Modeling Language (VRML) format. By using this function, the data of the molecular model displayed on Modrast-P are converted to a VRML format and can be displayed on a WWW browser. It has various representations, for example, whole structure of space-filling model (Figure 1), ball-and-stick model, and backbone model (Figures 2, 3), backbone model with specified part as spacefilling model (Figure 4), and enlarged ball-and-stick models of a part of compounds (Figures 5, 6). A platform-independent VRML file generated by this program is very efficient for the exchange of molecular information through the computer network.
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