Structural Annotation of Mycobacterium tuberculosis Proteome

Abstract

Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.

Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

“…Structural models of the Mtb proteome were obtained from a recent study by our group26. Crystal structures of 324 Mtb proteins available in PDB and 2737 comparative models that we generated in that study together account for about 70% of the proteome.…”

“…We also take advantage of the suite of computational algorithms that have been recently developed in our laboratory for binding site detection22, comparison2324 and functional characterization25. Using automated methods for comparing binding pockets2324, a first level function annotation was obtained in that study26. Here, we report (a) characterizing the pocketome to obtain proteome-wide ligand associations, (b) identifying number of pocket types present in Mtb proteome, (c) identifying clusters of similar pockets in the proteome, (d) estimating druggability among such pocket clusters and (e) identifying target sets with a polypharmacological potential.…”

Structural Annotation of the Mycobacterium tuberculosis Proteome

“…Automatically generated models using the Modeller package are made available in a dedicated database called MODBASE (31). For around 70% of the M. tuberculosis genome, structural models with reasonable confidence have been generated (17) (Fig. 1).…”

“…This approach has been utilized to obtain structural information for nearly 70% of the proteome (17). There are already a few excellent review articles on the structural biology of M. tuberculosis describing structural details of proteins involved in important biological processes (12,13,18,19).…”

Structural Analysis of Respirasomes in Electron Transfer Pathway of Acidithiobacillus ferrooxidans: A Computer-Aided Molecular Designing Study

“…Previously, Schoonman et al have suggested that the threading methods are able to predict more accurate models than comparative modeling in cases of low sequence identity (<30%) [43]. Thus, based on the recent studies of successful implementation of threading approach [44][45][46][47][48][49], we carried out template search against the fold databases using several threading algorithms including PHYRE, FUGUE, pGenTHREADER, SAMT02, Genesilico, and Pcons metaservers. Amongst all the results of threading algorithms, only the mosquitocidal holotoxin from Bacillus sphaericus (2VSE) proposed by pGenTHREADER had similar secondary structure as that of Cyc2 with a value of 0.0006, SolvE score of −4.2, and net score of 48.983 amid a high confidence prediction range.…”