Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

Background: One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results: Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with kn...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Leslie Regad, Juliette Martin, Anne-Claude Camproux
• Keywords: Biometrics, BMCBI 2011, Pattern Statistics, Protein Structures, Systematic Extraction