Wei-Zu Chen | Search PubMed

PubMed2005

Constructing HIV-1 integrase tetramer and exploring influences of metal ions on forming integrase-DNA complex.

HIV-1 integrase (IN) is essential for the replication of HIV-1 in human cells. At present, the complete structure of complex IN-DNA has not been resolved. In this paper, a HIV-1 IN tetramer model was built with homology modeling and molecular dynamics simulation approach, in which two Mg2+ ions were reasonably located in each catalytic core domain. Moreover, it was found that the AB and CD chains of HIV-1 IN tetramer were different in the structures and metal ions of HIV-1 IN tetramer might have great influences on DNA locating on IN. These findings may provide a more complete structural basis for guiding drug discovery and revealing integration mechanism.

Catalytic Domain↗

PubMed2003

A soft docking algorithm for predicting the structures of protein-protein complexes.

An efficient soft docking algorithm is described to predict the mode of binding between two proteins based on the three-dimensional structures of molecules. The molecular model used in this work was grounded on the "simplified protein" model used in Janin's docking algorithm. The side chain flexibility of the amino acid residues Arg, Lys, Asp, Glu and Met at the protein surface was considered through softening the molecular surface. A double filtering technique was used to eliminate most of the unlike binding modes. The energy minimization was performed on the retained structures, and then these structures were evaluated with the scoring function which included electrostatic, desolvation and van der Waals energy terms. The 26 complexes were used to test this docking algorithm and good results were obtained. The native-like conformations of all the complexes were all found, of which 20 were ranked in the top 10.

Algorithms↗