Refinement of herpesvirus B-capsid structure on parallel supercomputers.
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.
Zhou
Z H
ZH
Texas Center for Advanced Molecular Computation, University of Houston, 77204-3476, USA.
Chiu
W
W
Haskell
K
K
Spears
H
H
Jakana
J
J
Rixon
F J
FJ
Scott
L R
LR
D002213:Capsid / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D005615:Freezing; D008854:Microscopy, Electron; D008958:Models, Molecular; D011487:Protein Conformation; D018139:Simplexvirus / Q000737:chemistry* / Q000648:ultrastructure