Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins.

ABSTRACT: We examine the advantages of going beyond sequence similarity and use both protein three-dimensional (3D) structure prediction and then quaternary structure (docking) of inferred 3D structures to help evaluate whether comparable sequences can fold into homologous structures with sufficient lateral associations for quaternary structure formation. Our test case is the major vault protein (MVP) that oligomerizes in multiple copies to form barrel-like vault particles and is relatively widespread among eukaryotes. We used the iterative threading assembly refinement server (I-TASSER) to predict whether putative MVP sequences identified by BLASTp and PSI Basic Local Alignment Search Tool are structurally similar to the experimentally determined rodent MVP tertiary structures. Then two identical p

SUBMITTER: Daly TK 

PROVIDER: S-EPMC3595041 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature