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Protein homomers in point-group assembly: Symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains

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Title Protein homomers in point-group assembly: Symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains
 
Creator PEDNEKAR, D
DURANI, S
 
Subject escherichia-coli
allosteric transitions
biological recognition
binding
cation
electrostatics
biomolecules
interfaces
aspartate
residues
symmetry
hotspots
protein-protein interaction
pi-pi interaction
cation-pi interaction
 
Description Oligomerizing to point-group symmetry, protein oligomers need to have the symmetry broken for biologically crucial functions, such as, allosteric regulation, enzyme catalysis, and so forth. In the making of symmetry, based on self assembly, and the breaking of symmetry, based on intermolecular interactions, proteins may manifest, like their other functions, specific scripts over the coding alphabet in side chains. To address the possibility, we analyzed 82 protein homodimers in their C(2)-symmetry-related side chains across noncrystallographic interfaces, to know if they may be identical or distinct in conformation, and thus conserved or broken in symmetry. We find the propensity to conformational mismatch across interfaces correlated with side-chain chemical structure, low to very low in aromatic Trp, Tyr, His, Phe, and Arg, and high to very high in aliphatic Val, Pro, Met, Glu, Ser, Lys, Gln, Asn, and Asp, related not to polarity but, interestingly, to aromaticity of the structure. The organizational plan having aromatics embedded in a hub of aliphatic-nonpolar groups and a surrounding rim of aliphatic-polar groups, called "hotspot," has been known to direct protein-protein interaction. Finding conformational-mismatch propensities of side chains congruous with their specific chemical roles in protein-protein interaction, we propose that aromatic side chains will drive protein homomers to high symmetry, while polar- and nonpolar aliphatic side chains will drive them to the functionally-necessitated breaks of symmetry. Side chains are in their roles as protein-coding alphabet illuminated in the physics, which is discussed.
 
Publisher WILEY-LISS
 
Date 2011-09-01T13:40:49Z
2011-12-26T12:59:40Z
2011-12-27T05:52:18Z
2011-09-01T13:40:49Z
2011-12-26T12:59:40Z
2011-12-27T05:52:18Z
2010
 
Type Article
 
Identifier PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78(14), 3048-3055
0887-3585
http://dx.doi.org/10.1002/prot.22828
http://dspace.library.iitb.ac.in/xmlui/handle/10054/12793
http://hdl.handle.net/10054/12793
 
Language en