Structure based sequence analysis of viral and cellular protein assemblies.

Authors:
Ranjan V Mannige
Ranjan V Mannige
Harvard University
United States
Vijay S Reddy
Vijay S Reddy
The Scripps Research Institute
United States
Dr. Mauricio Carrillo-Tripp, PhD
Dr. Mauricio Carrillo-Tripp, PhD
Biomolecular Diversity Laboratory, Cinvestav
Associate Profesor
Computational Biophysics
Irapuato, Guanajuato | México

J Struct Biol 2016 12 29;196(3):299-308. Epub 2016 Jul 29.

Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico. Electronic address:

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.

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http://dx.doi.org/10.1016/j.jsb.2016.07.013DOI Listing

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December 2016
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