Biomedical subjects

Zihe Rao

Publications and source records attributed to Zihe Rao.

113 records · Page 7Linked to original sources

PubMed2002

SOFTDOCK: understanding of molecular recognition through a systematic docking study.

Molecular recognition and docking are essential to the biological functions of proteins. SOFTDOCK was one of the first molecular docking methods developed for protein-protein docking. Its ability to represent the molecular surface with different shapes and properties and to dock a variety of molecular complexes with certain conformational changes was demonstrated in a previous study. In the present work, we studied the effects of the docking parameters through statistical analysis. Seventy one typical binary complexes of different categories in PDB were also systematically docked for a test; 57 of them produced correct solutions with one set of docking parameters whereas the other 14 complexes required adjustment of the docking parameters, by decreasing the softness of the recognition and hence the background noise. We found that these 14 complexes had special structural features. Our results suggest that a variety of mechanisms may be involved in molecular recognition rather than the shape complementarity only, which is very helpful in developing more powerful methods for predicting molecular recognition.

Binding Sites↗

PubMed2002

Six-helix bundle assembly and characterization of heptad repeat regions from the F protein of Newcastle disease virus.

Paramyxoviruses may adopt a similar fusion mechanism to other enveloped viruses, in which an anti-parallel six-helix bundle structure is formed post-fusion in the heptad repeat (HR) regions of the envelope fusion protein. In order to understand the fusion mechanism and identify fusion inhibitors of Newcastle disease virus (NDV), a member of the Paramyxoviridae family, we have developed an E. coli system that separately expresses the F protein HR1 and HR2 regions as GST fusion proteins. The purified cleaved HR1 and HR2 have subsequently been assembled into a stable six-helix bundle heterotrimer complex. Furthermore, both the GST fusion protein and the cleaved HR2 show virus-cell fusion inhibition activity (IC(50) of 1.07-2.93 microM). The solubility of the GST-HR2 fusion protein is much higher than that of the corresponding peptide. Hence this provides a plausible method for large-scale production of HR peptides as virus fusion inhibitors.

Amino Acid Sequence↗

PubMed2002

Structure of equine infectious anemia virus matrix protein.

The Gag polyprotein is key to the budding of retroviruses from host cells and is cleaved upon virion maturation, the N-terminal membrane-binding domain forming the matrix protein (MA). The 2.8-A resolution crystal structure of MA of equine infectious anemia virus (EIAV), a lentivirus, reveals that, despite showing no sequence similarity, more than half of the molecule can be superimposed on the MAs of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV). However, unlike the structures formed by HIV-1 and SIV MAs, the oligomerization state observed is not trimeric. We discuss the potential of this molecule for membrane binding in the light of conformational differences between EIAV MA and HIV or SIV MA.

Amino Acid Sequence↗

PubMed2002

Crystallization and preliminary X-ray diffraction analysis of FKBP12 complexed with a novel neurotrophic ligand.

A novel neurotrophic ligand, (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-Leucine ethyl ester, has been complexed with FKBP12 and crystallized using the hanging-drop vapor-diffusion method. Crystals belong to P2(1) space group, with unit cell parameters a=41.2, b=29.6, c=41.5 A, beta=114.0 degrees. The crystals diffract to 1.8 A resolution limit.

Crystallography, X-Ray↗

PubMed2001

Crystallization and preliminary crystallographic analysis of a metastasis-inducing protein, human S100A4.

A metastasis-inducing protein, human S100A4, cDNA was overexpressed in Escherichia coli. The recombinant protein was purified by three chromatographic procedures. Crystals were obtained using polyethylene glycol as a precipitant. The native S100A4 crystals did not diffract sufficiently well for data collection, but the SeMet S100A4 crystal, grown using similar conditions as for the native, was found to be stable during exposure to X-rays and diffracted to 4 A resolution in-house. The crystal belongs to space group P6 or P3. The unit-cell parameters are a = b = 47.1, c = 175.6 A, alpha = beta = 90, gamma = 120 degrees. Complete data will be collected using synchrotron radiation.

Crystallography, X-Ray↗