More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology.

ABSTRACT: Large-scale genome sequencing gained general importance for life science because functional annotation of otherwise experimentally uncharacterized sequences is made possible by the theory of biomolecular sequence homology. Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. Having the same fold imposes strict conditions over the packing in the hydrophobic core requiring similarity of hydrophobic patterns. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal

SUBMITTER: Wong WC 

PROVIDER: S-EPMC2912341 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature