Recapitulation of protein family divergence using flexible backbone protein design

TitleRecapitulation of protein family divergence using flexible backbone protein design
Publication TypeJournal Article
Year of Publication2005
AuthorsSaunders, C. T., & Baker D.
JournalJournal of molecular biology
Volume346
Issue2
Pagination631-44
Date Published2005 Feb 18
ISSN0022-2836
KeywordsEvolution, Molecular, Models, Molecular, Molecular Structure, Primary Publication, Protein Conformation, Proteins, src Homology Domains, Structural Homology, Protein
Abstract

We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence search, and optimizing the backbone for a fixed amino acid sequence using atomic-resolution structure prediction. We find that such a flexible backbone design method better recapitulates protein family sequence variation than sequence optimization on fixed backbones or randomly perturbed backbone ensembles for ten diverse protein structures. For the SH3 domain, the backbone structure variation in the family is also better recapitulated than in randomly perturbed backbones. The potential application of this method as a model of protein family evolution is highlighted by a concerted transition to the amino acid sequence in the structural core of one SH3 domain starting from the backbone coordinates of an homologous structure.

Alternate JournalJ. Mol. Biol.
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