Refinement of herpesvirus B-capsid structure on parallel supercomputers

Zhou, Z.H., Chiu, W., Haskell, K., Spears, H., Jakana, J., Rixon, F.J. and Scott, L.R. (1998) Refinement of herpesvirus B-capsid structure on parallel supercomputers. Biophysical Journal, 74(1), pp. 576-588. (doi: 10.1016/S0006-3495(98)77816-6)

Abstract

Electron cryomicroscopy and icosahedral reconstruction are used to obtain the three-dimensional structure of the 1250-A-diameter herpesvirus B-capsid. The centers and orientations of particles in focal pairs of 400-kV, spot-scan micrographs are determined and iteratively refined by common-lines-based local and global refinement procedures. We describe the rationale behind choosing shared-memory multiprocessor computers for executing the global refinement, which is the most computationally intensive step in the reconstruction procedure. This refinement has been implemented on three different shared-memory supercomputers. The speedup and efficiency are evaluated by using test data sets with different numbers of particles and processors. Using this parallel refinement program, we refine the herpesvirus B-capsid from 355-particle images to 13-A resolution. The map shows new structural features and interactions of the protein subunits in the three distinct morphological units: penton, hexon, and triplex of this T = 16 icosahedral particle.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Rixon, Dr Frazer
• Authors: Zhou, Z.H., Chiu, W., Haskell, K., Spears, H., Jakana, J., Rixon, F.J., and Scott, L.R.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Research Group: Biophys. J.
• Journal Name: Biophysical Journal
• ISSN: 0006-3495
• ISSN (Online): 1542-0086