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:
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Proteins 2008 Apr;71(1):407-14
Yeast Structural Genomics, IBBMC Université Paris-Sud, CNRS UMR 8619, 91405-Orsay, France.
To evaluate the evolutionary constraints placed on viral proteins by the structure and assembly of the capsid, we calculate Shannon entropies in the aligned sequences of 45 polypeptide chains in 32 icosahedral viruses, and relate these entropies to the residue location in the three-dimensional structure of the capsids. Three categories of residues have entropies lower than the chain average implying that they are better conserved than average: residues that are buried within a subunit (the protein core), residues that contain atoms buried at an interface between subunits (the interface core), and residues that contribute to several such interfaces. The interface core is also conserved in homomeric proteins and in transient protein-protein complexes, which have only one interface whereas capsids have many. Read More
Proteins 2008 Nov;73(3):644-55
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Viral capsids are composed of multiple copies of one or a few chemically distinct capsid proteins and are mostly stabilized by inter subunit protein-protein interactions. There have been efforts to identify and analyze these protein-protein interactions, in terms of their extent and similarity, between the subunit interfaces related by quasi- and icosahedral symmetry. Here, we describe a new method to map quaternary interactions in spherical virus capsids onto polar angle space with respect to the icosahedral symmetry axes using azimuthal orthographic diagrams. Read More
Structure 1998 Feb;6(2):157-71
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
Background: Tobacco ringspot virus (TRSV) is a member of the nepovirus genus of icosahedral RNA plant viruses that cause disease in fruit crops. Nepoviruses, comoviruses and picornaviruses are classified in the picornavirus superfamily. Crystal structures of comoviruses and picornaviruses and the molecular mass of the TRSV subunit (sufficient to accommodate three beta-barrel domains) suggested that nepoviruses may represent a link in the evolution of the picornavirus capsids from a T = 3 icosahedral virus. Read More
Structure 1995 Oct;3(10):1021-30
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Background: Sobemoviruses are a group of RNA plant viruses that have a narrow host range. They are characterized in vitro by their stability, high thermal inactivation point and longevity. The three-dimensional structure of only one virus belonging to this group, southern bean mosaic virus (SBMV), is known. Read More