A short survey on protein blocks

Abstract

Protein structures are classically described in terms of secondary structures. Even if the regular secondary structures have relevant physical meaning, their recognition from atomic coordinates has some important limitations such as uncertainties in the assignment of boundaries of helical and β-strand regions. Further, on an average about 50% of all residues are assigned to an irregular state, i.e., the coil. Thus different research teams have focused on abstracting conformation of protein backbone in the localized short stretches. Using different geometric measures, local stretches in protein structures are clustered in a chosen number of states. A prototype representative of the local structures in each cluster is generally defined. These libraries of local structures prototypes are named as “structural alphabets”. We have developed a structural alphabet, named Protein Blocks, not only to approximate the protein structure, but also to predict them from sequence. Since its development, we and other teams have explored numerous new research fields using this structural alphabet. We review here some of the most interesting applications.

Species specific amino acid sequence–protein local structure relationships: An analysis in the light of a structural alphabet

“…Figure 1), described as a series of (, ) dihedral angles corresponding to 5 residues (Joseph et al, 2010a;Joseph et al, 2010b). They were obtained using an unsupervised classifier similar to Kohonen Maps (Kohonen, 2001) and Hidden Markov Models (Rabiner, 1989).…”

“…The 16-state description of local structures in terms of Protein Blocks (PBs) is expected to highlight finer differences in the amino acid preferences in each species (Joseph et al, 2010b).…”

“…The number of prototypes in a library is important for characterizing the local fold (Hunter and Subramaniam, 2003;Martin et al, 2008;Sander et al, 2006;Tung et al, 2007;Unger et al, 1989). The structural alphabet used in this study, is composed of 16 local structure prototypes that are 5 residues long, called Protein Blocks (PBs, see Figure 1) (de Brevern et al, 2000;Joseph et al, 2010a;Joseph et al, 2010b). They efficiently approximate every part of protein structures (de Brevern, 2005) From different eukaryotic kingdoms, three species namely Arabidopsis thaliana (At), Plasmodium falciparum (Pf) and Saccharomyces cerevisiae (Sc) were chosen for the study.…”

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

“…These methods are based on libraries of local backbone structures that represent the frequently occurring regular backbone conformations. With the premise that the secondary structure description in terms of α-helix and β-strands covers only about 50% of all local conformations, several studies attempted to characterize most or all of the backbone structure [22,23]. A library of local backbone conformations that can be used to abstract a complete protein backbone is called as a Structural Alphabet (SA).…”

“…A widely used SA, named Protein Blocks (PBs) [22,[34][35][36][37], was used to develop an efficient method for comparing two protein structures [38]. The structures were translated into PB sequences followed by the alignment of the PB sequences.…”