Protein domain assignment from the recurrence of locally similar structures

作者：Tai Chin Hsien; Sam Vichetra; Gibrat Jean Francois; Garnier Jean; Munson Peter J; Lee Byungkook^*

来源：Proteins: Structure, Function, and Genetics , 2011, 79(3): 853-866.

DOI：10.1002/prot.22923

• domain parsing
• structure comparisons
• clustering
• LSSP
• secondary structures
• symmetric matrix factorization
• singular value decomposition
• pairwise correlation method

Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that arc comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, tor secondary structure elements. In addition it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies.

• 出版日期2011-3