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.
The most softwares for protein-protein docking are regarded as two proteins being rigid, and take no account of the flexibility of proteins, which causes conformation variety of the interface because of interaction of...
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The most softwares for protein-protein docking are regarded as two proteins being rigid, and take no account of the flexibility of proteins, which causes conformation variety of the interface because of interaction of the interface amino acids. On the premise of the rigidity of protein-protein docking, by the method of molecular dynamic simulation, we search the protein-protein interface conformations of the complexes which grounded on the rigid docking. Since the interaction of the amino acid was taken into account, to a certain extent, the complex conformations are more perfect.
The potential felt by a single electron within a molecule represents the total interaction energy of this electron with all nuclei and the rest electrons in the molecule and is an important quantity. It is formulated ...
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The potential felt by a single electron within a molecule represents the total interaction energy of this electron with all nuclei and the rest electrons in the molecule and is an important quantity. It is formulated and then calculated by using the ab initio MELD program plus a separate calculation program. We have systematically investigated and discussed this kind of potentials for a series of molecules. In terms of the three dimensional graph, the variation of the potential acting on the single electron within a molecule has clearly and visually been shown, and hence the electronic movement and the chemical bonding can be deeply understood.
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