Parallel Computing Applied to High-Resolution 3D Structure
            Determination of Supra-molecular Complexes
   
                        Z. Hong Zhou

                     University of Texas 
                   Houston Medical School  
          Dept. of Pathology & Laboratory Medicine
                     Houston, TX 77030

                hong@casper.med.uth.tmc.edu


The explosion of sequence data resulting from large-scale genome sequencing
has created unprecedented challenges for structural and computational
scientists.  X-ray crystallography and NMR, which are the primary tools for
determining atomic structures of macromolecules, can no longer keep pace
with this rapid development, thus posing a need for novel approaches to
high-resolution structural determination, particular for supramolecular
assemblies that are difficult to study by traditional means.  Recently,
three-dimensional (3D) reconstruction by electron cryomicroscopy (cryoEM)
has become an increasingly powerful tool for studying large assemblies at a
moderate resolution.  However, significant computational advancement has yet
to be made in cryoEM in order to reconstruct large complexes to atomic
detail.

The major goal of our research is to determine the high-resolution
structures of human herpesviruses by cryoEM reconstruction.  The 2000-Angstrom
diameter herpesviruses are among the most complex viruses, and are the
causative agents of cold sores, birth abnormalities and complications in
immuno-suppressed individuals.  To establish cryoEM reconstruction
procedures for reconstructing such a large virus to high resolution, we
chose to first study an insect reovirus, the cytoplasmic polyhedrosis virus
(CPV), as a model system because of its structural stability and the
availability of atomic structures of other reoviruses for validation.  We
have developed high performance parallel computing programs to process
thousands of images to reconstruct CPV to an unprecedented 8-Angstrom resolution.
This map has revealed density rods attributable to ten a helices and two
b-sheet rich regions in each shell protein.  In addition, comparison between
the CPV capsids with and without its RNA genome has allowed the
identification of the viral transcriptional complex and its interaction with
the ordered viral RNA inside the full capsid.

Using the parallel reconstruction procedures, we have reconstructed the 3D
structure of the herpesvirus capsid to 8.5-Angstrom resolution.  Most of the
molecular boundaries of the capsid proteins have been identified, revealing
a novel structural arrangement in each heterotrimer.  In addition, 18
rod-shaped densities, representing putative a helices, have been identified
in the each major capsid protein.   One floor helix connects adjacent
subunits and is interpreted as the N-terminus, which plays a critical role
in capsid assembly.  A group of five a helices is located adjacent to the
constriction inside the capsomer channel, suggesting a mechanism for
regulating viral DNA packaging and release.
Selected recent publications:



1. Zhou, Z.H., Macnab, S.J., Jakana, J., Scott, L.R., Chiu, W., Rixon, F.J.
(1998), Proc. Natl. Acad. Sci. USA, 95 (6), 2778-2783.

2. Zhang, H., Zhang, J., Yu, X., Lu, X., Zhang, Q., Jakana, J., Chen, D.,
Zhang, X., Zhou, Z.H. (1999)  J. Virology, 73 (2), 1624-1629.

3. Zhou, Z.H., Chen, D.H., Jakana, J., Rixon, F.J., Chiu, W. (1999) J.
Virology, 73 (4), 3210-3218.

4. Chen, D. H., Jiang, H., Lee, M., Liu, F., Zhou, Z.H. (1999) Virology,
260, 10-16.