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.
New transition metal sandwich compounds, [(η 5-C 5H 5)M(MeSiB 10H 10)] -(M=Co, Rh and Ir) have been investigated by using DFT/B3LYP method with relativistic pseudopotentials to study the optimized geometry and the el...
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New transition metal sandwich compounds, [(η 5-C 5H 5)M(MeSiB 10H 10)] -(M=Co, Rh and Ir) have been investigated by using DFT/B3LYP method with relativistic pseudopotentials to study the optimized geometry and the electronic *** results obtained are in good agreement with the experimental *** is concluded that silaborane cage has stronger coordination abilities and the metal-Si bond length is very *** electronic structure characters indicate that these sandwich cpmplexes satisfy the 18-electron rule, although they are thermally stable, and they may be photochemically active.
SARS is a positive-stranded virus featuring the largest viral RNA genomes today. The viral main proteinase(Hydrolase), controlling the activities of SARS virus replication , is an attractive target for therapy. We det...
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SARS is a positive-stranded virus featuring the largest viral RNA genomes today. The viral main proteinase(Hydrolase), controlling the activities of SARS virus replication , is an attractive target for therapy. We determined crystal structure for transmissible gastroenteritis virus(TGEV) hydrolase, and constructed a homology model for SARS coronavirus proteinase on Silicon Graphics station by Insight Ⅱ molecule simulation software. The structure may reveal remarkable degree of conservation of the substrate binding sites. We design an imaginable peptide precursor for inhibitor, and the base shape of pocket and property of the residues may be used as a basis for designing anti-SARS drugs.
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