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Search Results: 1 - 7 of 7 matches for " Danishuddin "
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Analysis of PB2 protein from H9N2 and H5N1 avian flu virus
Danishuddin,Asad Ullah Khan
Bioinformation , 2008,
Abstract: Influenza A viruses of subtype H9N2 are wide spread among poultry and other mammalian species. Crossing the species barrier from poultry to human occurred in recent years creating a pandemic of H9N2 virus. It is known that the pathogenicity of H9N2 is lower than H5N1. Nonetheless, it is important to establish the molecular functions of H9N2 viral proteins. We studied mutations in the polymerase protein PB2 of H9N2 from different strains and compared it with the highly pathogenic H5N1. The mutation M294T was found to be important in the N-myristoylation domain of Ck/UP/2573/India/04(H9N2) isolate. Prediction of secondary structures and PROSITE motif assignments were performed for PB2 to gain functional insight. Subsequently, the effect of mutations in secondary structures among strains is discussed.
Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.)
Mohd Danishuddin,Ravish Chatrath,Rajender Singh
Bioinformation , 2011,
Abstract: Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis depicts the involvement of six amino acids in hydrogen bonding (AGP-SThr422-AGP-LMet138, AGP- SArg420-AGP-LGly47, AGP-SSer259-AGP-LSer306, AGP-SGlu241-AGP-LIle311, AGP- SGln113-AGP-LGlu286 and AGP-SGln70-AGP-LLys291). Fifteen amino acids of small subunit were able to make hydrophobic contacts with seventeen amino acids of large subunit. Furthermore, decrease in the solvent accessible surface area in the amino acids involved in interaction were also reported. All the distances were formed in between 2.27 to 3.78 . The present study focussed on heterodimeric structure of (AGPase). This predicted complex not only enhance our understanding of the interaction mechanism between these subunits (AGP-L and AGP-S) but also enable to further study to obtain better variants of this enzyme for the improvement of the plant yield.
Mining and survey of simple sequence repeats in wheat rust Puccinia sp
Rajender Singh,Bharati Pandey,Mohd Danishuddin,Sonia Sheoran
Bioinformation , 2011,
Abstract: The abundance and inherent potential for extensive allelic variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in eukaryotes. In this study, we analyzed and compared the abundance and organisation of SSR in the genome of two important fungal pathogens of wheat, brown or leaf rust (Puccinia triticina) and black or stem rust (Puccinia graminis f. sp. tritici). P. triticina genome with two fold genome size as compared to P. graminis tritici has lower relative abundance and SSR density. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of dinucleotide followed by trinucleotide repeats. More than two-hundred different types of repeat motifs were observed in the genomes. The longest SSR motifs varied in both genomes and some of the repeat motifs are found in higher frequency. The information about survey of relative abundance, relative density, length and frequency of different repeat motifs in Puccinia sp. will be useful for developing SSR markers that could find several applications in analysis of fungal genome such as genetic diversity, population genetics, race identification and acquisition of new virulence.
Phylogenetic analysis of surface proteins of novel H1N1 virus isolated from 2009 pandemic
Mohd Danishuddin,Shahper N Khan,Asad U Khan
Bioinformation , 2009,
Abstract: Swine Influenza Virus (H1N1) is a known causative agent of swine flu. Transmission of Swine Influenza Virus form pig to human is not a common event and may not always cause human influenza. The 2009 outbreak by subtype H1N1 in humans is due to transfer of Swine Influenza Virus from pig to human. Thus to analyze the origin of this novel virus we compared two surface proteins (HA and NA) with influenza viruses of swine, avian and humans isolates recovered from 1918 to 2008 outbreaks. Phylogenetic analyses of hemagglutinin gene from 2009 pandemic found to be clustered with swine influenza virus (H1N2) circulated in U.S.A during the 1999-2004 outbreaks. Whereas, neuraminidase gene was clustered with H1N1 strains isolated from Europe and Asia during 1992-2007 outbreaks. This study concludes that the new H1N1 strain appeared in 2009 outbreak with high pathogenicity to human was originated as result of re-assortment (exchange of gene). Moreover, our data also suggest that the virus will remain sensitive to the pre-existing therapeutic strategies.
Biochemical Characterization of CTX-M-15 from Enterobacter cloacae and Designing a Novel Non-β-Lactam-β-Lactamase Inhibitor
Mohammad Faheem, Md Tabish Rehman, Mohd Danishuddin, Asad U. Khan
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056926
Abstract: The worldwide dissemination of CTX-M type β-lactamases is a threat to human health. Previously, we have reported the spread of blaCTX-M-15 gene in different clinical strains of Enterobacteriaceae from the hospital settings of Aligarh in north India. In view of the varying resistance pattern against cephalosporins and other β-lactam antibiotics, we intended to understand the correlation between MICs and catalytic activity of CTX-M-15. In this study, steady-state kinetic parameters and MICs were determined on E. coli DH5α transformed with blaCTX-M-15 gene that was cloned from Enterobacter cloacae (EC-15) strain of clinical background. The effect of conventional β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) on CTX-M-15 was also studied. We have found that tazobactam is the best among these inhibitors against CTX-M-15. The inhibition characteristic of tazobactam is defined by its very low IC50 value (6 nM), high affinity (Ki = 0.017 μM) and better acylation efficiency (k+2/K′ = 0.44 μM?1s?1). It forms an acyl-enzyme covalent complex, which is quite stable (k+3 = 0.0057 s?1). Since increasing resistance has been reported against conventional β-lactam antibiotic-inhibitor combinations, we aspire to design a non-β-lactam core containing β-lactamase inhibitor. For this, we screened ZINC database and performed molecular docking to identify a potential non-β-lactam based inhibitor (ZINC03787097). The MICs of cephalosporin antibiotics in combination with this inhibitor gave promising results. Steady-state kinetics and molecular docking studies showed that ZINC03787097 is a reversible inhibitor which binds non-covalently to the active site of the enzyme through hydrogen bonds and hydrophobic interactions. Though, it’s IC50 (180 nM) is much higher than tazobactam, it has good affinity for CTX-M-15 (Ki = 0.388 μM). This study concludes that ZINC03787097 compound can be used as seed molecule to design more efficient non-β-lactam containing β-lactamase inhibitor that could evade pre-existing bacterial resistance mechanisms.
Efficacy of E. officinalis on the Cariogenic Properties of Streptococcus mutans: A Novel and Alternative Approach to Suppress Quorum-Sensing Mechanism
Sadaf Hasan, Mohd Danishuddin, Mohd Adil, Kunal Singh, Praveen K. Verma, Asad U. Khan
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040319
Abstract: The present study was focused on evaluating the potential of Emblica officinalis against cariogenic properties of Streptococcus mutans, a causative microorganism for caries. The effect of crude extract and ethanolic fraction from Emblica officinalis fruit was analysed against S. mutans. The sub-MIC concentrations of crude and ethanolic fraction of E. officinalis were evaluated for its cariogenic properties such as acid production, biofilm formation, cell-surface hydrophobicity, glucan production, sucrose-dependent and independent adherence. Its effect on biofilm architecture was also investigated with the help of confocal and scanning electron microscopy (SEM). Moreover, expression of genes involved in biofilm formation was also studied by quantitative RT- PCR. This study showed 50% reduction in adherence at concentrations 156 μg/ and 312.5 μg/ml of crude extract and ethanolic fraction respectively. However, the biofilm was reduced to 50% in the presence of crude extract (39.04 μg/ml) and ethanolic fraction (78.08 μg/ml). Furthermore, effective reduction was observed in the glucan synthesis and cell surface hydrophobicity. The qRT-PCR revealed significant suppression of the genes involved in its virulence. Confocal and scanning electron microscopy clearly depicted the obliteration of biofilm structure with reference to control. Hence, this study reveals the potential of E. officinalis fruit extracts as an alternative and complementary medicine for dental caries by inhibiting the virulence factors of Streptococcus mutans.
Inhibition of N-Terminal Lysines Acetylation and Transcription Factor Assembly by Epirubicin Induced Deranged Cell Homeostasis
Shahper N. Khan, Mohd Danishuddin, Bhavna Varshney, Sunil K. Lal, Asad U. Khan
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051850
Abstract: Epirubicin (EPI), an anthracycline antitumour antibiotic, is a known intercalating and DNA damaging agent. Here, we study the molecular interaction of EPI with histones and other cellular targets. EPI binding with histone core protein was predicted with spectroscopic and computational techniques. The molecular distance r, between donor (histone H3) and acceptor (EPI) was estimated using F?rster’s theory of non-radiation energy transfer and the detailed binding phenomenon is expounded. Interestingly, the concentration dependent reduction in the acetylated states of histone H3 K9/K14 was observed suggesting more repressed chromatin state on EPI treatment. Its binding site near N-terminal lysines is further characterized by thermodynamic determinants and molecular docking studies. Specific DNA binding and inhibition of transcription factor (Tf)-DNA complex formation implicates EPI induced transcriptional inhibition. EPI also showed significant cell cycle arrest in drug treated cells. Chromatin fragmentation and loss of membrane integrity in EPI treated cells is suggestive of their commitment to cell death. This study provides an analysis of nucleosome dynamics during EPI treatment and provides a novel insight into its action.
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