Abstract
A large fraction of the proteome is made by proteins that are not permanently monomeric but form oligomeric assemblies, which can be either homo- or hetero-oligomeric. Here it is described that protomers of hetero-oligomeric proteins tend to resemble each other more than expected. This is verified by comparing the level of similarity of pairs of hetero-oligomeric protein protomers and of pairs of proteins that do not interact with each other. This observation, interesting per se, might reflect the evolution of hetero-oligomers from ancestral homo-oligomers, through gene duplication and paralogs divergence. However, other hypotheses cannot be excluded and the observed structural similarity might result from several causes.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-3-680) contains supplementary material, which is available to authorized users.
Highlights
Many proteins associate in vivo with other proteins and form supramolecular assemblies, which may contain (i) two or more copies of the same polypeptide chain (ii) two or more polypeptide chains that have different amino acid sequence, (iii) and even other types of biopolymers, like for example RNA.The reason why proteins are not systematically monomeric is, in general, unknown
The TATA-binding protein (TBP), together with several transcription factors (TFs) and RNA polymerase II, can form the RNA polymerase II preinitiation complex (Lee and Young 2000): TBP is able to recognize the so-called TATA box, a DNA sequence segment that is found about 30 base pairs upstream of the transcription site in some eukaryotic gene promoters; due to its binding to DNA, TBP is recognized by the TFs and forms a heterooligomeric complex that is recognized by RNA polymerase II; each protomer has a different function in the final product (Lee and Young 2000)
Distances on the Proteomic Ramachandran plot (PRplot) The Proteomic Ramachandran Plot (PRplot) is a generalization of the Ramachandran plot, where a protein structure is represented by the average values of the main-chain phi and psi torsion angles (Carugo and Djinović-Carugo 2013)
Summary
Many proteins associate in vivo with other proteins and form supramolecular assemblies, which may contain (i) two or more copies of the same polypeptide chain (ii) two or more polypeptide chains that have different amino acid sequence, (iii) and even other types of biopolymers, like for example RNA.The reason why proteins are not systematically monomeric is, in general, unknown. The TATA-binding protein (TBP), together with several transcription factors (TFs) and RNA polymerase II, can form the RNA polymerase II preinitiation complex (Lee and Young 2000): TBP is able to recognize the so-called TATA box, a DNA sequence segment that is found about 30 base pairs upstream of the transcription site in some eukaryotic gene promoters; due to its binding to DNA, TBP is recognized by the TFs and forms a heterooligomeric complex that is recognized by RNA polymerase II; each protomer has a different function in the final product (Lee and Young 2000) Another example is the [Fe, Ni]-hydrogenase: while the larger subunit of this hetero-dimeric enzyme hosts a bimetallic. There are examples of monomeric Cu, Zn-superoxide dismutases that are perfectly functional and both monomeric and dimeric Cu, Zn-superoxide dismutases are expressed in different strains of E. coli (Bordo et al 1999)
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