Praveen Bioperl IJPT 2013

International Journal of Computer Applications, 2012

The prediction for the unknown proteins from Mycobacterium tuberculosis KZN 1435 were carried out for characterization of the proteins in their respective families. In Mycobacterium tuberculosis KZN 1435 out of 1560 genes for hypothetical proteins, functions were predicted for 1221 hypothetical protein whereas, structures for 803 unknown proteins were revealed. The Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs were used for the prediction of functions in the proteins by searching protein databases for the presence of conserved domains; whereas, tertiary structures were constructed using PS2 Server-Protein Structure Prediction server. This study was helpful in understanding functional characteristics of hypothetical proteins in Mycobacterium tuberculosis KZN 1435 as well as their role in the life cycle of the bacterium.

Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen’s proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins making up nearly 70% of the Mycobacterium tuberculosis proteome are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of its genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site–based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.

ijpsr.com

Mycobacterium tuberculosis is a deadly infectious disease, there is rising death of humans every year because of this disease, availability of genome sequences of Mycobacterium tuberculosis has provided tremendous amount of information that can be useful in drug target and new vaccine development. Sequence similarity provides accurate annotation for genes in newly sequenced genomes. In this present work about 107 hypothetical proteins of Mycobacetrium tuberculosis were taken and its functions were predicted using bioinformatics tools BLAST, BLOCKS, COGs, InterProScan and PFP. From our analysis of 107 hypothetical proteins only two shows 100% functions these proteins may serve as target for few antibiotics.

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.

Microbial Informatics and Experimentation, 2012

The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have killed human and other mammals since millennia. Additionally, with the many different mycobacterial sequences available, there is a crucial need for the visualization and the simplification of their data. In this present study, we aim to highlight a comparative genome, proteome and phylogeny analysis between twenty-one mycobacterial (Tuberculosis and non tuberculosis) strains using a set of computational and bioinformatics tools (Pan and Core genome plotting, BLAST matrix and phylogeny analysis). Results: Considerably the result of pan and core genome Plotting demonstrated that less than 1250 Mycobacterium gene families are conserved across all species, and a total set of about 20,000 gene families within the Mycobacterium pan-genome of twenty one mycobacterial genomes. Viewing the BLAST matrix a high similarity was found among the species of the complex Mycobacterium tuberculosis and less conservation is found with other slow growing pathogenic mycobacteria. Phylogeny analysis based on both protein conservation, as well as rRNA clearly resolve known relationships between slow growing mycobacteria.

Electrophoresis, 2000

Human tuberculosis is caused by the intracellular pathogen Mycobacterium tuberculosis. Sequencing of the genome of M. tuberculosis strain H37Rv has predicted 3924 open reading frames, and enabled identification of proteins from this bacterium by peptide mass fingerprinting. Extracellular proteins from the culture medium and proteins in cellular extracts were examined by two-dimensional gel electrophoresis using immobilized pH gradient technology. By mass spectrometry and immunodetection, 49 culture filtrate proteins and 118 lysate proteins were identified, 83 of which were novel. To date, 288 proteins have been identified in M. tuberculosis proteome studies, and a list is presented which includes all identified proteins (available at http://www.ssi.dk/publichealth/tbimmun). The information obtained from the M. tuberculosis proteome so far is discussed in relation to the information obtained from the complete genome sequence.

Biochemical and Biophysical Research Communications, 1998

Proteome studies complement current molecular approaches through analysis of the actively translated portion of the genome (the "functional proteome"). Twodimensional gel electrophoresis (2-DGE) utilising immobilized pH gradients of pH 2.3-5.0 and pH 6.0 -11.0, developed with predetermined regions of overlap compatible with commercially available pH 4.0 -7.0 gradients, permitted the display of a significant portion of the proteome of Mycobacterium tuberculosis H37Rv. A significant portion of the M. tuberculosis proteome, in the molecular mass (M r ) window 5 kDa to 200 kDa and with isoelectric point (pI) between pH 2.3 and 11.0, was visualised for the first time. A total of 493 protein spots were effectively resolved, including 126 spots that could not be seen using standard pH 4.0 -7.0 gradients. These results were used to compare the physical properties of the observed proteins to the theoretical predictions of the recently completed M. tuberculosis H37Rv genome. Most proteins were found in the pI and mass window of pH 4.0 -7.0 and 10 -100 kDa. Analysis of the predicted proteome revealed a bimodal pI distribution, with substantial numbers of proteins in the pI regions 4.0 -7.0 and 9.0 -12.0 as has been seen for the majority of completed genomes. Such data may reveal current limitations in experimental extraction and separation of extremely basic, high M r and hydrophobic proteins via 2-DGE. Conversely, 13 acidic proteins were observed with pI less than the lowest value predicted by the genome. In addition, a subset of small proteins (<10 kDa) were observed within the pI region of pH 5.0 -8.0 that were not predicted by the complete genomic sequence, reflecting the current inability to distinguish small genes from within DNA sequence. This work represents the foundation for comparing the protein expression patterns of different pathogenic and nonpathogenic M. tuberculosis strains. The characterization of M. tuberculosis protein expression, further facilitated by the recent completion of the genome sequence, could aid in developing more effective diagnostic or therapeutic reagents. FIG. 3. Two-dimensional plot of the observed pI and M r of the 493 M. tuberculosis proteins visualised within a series of silver-stained 2D gels. Dashed line represents pI value at which protein expression is greatly reduced. FIG. 4. Two-dimensional plot of the observed pI and M r of 493 M. tuberculosis proteins visualised, and superimposed on the predicted values from 3, 924 conceptually translated ORFs from the complete M. tuberculosis genome. The blue crosses represent the pI and M r of the silver-stained 2-DGE spots and the red circles represent the pI and M r of the conceptually translated ORFs. Dashed boxes serve to highlight the presence of proteins of (i) extremely acidic pI, and (ii) M r Յ 10 kDa, observed experimentally but not represented following predicted proteome plot. Vol. 253, No. 1, 1998 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 72 FIG. 5. (A) Distribution of proteins according to pI for the predicted M. tuberculosis proteome. (B) Distribution of proteins according to pI for the observed M. tuberculosis H37Rv proteome.

Tuberculosis, 2013

Hundreds of putative enzymes from Mycobacterium tuberculosis as well as other mycobacteria remain categorized as "conserved hypothetical proteins" or "hypothetical proteins", offering little or no information on their functional role in pathogenic and non-pathogenic processes. In this study we have predicted the fold and 3-D structure of more than 99% of all proteins encoded in the genome of M. tuberculosis H37Rv. Fold-recognition, database search, 3-D modelling was performed using Protein Homology/analogy Recognition Engine V 2.0 (Phyre 2). These results are used to tentatively assign potential function for unannotated enzymes and proteins. In summary, fold-recognition and structural homology might be used as a complementary tool in genome annotation efforts and furthermore, it can deliver primary sequence-independent information regarding structure, ligands and even substrate specificity for enzymes that display low primary sequence identity with potential homologues in other species.

International Journal of Mycobacteriology, 2013

Background: Mycobacterium tuberculosis (MTB) H 37 Ra is an attenuated tubercle bacillus closely related to the virulent type strain MTB H 37 Rv. In spite of extensive study, variation in virulence between the MTB H 37 Rv and MTB H 37 Ra strains is still to be understood. The difference in protein expression or structure due to mutation may probably be an important factor for the virulence property of MTB H 37 Rv strain. Methods:In this study, a whole proteome comparison between these two strains was carried out using bioinformatics approaches to elucidate differences in their protein sequences. Results:On comparison of whole proteome using NCBI standalone BLAST program between these two strains, 3759 identical proteins in both the strains out of 4003 proteins were revealed in MTB H 37 Rv and 4034 proteins were revealed in MTB H 37 Ra; 244 proteins of MTB H 37 Rv and 260 proteins of MTB H 37 Ra were found to be non-identical. A total of 172 proteins were identified with mutations (Insertions/deletions/substitutions) in MTB H 37 Ra while 53 proteins of MTB H 37 Rv and 85 proteins of MTB H 37 Ra were found to be distinct. Among 244 non-identical proteins, 19 proteins were reported to have an important biological function; In this study, mutation was shown in these proteins of MTB H 37 Ra. This study reports the protein differences with mutations between MTB H 37 Rv and H 37 Ra, which may help in better understanding the pathogenesis and virulence properties of MTB H 37 Rv.

Genome …, 2003

2003 Strong et al. Volume 4, Issue 9, Article R59 Method ... Inference of protein function and protein linkages in Mycobacterium ... Addresses: * Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, University ...