Constraints on the assembly of spherical virus particles.

Examination of protein structure shows that it is not possible to deform protein domains to the extent required by the Caspar-Klug quasi-symmetry surface lattices for the description of viral capsids (D. L. D. Caspar and A. Klug (1962). Cold Spring Harbor Symp. Quant. Biol. 27, 1-24). However, flexibility in proteins can be achieved by a number of ligand-induced events. One type of alteration is that of quaternary structural changes in oligomers. This strategy has been used by southern bean mosaic virus and tomato bushy stunt virus where dimers attain two different states in the assembled capsid. Alterations of subunit interactions can be induced by association with RNA, cations, or other oligomeric units and, hence, successful assembly results from a stepwise aggregation. The nature of the oligomers (dimers, trimers, or pentamers) must be the underlying reason for the occurrence of the Caspar-Klug lattices and the organization into icosahedra. An analysis of the surface lattices shows which types of oligomers will be necessary for assembly.

Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three-dimensional structure of the virus.

The amino acid sequence of the coat protein of southern bean mosaic virus has been determined. Chemical techniques were supplemented by a 2.8-A-resolution electron-density map which helped in assigning absolute positions for each peptide. Four amino acids and the placement of one heptapeptide near the amino terminus of the protein were interpolated by comparison with the partially known southern bean mosaic virus RNA sequence. The subunit is heavily lined with basic residues on the side facing the RNA. Subunit-subunit interactions are hydrophobic and ionic. The calcium site on the quasi-threefold axis has three glutamic residues as ligands. There is a disulfide bond, between Cys 168 and 176, within a sequence which is inserted in southern bean mosaic virus relative to the tomato bushy stunt virus structure. This portion is a helix nestling between the "beta-barrel" subunit structure and the RNA interior.

Molecular asymmetry in an abortive ternary complex of lobster glyceraldehyde-3-phosphate dehydrogenase.

An abortive ternary complex of lobster glyceraldehyde-3-phosphate dehydrogenase was produced by the covalent attachment of 3,3,3-trifluoroacetone to Cys- 149 in each subunit. X-ray diffraction analysis of the glyceraldehyde-3-phosphate dehydrogenase-trifluoroacetone-nicotinamide adenine dinucleotide complex showed asymmetry with respect to the active-site conformations of the trifluoroacetone substrate analogue and some catalytic groups. These results are consistent with 19F nuclear magnetic resonance observations of this complex (Bode, J., Blumenstein, M., and Raftery, M. A. (1975), Biochemistry 14, 1153--1160). Different substrate conformations were found on opposite sides of the molecular diad relating subunits whose active centers are in close proximity (the R axis).

Sequence variability and structure of D-glyceraldehyde-3-phosphate dehydrogenase.

The amino acid sequences of pig muscle and of yeast glyceraldehyde-3-phosphate dehydrogenase are compared with the three-dimensional structure of the lobster muscle enzyme. Residues in sheet and helical regions, on the exterior and interior, in subunit and domain interfaces, as well as residues in the active site have been examined for evolutionary conservation. The residues in the first (NAD binding) domain (1-147) are less conserved than residues in the second (catalytic) domain (148-334) probably because there are fewer internal residues and fewer residues involved in interactions between subunits. Residues in subunit interface are conserved to a significantly greater extent than others, and those involved in catalysis are conserved most of all. Patterns of residues in helices and sheets follow those found for other proteins.