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Allahābād, India

Singh S.,JSBB | Singh A.K.,Indian Institute of Technology Bombay | Wadhwa G.,Apex Bioinformatics Center | Singh D.B.,Chhatrapati Shahu Ji Maharaj University | And 3 more authors.
Interdisciplinary Sciences: Computational Life Sciences

Determination of the native geometry of the enzymes and ligand complexes is a key step in the process of structure-based drug designing. Enzymes and ligands show flexibility in structural behavior as they come in contact with each other. When ligand binds with active site of the enzyme, in the presence of cofactor some structural changes are expected to occur in the active site. Motivation behind this study is to determine the nature of conformational changes as well as regions where such changes are more pronounced. To measure the structural changes due to cofactor and ligand complex, enzyme in apo, holo and ligand-bound forms is selected. Enzyme data set was retrieved from protein data bank. Fifteen triplet groups were selected for the analysis of structural changes based on selection criteria. Structural features for selected enzymes were compared at the global as well as local region. Accessible surface area for the enzymes in entire triplet set was calculated, which describes the change in accessible surface area upon binding of cofactor and ligand with the enzyme. It was observed that some structural changes take place during binding of ligand in the presence of cofactor. This study will helps in understanding the level of flexibility in protein–ligand interaction for computer-aided drug designing. © 2015, International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg. Source

Saha S.B.,JSBB | Uttam V.,JSBB | Verma V.,Chonnam National University
Journal of Clinical Pathology

Background and aims Despite medical advancements, Escherichia coli-associated infections remain a major public health concern and although an abundant information about E. coli and its antibiotic resistance mechanisms is available, no effective tool exists that integrates gene and genomic data in context to drug resistance, thus raising a need to develop a repository that facilitates integration and assimilation of factors governing drug resistance in E. coli. Descriptions User-friendly Comprehensive Antibiotic resistance Repository of Escherichia coli (u-CARE) is a manually curated catalogue of 52 antibiotics with reported resistance, 107 genes, transcription factors and single nucleotide polymorphism (SNPs) involved in multiple drug resistance of this pathogen. Each gene page provides detailed information about its resistance mechanisms, while antibiotic page consists of summary, chemical description and structural descriptors with links to external public databases like GO, CDD, DEG, Ecocyc, KEGG, Drug Bank, PubChem and UniProt. Moreover, the database integrates this reductive information to holistic data such as strain-specific and segment-specific pathogenic islands and operons. In addition, the database offers rich user interface for the visualisation and retrieval of information using various search criteria such as sequence, keyword, image and class search. Conclusions u-CARE is aimed to cater to the needs of researchers working in the field of antimicrobial drug resistance with minimal knowledge of bioinformatics. This database is also intended as a guide book to medical practitioners to avoid use of antibiotics against which resistance has already been reported in E. coli. Source

Singh S.,JSBB | Sablok G.,Research and Innovation Center | Farmer R.,JSBB | Singh A.K.,Indian Institute of Technology Bombay | And 2 more authors.
BioMed Research International

In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5-TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10 ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was -0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (-13.0 Kcal/Mol) and a log P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection. © 2013 Satendra Singh et al. Source

Singh S.,SHIATS | Yadav S.K.,SHIATS | Mishra P.,SHIATS | Maurya R.,SHIATS | And 5 more authors.
Journal of Pure and Applied Microbiology

1-aminocyclopropane-1-carboxylate (ACC) deaminase promotes plant growth by sequestering and cleaving the ethylene precursor ACC to α-ketobutyrate and ammonium. Many plant growth promoting rhizobacteria producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase as a source of nitrogen has an eminent role in plant nutrition. In this work to perform comparative proteomics analysis of ACCD producing plant growth-promoting rhizobacteria (PGPR) i.e., Azospirillum lipoferum, Phyllobacterium brassicacearum, Pseudomonas fluorescens, Francisella tularensis subsp. holarctica OSU18 and Bacillus cereus. The sequence and phylogenetic analysis of ACCD producing PGPR species represents the common conserved domain belonging to the tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily and closely related to each other. The predicted homology models of ACCD of PGPR have similar protein structure with similar folds often share similar function. This analysis represents the evolutionary conservation and same biochemical function of ACCD producing plant growth-promoting rhizobacteria. Source

Kumawat M.,JSBB | Ahlawat S.,JSBB | Ahlawat N.,SSAHD | Pesingi P.K.,4Veterinary Public Health | And 3 more authors.
Journal of Pure and Applied Microbiology

Salmonella enterica subspecies enterica serovar Enteritidis (SE) and Salmonella enterica subspecies enterica serovar Typhimurium (ST) are the zoonotic Salmonella that colonizes in the intestine of poultry asymptomatically and are transmitted to human by consumption of contaminated foods like meat, eggs and egg products. The PPIases are enzymes that accelerate folding of proline-containing proteins by catalyzing the cis-trans isomerisation, which plays important roles in a variety of stress responses in bacterium. In this study, the Peptidyl prolyl cis-trans isomerases C (ppiC) gene from ST was cloned, sequenced, analyzed and submitted to gene bank (accession number KR054755). The retrieved sequence data analysis, suggested that gene belongs to the parvulin family of peptidyl-prolyl cis/trans isomerases (PPIases, EC of ST. Entertainingly, the ppiC sequence shows about 100% -99% with other Salmonella serovars. The conclusion of this study effectively indicate that ppiC gene of Salmonella is highly conserved in most of the pathogenic Salmonella spp. as analogous to patterns of other serovars. Source

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