Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active...
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Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active closed structure. During change from non-active opened structure to active closed structure, the protein loop connecting domain α to domain α/β becomes bent remarkablely, which results in two domains closed up, and binding pocket reduce obviously. Setting about from the inactive-open X-ray structure, applying the method of molecular dynamic simulation, putting the ligand in the active-pocket, we carry out a dynamic simulation in the CVFF force-field for the entire system. The structures obstained are more approximately to the active-close X-ray structures, it proves that the rigid movement of the domains is arouse by the inducing effect of the ligand molecules.
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