Comparative architecture of octahedral protein cages. II. Interplay between structural elements.
In paper I [Janner (2008). Acta Cryst. A64, 494-502], the enclosing forms of the monomers of four octahedral holoenzymes (bacterio and mitochondrial ferritins, small heat-shock protein and sulfur oxygenase reductase) were derived, with vertices at points of a cubic lattice and indexed accordingly. The correspondence between vertices and neighboring residues allows a sequential ordering of the vertices within the polyline defined by the C(alpha) atoms of the primary structure. The alignment of these sequences shows that the form vertices denoted as turning points delimit the elements of the secondary structure (alpha-helices, beta-strands and loops). This relation is analyzed further in a plot of angular changes in orientations of the polyline segments and planes as a function of the residue numbers and of the form vertices, respectively, leading to an alternative characterization of the ternary structure. Finally, two simple connectivity models of monomers, oriented according to the symmetry axes of the octahedral point group 432, suggest possible patterns in the self-assembly process from clusters of monomers to the quaternary structure of the cubic cage.
Janner
Aloysio
A
Theoretical Physics, Radboud University, Toernooiveld, NL-6525 ED Nijmegen, The Netherlands. a.janner@science.ru.nl
D041541:Acidianus / Q000737:chemistry; D000465:Algorithms; D003461:Crystallography; D045285:Desulfovibrio desulfuricans / Q000737:chemistry; D005293:Ferritins / Q000737:chemistry*; D006360:Heat-Shock Proteins / Q000737:chemistry*; D006801:Humans; D017017:Methanococcus / Q000737:chemistry; D008928:Mitochondria / Q000737:chemistry; D008958:Models, Molecular; D010088:Oxidoreductases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry
D006360:Heat-Shock Proteins; D011994:Recombinant Proteins; D005293:Ferritins; D010088:Oxidoreductases