Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids

IRAM: virus capsid database and analysis resource

IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1-5 Å). Each capsid's structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences. The diverse functionality of IRAM is valuable to researchers because it integrates different aspects of virus capsids via a user-friendly interface. Such data are critical for studying capsid evolution and patterns of conservation. The IRAM database can also provide initial necessary information for the design of synthetic capsids for various biotechnological applications.

Structure based sequence analysis of viral and cellular protein assemblies

It is well accepted that, in general, protein structural similarity is strongly related to the amino acid sequence identity. To analyze in great detail the correlation, distribution and variation levels of conserved residues in the protein structure, we analyzed all available high-resolution structural data of 5245 cellular complex-forming proteins and 293 spherical virus capsid proteins (VCPs). We categorized and compare them in terms of protein structural regions. In all cases, the buried core residues are the most conserved, followed by the residues at the protein-protein interfaces. The solvent-exposed surface shows greater sequence variations. Our results provide evidence that cellular monomers and VCPs could be two extremes in the quaternary structural space, with cellular dimers and oligomers in between. Moreover, based on statistical analysis, we detected a distinct group of icosahedral virus families whose capsid proteins seem to evolve much slower than the rest of the protein complexes analyzed in this work.