On the origin and highly likely completeness of single-domain protein structures.

ABSTRACT: The size and origin of the protein fold universe is of fundamental and practical importance. Analyzing randomly generated, compact sticky homopolypeptide conformations constructed in generic simplified and all-atom protein models, all have similar folds in the library of solved structures, the Protein Data Bank, and conversely, all compact, single-domain protein structures in the Protein Data Bank have structural analogues in the compact model set. Thus, both sets are highly likely complete, with the protein fold universe arising from compact conformations of hydrogen-bonded, secondary structures. Because side chains are represented by their Cbeta atoms, these results also suggest that the observed protein folds are insensitive to the details of side-chain packing. Sequence specificity ent

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC1413790 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature