Dr. Z. Hong Zhou

Computational and Structural Studies of Viruses
and Supra-molecular Complexes

Our research focuses on establishing structure-function relationships in viruses and supra-molecular complexes using electron cryomicroscopy (cryoEM) and three-dimensional (3D) computer reconstruction techniques.

The first area of interest is human herpesvirus (HHV), a family of dsDNA viruses that are causative agents of cold sores, blindness, cancers and life-threatening conditions in immunosuppressed individuals. Our current efforts focus on the structural and assembly studies of cytomegaloviruses (HHV-5), Kaposi's sarcoma-associated herpesvirus and other cancer-associated herpesviruses. Comparative 3D structural analyses of these viruses and herpes simplex virus (studies previously carried out in our groups) provide a unified picture of the molecular mechanisms underlying the morphogenesis and pathogenesis of these different herpesviruses.

The second area of research concerns the structural basis of RNA transcription within intact dsRNA viruses, using cytoplasmic polyhedrosis virus (CPV) and rice dwarf virus as model systems. These viruses share many features in RNA transcription but differ substantially in 3D structure from human reoviruses that have been studied previously. Our structural studies of these viruses would also lead to a better understanding of the structural basis of the host diversity of reovirus infectivities.

The third research area relates to the 3D structural studies of human pyruvate dehydrogenase complexes (hPDC), one of the largest multienzyme systems and an essential component of metabolic pathways in human heart. Structural comparisons of hPDC complexes with different molecular components provide a structural framework for understanding its dynamic and multifunctional activities. A final major effort in our group is to develop state-of-the-art cryoEM reconstruction software for high resolution structural studies by integrating modern programming technologies, relational database management, as well as sequence-based atomic modeling. Graduate students carrying out tutorial or thesis research in the group would gain valuable research experience in structural and computational biology and master techniques ranging from cell culture, protein and virus purification, conventional and cryo-EM, modern computer programming, relational database design and management, 3D structure visualization to bioinformatics.

Schematic illustration of RNA transcription mechanism elucidated in a single shelled dsRNA virus, cytoplasmic polyhedrosis virus (CPV). The plus and minus strands of the genomic RNA are shown in blue and pink, respectively. (A) Transcription machinery at its quiescent state. The RNA genome is anchored to the TEC and the 3' end of the minus strand is positioned in the RNA-binding cleft of the TEC, forming an initiation complex. (B) Transcription machinery at the initial stage of the transcription process. The 3' end of the minus strand is driven passing through the channel of the transcription enzyme complex (TEC) and re-associates with the plus strand, while the newly synthesized mRNA is simultaneously capped by methyltransferase at the inner surface of the turret complex. The small arrows along the genomic RNA depict directions of the continuous movement of the RNA template chains. (C) Transcription machinery during elongation. The TEC keeps on adding NTP to the 3' termini of the mRNA; the capped mRNA is being released through the central channel of the turret simultaneously during elongation. The rejoined parental strands are propelled towards the center of the capsid, where steric hindrance posed by neighboring RNA segments would eventually force it to coil upward. The requirement to overcome this steric hindrance and the bending energy barrier would ultimately lead to a spiral shape organization of each segment RNA molecule. Upon completion of one round of transcription, new cycles of transcription iterate. Bottom: a zoom-in view of the 3D structure of CPV containing its dsRNA genome (red) and TEC (blue) inside the capsid, determined by cryoEM and 3D reconstruction.

Selected References

Zhang, H., Yu, X.-K., Lu, X.-Y., Zhang, J.-Q., Zhou, Z.H. (2002) Molecular interactions and viral stability revealed by structural analyses of chemically-treated cypovirus capsids. Virology, 298, 45-52. (cover article)

Liang, Y., Ke, E.Y., Zhou, Z.H. (2002) Design and Integration of a SQL Image Database in a High-Resolution 3D Reconstruction Package. J. Struct. Biol. 137, 292-304.

Chiu, W., Baker, M.L., Jiang, W., Zhou, Z.H. (2002) Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics. Curr. Opin. Struct. Biol., 12(2):263-269. (cover article)

Zhou, Z.H., McCarthy, D.B., O'Connor, C.M., Reed, L.J., Stoops, J.K. (2001) The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes. Proc. Natl. Acad. Sci. 98(26):14802-14807.

Zhou, Z.H., M.L. Baker, W. Jiang, M. Dougherty, J. Jakana, G. Dong, G. Lu, W. Chiu (2001) Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nature Struct. Biol., 8(10):868-873. (cover article)

Zhou, Z.H., Liao, W., Cheng, R.H., Lawson, J.E., McCarthy, D.B., Reed, L.J., Stoops, J.K. Direct Evidence for the Size and Conformational Variability of the Pyruvate Dehydrogenase Complex Revealed by 3-D Electron Microscopy: the "Breathing" Core and its Functional Relationship to Protein Dynamics. J. Biol. Chem. 276, 21704-21713, 2001.

Zhou, Z.H., Dougherty, M., Jakana, J., He, J., Rixon, F.J., Chiu, W. Seeing the herpesvirus capsid at 8.5 ?. Science, 288, 877-880, 2000.

Wu, L., Lo, P., Yu, X.K., Stoops, J.K, Forghani, B., Zhou, Z.H. (2000) Three-dimensional structure of human herpesvirus 8 capsid. J. Virol. Vol. 74(20):9646-9654. (cover article)

Computational and Structural Studies of Viruses and Supra-molecular Complexes

Computational and Structural Studies of Viruses
and Supra-molecular Complexes