Refinement of herpesvirus B-capsid structure on parallel supercomputers

Biophys J. 1998 Jan;74(1):576-88. doi: 10.1016/S0006-3495(98)77816-6.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Capsid / chemistry*
  • Capsid / ultrastructure*
  • Computer Simulation
  • Freezing
  • Microscopy, Electron
  • Models, Molecular
  • Protein Conformation*
  • Simplexvirus / chemistry*
  • Simplexvirus / ultrastructure