Emergence of symmetry in homooligomeric biological assemblies

TitleEmergence of symmetry in homooligomeric biological assemblies
Publication TypeJournal Article
Year of Publication2008
AuthorsAndré, I., Strauss C. E. M., Kaplan D. B., Bradley P., & Baker D.
JournalProceedings of the National Academy of Sciences of the United States of America
Volume105
Issue42
Pagination16148-52
Date Published2008 Oct 21
ISSN1091-6490
KeywordsComputer Simulation, Models, Biological, Models, Molecular, Primary Publication, Protein Binding, Protein Structure, Quaternary, Proteins
Abstract

Naturally occurring homooligomeric protein complexes exhibit striking internal symmetry. The evolutionary origins of this symmetry have been the subject of considerable speculation; proposals for the advantages associated with symmetry include greater folding efficiency, reduced aggregation, amenability to allosteric regulation, and greater adaptability. An alternative possibility stems from the idea that to contribute to fitness, and hence be subject to evolutionary optimization, a complex must be significantly populated, which implies that the interaction energy between monomers in the ancestors of modern-day complexes must have been sufficient to at least partially overcome the entropic cost of association. Here, we investigate the effects of this bias toward very-low-energy complexes on the distribution of symmetry in primordial homooligomers modeled as randomly interacting pairs of monomers. We demonstrate quantitatively that a bias toward very-low-energy complexes can result in the emergence of symmetry from random ensembles in which the overall frequency of symmetric complexes is vanishingly small. This result is corroborated by using explicit protein-protein docking calculations to generate ensembles of randomly docked complexes: the fraction of these that are symmetric increases from 0.02% in the overall population to >50% in very low energy subpopulations.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
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