Archana,University of Lucknow |
Pandey N.,University of Lucknow |
Indian Journal of Agricultural Biochemistry | Year: 2017
To determine the effect of boron (B) on growth and ascorbate-non-protein thiols-cysteine in the leaves and roots of linseed (Linum usitatissimum L. var R-552), seedlings were raised in solution culture with variable boron supply (0.0033, 0.33 and 33 mg B L-1) under controlled conditions in green house. Optimum seedling growth was observed at 0.33 mg B L-1 supply whereas below and above this level seedlings showed growth retardation. Photosynthetic pigments were found to decrease more under excess boron (33 mg B L-1) than deficient (0.0033 mg B L-1). Accumulation of proline, hydrogen peroxide (H2O2) and lipid peroxidation was observed in both leaves and roots under deficient and excess boron supply. The concentration of ascorbate and non-protein thiols decreased with increased activity of ascorbate peroxidase (APX) and glutathione reductase (GR) enzymes was observed in both parts under boron stress. Cysteine concentration was elevated in leaves and decreased in roots. © 2017, Indian Society of Agricultural Biochemists. All rights reserved.
International Journal of Pharmaceutical Sciences Review and Research | Year: 2012
A cervical carcinoma that contained human Papillomavirus (HPV)-16 homologous DNA was analyzed. Each tumour cell genome contained a single, incomplete copy of HPV-16 DNA. The E6 and E7 open reading frames (ORFs) were completely conserved relative to other published HPV-16 sequences. Much of the non-coding region (NCR) was free of base changes, including complete conservation of several regulatory elements. Multiple mutations were identified in the remaining integrated HPV-16 DNA, which was composed of parts of The L1 and E1 ORFs. The extraordinary conservation of the E6/E7 DNA sequence, as compared with other regions of the integrated HPV-16 DNA, supports the role of E6/E7 in tumorigenesis. In the present work T-cell and B-cell epitopes were predicted for HPV Type-16 E7 protein expressed in cervical cancer of human. MHC-1 and MHC-2 epitopes were predicted by ANNPred and MHC2Pred servers respectively and B-cell epitopes were predicted by ABCPred server. In order to find most relevant epitopes among the MHC-1 and MHC-2 predicted epitopes; protein-protein docking studies were carried out. These predicted epitopes might be promising candidates for the vaccine-designing for human Papilloma virus-type 16 E7 protein expressed in cervical cancer.
PubMed | JSBB, Gautam Buddha University, Chhatrapati Shahu Ji Maharaj University, Apex Bioinformatics Center and 2 more.
Type: Journal Article | Journal: Interdisciplinary sciences, computational life sciences | Year: 2016
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.
Saha S.B.,JSBB |
Uttam V.,JSBB |
Verma V.,Chonnam National University
Journal of Clinical Pathology | Year: 2015
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.
Shukla S.,JSBB |
International Journal of Pharma and Bio Sciences | Year: 2015
In the present study E. coli was used for the production of alkaline protease in eight different fermentation media. This bacterium was isolated from soil sample and screened for protease production. The enzyme production from E. coli was estimated using casein as substrate and its molecular weight was determined by SDS-PAGE. The enzyme activity was also studied at different parameters like pH, temperature, carbon source, nitrogen source, metal ions concentration and effect of inhibitors.
Mishra S.K.,JSBB |
Biosciences Biotechnology Research Asia | Year: 2016
Laccase is the model enzymes for multi-copper oxidases can be used in bioremediation, beverage processing, ascorbic acid determination, baking, as a biosensor and to improve food sensory factors. An attempt was made to screen, optimize and production laccase enzyme produced by the consortium of laccase producing Bacillus subtilis. To date, laccases connect mostly been unaided and characterized from flora and fauna and fungi, and unaided fungal laccases are used currently in biotechnological applications. In contrast, tiny is known just approximately bacterial laccases, although recent immediate assume ahead in the combined genome analysis suggests that the enzymes are widespread in bacteria. Since bacterial genetic tools and biotechnological processes are skillfully conventional, therefore developing bacterial laccases would be significantly important. Laccase activity was determined by measuring the oxidation of guaiacol at 530 nm. Laccase activity was maximum when manage at the following conditions, 60 hrs incubation, 30 °C temperature, and pH-5, 2% nitrogen sources, 3 % peptone and beef extract and 2 % carbon sources, glucose and sucrose in the production medium. This research summarizes the distribution of laccases among bacteria, and able to producing maximum laccases at the most favorable conditions.
PubMed | JSBB and Omar Al-Mukhtar University
Type: Journal Article | Journal: Bioinformation | Year: 2014
In the development of multicellularity, signaling proteins has played a very important role. Among them, RAS family is one of the most widely studied protein family. However, evolutionary analysis has been carried out mainly on super family level leaving sub family information in scanty. Thus, a subfamily evolutionary study on RAS evolutionary expansion is imperative as it will aid in better drug designing against dreadful diseases like Cancer and other developmental diseases. The present study was aimed to understand RAS evolution on both holistic as well as reductive level. All human RAS family genes and protein were subjected to BLAST tools to find orthologs and paralogs with different parameters followed by phylogenetic tree generation. Our results clearly showed that H-RAS is the most primitive RAS in higher eukaryotes and then diverged into other RAS family members due to different gene modification events. Furthermore, a site specific selection pressure analysis was carried out using SELECTON server which showed that H-RAS, M-RAS and N-RAS are evolving faster than K-RAS and R-RAS. Thus, the results ascertain a new ground to cancer biologists to exploit negatively selected K-RAS and R-RAS as potent drug targets in cancer therapeutics.
PubMed | JSBB
Type: | Journal: BioMed research international | Year: 2013
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.
PubMed | JSBB
Type: | Journal: Interdisciplinary sciences, computational life sciences | Year: 2015
Determination of the native geometry of the enzymes and ligand complexe 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 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 form is selected. Enzyme data set was retrieved from protein data bank (PDB). 15 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 presence of cofactor. This study will helps in understanding the level of flexibility in protein-ligand interaction for computer aided drug designing.
PubMed | JSBB
Type: Journal Article | Journal: Bioinformation | Year: 2012
The emergence of multidrug-resistant strain of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strain has highlighted the urgent need for the alternative and effective therapeutic approach to combat the menace of this nosocomial pathogen. In the present work novel potential therapeutic drug targets have been identified through the metabolic pathways analysis. All the gene products involved in different metabolic pathways of CA-MRSA in KEGG database were searched against the proteome of Homo sapiens using the BLASTp program and the threshold of E-value was set to as 0.001. After database searching, 152 putative targets were identified. Among all 152 putative targets, 39 genes encoding for putative targets were identified as the essential genes from the DEG database which are indispensable for the survival of CA-MRSA. After extensive literature review, 7 targets were identified as potential therapeutic drug target. These targets are Fructose-bisphosphate aldolase, Phosphoglyceromutase, Purine nucleoside phosphorylase, Uridylate kinase, Tryptophan synthase subunit beta, Acetate kinase and UDP-N-acetylglucosamine 1-carboxyvinyltransferase. Except Uridylate kinase all the identified targets were involved in more than one metabolic pathways of CA-MRSA which underlines the importance of drug targets. These potential therapeutic drug targets can be exploited for the discovery of novel inhibitors for CA-MRSA using the structure based drug design (SBDD) strategy.