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2024-03-29T00:47:34Z
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2012-02-28T16:07:47Z
2012-02-28T16:07:47Z
http://crdd.osdd.net/open/id/eprint/1116
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1116
2012-02-28T16:07:47Z
Interaction between Vibrio mimicus and Acanthamoeba castellanii.
Vibrio mimicus is a Gram-negative bacterium, which causes gastroenteritis and is closely related to Vibrio cholerae. The environmental reservoir of this bacterium is far from defined. Acanthamoeba as well as Vibrio species are found in diverse aquatic environments. The present study was aimed to investigate the ability of A. castellanii to host V. mimicus, the role of bacterial protease on interaction with A. castellanii and to disclose the ability of cysts to protect intracellular V. mimicus. Co-cultivation, viable counts, gentamicin assay, electron microscopy and statistical analysis showed that co-cultivation of wild type and luxO mutant of V. mimicus strains with A. castellanii did not inhibit growth of the amoeba. On the other hand co-cultivation enhanced growth and survival of V. mimicus strains. Vibrio mimicus showed intracellular behaviour because bacteria were found to be localized in the cytoplasm of amoeba trophozoites and remain viable for 14 days. The cysts protected intracellular V. mimicus from high level of gentamicin. The intracellular growth of V. mimicus in A. castellanii suggests a role of A. castellanii as a host for V. mimicus.
Hadi Abd
Soni Priya Valeru
Susan Marouf Sami
Amir Saeed
Saumya Raychaudhuri
Gunnar Sandström
2012-09-11T06:09:57Z
2012-09-11T06:09:57Z
http://crdd.osdd.net/open/id/eprint/1186
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1186
2012-09-11T06:09:57Z
Development of Bioinformatics tools for understanding RNA interference pathway.
Firoz Ahmed
2011-12-08T19:32:12Z
2011-12-08T19:32:12Z
http://crdd.osdd.net/open/id/eprint/539
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/539
2011-12-08T19:32:12Z
Redox-mediated interactions of VHb (Vitreoscilla haemoglobin) with OxyR: novel regulation of VHb biosynthesis under oxidative stress.
The bacterial haemoglobin from Vitreoscilla, VHb, displays several unusual properties that are unique among the globin family. When the gene encoding VHb, vgb, is expressed from its natural promoter in either Vitreoscilla or Escherichia coli, the level of VHb increases more than 50-fold under hypoxic conditions and decreases significantly during oxidative stress, suggesting similar functioning of the vgb promoter in both organisms. In the present study we show that expression of VHb in E. coli induced the antioxidant genes katG (catalase-peroxidase G) and sodA (superoxide dismutase A) and conferred significant protection from oxidative stress. In contrast, when vgb was expressed in an oxyR mutant of E. coli, VHb levels increased and the strain showed high sensitivity to oxidative stress without induction of antioxidant genes; this indicates the involvement of the oxidative stress regulator OxyR in mediating the protective effect of VHb under oxidative stress. A putative OxyR-binding site was identified within the vgb promoter and a gel-shift assay confirmed its interaction with oxidized OxyR, an interaction which was disrupted by the reduced form of the transcriptional activator Fnr (fumurate and nitrate reductase). This suggested that the redox state of OxyR and Fnr modulates their interaction with the vgb promoter. VHb associated with reduced OxyR in two-hybrid screen experiments and in vitro, converting it into an oxidized state in the presence of NADH, a condition where VHb is known to generate H2O2. These observations unveil a novel mechanism by which VHb may transmit signals to OxyR to autoregulate its own biosynthesis, simultaneously activating oxidative stress functions. The activation of OxyR via VHb, reported in the present paper for the first time, suggests the involvement of VHb in transcriptional control of many other genes as well.
Arvind Anand
Brian T Duk
Sandeep Singh
Meltem Y Akbas
Dale A Webster
Benjamin C Stark
Kanak L Dikshit
2012-09-11T04:06:08Z
2012-09-11T04:06:08Z
http://crdd.osdd.net/open/id/eprint/1172
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1172
2012-09-11T04:06:08Z
Studies on the catalytic mechanism of plasminogen activation by streptokinase.
Rachna Aneja
2012-02-28T16:09:28Z
2012-02-28T16:09:28Z
http://crdd.osdd.net/open/id/eprint/1104
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1104
2012-02-28T16:09:28Z
Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake.
A novel Gram-stain-negative, rod-shaped, non-motile bacterium, strain LW1(T), was isolated from a water sample collected at a depth of 3.5 m from Lonar Lake, Buldhana district, Maharashtra, India. The cell suspension was reddish-orange due to the presence of carotenoids. Strain LW1(T) was positive for catalase, oxidase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase, urease and lipase. Fatty acids were dominated by branched-chain fatty acids (>76 %), with a high abundance of iso-C(15 : 0) (48 %), anteiso-C(15 : 0) (7 %) and iso-C(17 : 0) 3-OH (11 %). Strain LW1(T) contained MK-4 and MK-7 as the major respiratory quinones and phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as the major phospholipids. A blast sequence similarity search based on 16S rRNA gene sequences indicated that members of the genera Belliella and Aquiflexum were the nearest phylogenetic neighbours with similarities of 91.8-92.3 %. Phylogenetic analyses indicated that strain LW1(T) formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Aquiflexum, Cyclobacterium, Echinicola and Algoriphagus. Based on the above-mentioned phenotypic and phylogenetic characteristics, it is proposed that strain LW1(T) represents a novel species in a new genus, Indibacter alkaliphilus gen. nov., sp. nov. (type strain LW1(T)=KCTC 22604(T)=CCUG 57479(T)). The genomic DNA G+C content of strain LW1(T) is 42.7+/-1 mol%.
P Anil Kumar
T N R Srinivas
S Madhu
R Manorama
S Shivaji
2012-02-28T16:09:35Z
2012-02-28T16:09:35Z
http://crdd.osdd.net/open/id/eprint/1103
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1103
2012-02-28T16:09:35Z
Nitritalea halalkaliphila gen. nov., sp. nov., an alkaliphilic bacterium of the family 'Cyclobacteriaceae', phylum Bacteroidetes.
A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7(T), was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids were dominated by large amounts of iso-C₁₅:₀ (59.6 %) and iso-C₁₇:₀ 3-OH (8.9 %). Strain LW7(T) contained MK-4 and MK-5 as the major respiratory quinones and phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. 16S rRNA gene sequence analysis indicated that Belliella baltica, a member of family 'Cyclobacteriaceae' (phylum Bacteroidetes), is the closest related species, with a sequence similarity of 94.0 % to the type strain. Other members of the family 'Cyclobacteriaceae' had sequence similarities of < 93.3 %. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain LW7(T) is proposed as a representative of a new genus and species, Nitritalea halalkaliphila gen. nov., sp. nov. The type strain of Nitritalea halalkaliphila is LW7(T) (=CCUG 57665(T) =JCM 15946(T) =NCCB 100279(T)). The genomic DNA G+C of strain LW7(T) is 49 mol%.
P Anil Kumar
T N R Srinivas
P Pavan Kumar
S Madhu
S Shivaji
2011-12-08T19:32:41Z
2011-12-08T19:32:41Z
http://crdd.osdd.net/open/id/eprint/543
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/543
2011-12-08T19:32:41Z
AntigenDB: an immunoinformatics database of pathogen antigens.
The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning pathogens, virulence factors and antigenic epitopes has resulted in many useful databases. However, most such immunological databases focus almost exclusively on antigens where epitopes are known and ignore those for which epitope information was unavailable. We have compiled more than 500 antigens into the AntigenDB database, making use of the literature and other immunological resources. These antigens come from 44 important pathogenic species. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases. We shall update AntigenDB on a rolling basis, regularly adding antigens from other organisms and extra data analysis tools. AntigenDB is available freely at http://www.imtech.res.in/raghava/antigendb and its mirror site http://www.bic.uams.edu/raghava/antigendb.
Hifzur Rahman Ansari
Darren R Flower
G.P.S. Raghava
2011-12-08T19:30:25Z
2012-03-22T09:45:11Z
http://crdd.osdd.net/open/id/eprint/525
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/525
2011-12-08T19:30:25Z
Identification of NAD interacting residues in proteins.
For the first time a sequence-based method has been developed for the prediction of NAD binding proteins and their interacting residues, in the absence of any prior structural information. The present model will aid in the understanding of NAD+ dependent mechanisms of action in the cell. To provide service to the scientific community, we have developed a user-friendly web server, which is available from URL http://www.imtech.res.in/raghava/nadbinder/.
Hifzur Rahman Ansari
G.P.S. Raghava
2011-12-08T18:57:18Z
2011-12-08T18:57:18Z
http://crdd.osdd.net/open/id/eprint/491
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/491
2011-12-08T18:57:18Z
Identification of conformational B-cell Epitopes in an antigen from its primary sequence.
This study demonstrates that prediction of conformational B-cell epitope in an antigen is possible from is primary sequence. This study will be very useful in predicting conformational B-cell epitopes in antigens whose tertiary structures are not available. A web server CBTOPE has been developed for predicting B-cell epitope http://www.imtech.res.in/raghava/cbtope/.
Hifzur Rahman Ansari
G.P.S. Raghava
2012-02-28T16:09:15Z
2015-01-09T09:45:01Z
http://crdd.osdd.net/open/id/eprint/1106
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1106
2012-02-28T16:09:15Z
Isolation and characterization of a Pseudomonas sp. strain IITR01 capable of degrading α-endosulfan and endosulfan sulfate.
This study describes toxic ES degradation by a Pseudomonas species that may be utilized for the bioremediation of the industrial soils contaminated with ES residues.
A Bajaj
Anuj Pathak
M R Mudiam
Shanmugam Mayilraj
Natesan Manickam
2012-02-28T16:09:04Z
2012-02-28T16:09:04Z
http://crdd.osdd.net/open/id/eprint/1108
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1108
2012-02-28T16:09:04Z
Actinomycetal diversity of western region of Madhya Pradesh
Actinomycetes are peculiar group of microorganisms with numerous members having different
kinds of features and extensive commercial importance. The strains present in the soil depend on the
geographical area and climatic conditions. A collection of Actinomycetes was developed, predominating
Streptomycetes. Enzyme profiling for all the cultures was performed. The selected cultures were
characterized biochemically. 16S rRNA sequencing was performed to identify the isolates to genus
level.
S. Bhasin
Swaranjit Singh Cameotra
H.A. Modi
2012-09-11T06:32:30Z
2012-09-11T06:32:30Z
http://crdd.osdd.net/open/id/eprint/1191
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1191
2012-09-11T06:32:30Z
Molecular and Biochemical studies of the genes involved in xylose metabolism in debaryomyces hansenii.
Dipanwita Biswas
2011-12-08T18:59:01Z
2012-04-02T06:43:16Z
http://crdd.osdd.net/open/id/eprint/501
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/501
2011-12-08T18:59:01Z
Cloning and characterization of thermotolerant xylitol dehydrogenases from yeast Pichia angusta.
Pichia angusta (syn. Hansenula polymorpha) represents one of the rare yeast that can grow and ferment both xylose and glucose at higher temperature (50°C). However, little is known about the enzymes involved in xylose utilization from this species. Previous studies indicated the presence of one xylose reductase and two xylitol dehydrogenase genes in P. angusta. In this study, we have expressed both xylitol dehydrogenases (PaXdh1p and PaXdh2p) in Escherichia coli and purified them as 6X-Histidine-tagged proteins. Biochemical characterization of the recombinant proteins reveals that both PaXdh1p and PaXdh2p are thermotolerant enzymes. PaXdh2p contains a catalytic and a structural Zn atom. However, the structural Zn atom is not present in PaXdh1p. Both enzymes also differ in their affinity for the substrate as well as in the catalytic efficiency. Through mutagenesis and modeling approaches, we have also identified residues important for catalysis and substrate binding.
Dipanwita Biswas
Manish Datt
K Ganesan
Alok K Mondal
2012-09-11T06:26:41Z
2012-09-11T06:26:41Z
http://crdd.osdd.net/open/id/eprint/1189
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1189
2012-09-11T06:26:41Z
Immunochemical methods for Biomonitoring of 2, 4-dichlorophe.
Robin C Boro
2012-02-28T16:07:10Z
2015-01-08T10:33:13Z
http://crdd.osdd.net/open/id/eprint/1121
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1121
2012-02-28T16:07:10Z
Biosurfactant-enhanced bioremediation of hydrophobic pollutants.
Biosurfactants are surface-active compounds synthesized by a wide variety of micro-organisms. They are molecules that have both hydrophobic and -philic domains and are capable of lowering the surface tension and the interfacial tension of the growth medium. Biosurfactants possess different chemical structures—lipopeptides, glycolipids, neutral lipids, and fatty acids. They are nontoxic biomolecules that are biodegradable. Biosurfactants also exhibit strong emulsification of hydrophobic compounds and form stable emulsions. Polycyclic aromatic hydrocarbons (PAHs), crude oil sludge, and pesticides can be toxic, mutagenic, and carcinogenic compounds that pollute the environment. They are released into the environment as a result of oil spillage and by-products of coal treatment processes. The low water solubility of these compounds limits their availability to microorganisms, which is a potential problem for bioremediation of contaminated sites. Microbially produced surfactants enhance the bioavailability of these hydrophobic compounds for bioremediation. Therefore, biosurfactant-enhanced solubility of pollutants has potential bioremediation applications
Swaranjit Singh Cameotra
R S Makkar
2012-09-11T04:18:53Z
2012-09-11T04:18:53Z
http://crdd.osdd.net/open/id/eprint/1174
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1174
2012-09-11T04:18:53Z
Archana Chauhan (2010). Molecular and Biochemical Characterization of p- Nirophenol/chlorontrophenol Degradation pathways of Bacteria.
Archana Chauhan
2011-12-08T19:19:07Z
2012-04-03T07:03:14Z
http://crdd.osdd.net/open/id/eprint/518
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/518
2011-12-08T19:19:07Z
Biodegradation: gaining insight through proteomics.
Biodegradation, a generic term used to describe methodologies to affect cleanup of environmental pollutants, has come up as an improved substitute for ineffective and expensive physico-chemical remediation methods. However, lack of information about the factors controlling the growth and metabolism of microorganisms in the polluted environment often limits its implementation. Recent advances in the understanding of biogeochemical processes and genomics have opened up new perspectives towards new opportunities of pollution abatement. High throughput genomic techniques have revolutionized the remediation process leading to breakthroughs in characterizing proteomes, metabolomes and phenotypes for organisms, communities and populations. These new techniques have allowed us to address longstanding questions regarding the molecular mechanisms that may control the mineralization processes and have an in-depth understanding of microbial community structure and stress responses. In order to explore insights of biodegradation this article discusses ways in which proteomics may be able to meet challenges in biodegradation.
Archana Chauhan
R K Jain
2011-12-08T19:17:51Z
2011-12-08T19:17:51Z
http://crdd.osdd.net/open/id/eprint/514
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/514
2011-12-08T19:17:51Z
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information.
These results show that PSSM based method performs better than single sequence based method. The prediction models based on dipeptides or tripeptides are more accurate than the traditional model based on single residue. A web server "GTPBinder" http://www.imtech.res.in/raghava/gtpbinder/ based on above models has been developed for predicting GTP interacting residues in a protein.
Jagat S Chauhan
Nitish K Mishra
G.P.S. Raghava
2012-02-28T16:09:41Z
2012-03-29T09:36:33Z
http://crdd.osdd.net/open/id/eprint/1102
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1102
2012-02-28T16:09:41Z
The role of culture collections as an interface between providers and users: the example of yeasts.
The importance and species diversity of yeasts in food production are described, including a listing of agricultural applications. Two yeast species were selected for case studies on distribution patterns from microbial culture collections: the high representation of Saccharomyces cerevisiae in culture collections enabled global comparison, while Dekkera bruxellensis deposits and distributions were analyzed from the perspective of a single culture collection. In conclusion, culture collections need to cover temporal gaps between deposit and application of strains. The further development of culture collections in countries of high but underexplored species diversity should facilitate the conservation and management of microbial resources.
H M Daniel
G S Prasad
2012-09-11T04:35:49Z
2012-09-11T04:35:49Z
http://crdd.osdd.net/open/id/eprint/1179
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1179
2012-09-11T04:35:49Z
Studies on Nucleoside Diphosphate kinase from Intracellular pathogens.
Haider Hussain Dar
2011-12-08T19:16:14Z
2011-12-08T19:16:14Z
http://crdd.osdd.net/open/id/eprint/510
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/510
2011-12-08T19:16:14Z
Intermolecular phosphotransfer is crucial for efficient catalytic activity of nucleoside diphosphate kinase.
NDK (nucleoside diphosphate kinase) is primarily involved in maintaining cellular nucleotide pools in both prokaryotes and eukaryotes. We cloned ndk from Salmonella typhimurium and expressed it in Escherichia coli as a histidine-tagged protein. The Ni-NTA (Ni(2+)-nitrilotriacetate)-purified protein (sNDK) was found to be tetrameric with a monomeric unit molecular mass of approximately 18 kDa. The sNDK exhibited bivalent-cation-dependent autophosphorylation at a wide range of pH values and the phosphorylation withstands acid or alkali treatment. Surprisingly, nucleoside diphosphates did not behave as 'true inhibitors' of autophosphorylation activity. The sNDK displayed phosphotransfer activity from nucleoside triphosphates to nucleoside diphosphates; however, it was Mg(2+)/Mn(2+)-dependent. Mutational analysis established His(117) as the predominantly phosphorylating residue in sNDK. Although it is a histidine kinase, we found that substitution of Ser(119) with alanine/glutamate significantly affected the autophosphorylation, as well as the NTP-synthesizing ability of sNDK. Interestingly, the mixture of inactive (H117A) and partially active (S119A) proteins was found to be catalytically more efficient than the presence of corresponding amounts of active population, advocating transfer of phosphate from phospho-His(117) to Ser(119). Consistent with this observation, the Ni-NTA-purified H117A protein, obtained following co-expression of both of the mutant constructs [His-tagged H117A and GST (glutathione transferase)-tagged S119A] in E. coli, exhibited autophosphorylation, thereby alluding to intermolecular phosphotransfer between His(117) and Ser(119). Although this housekeeping enzyme has long been discovered and characterized from different sources, the results of the present study portray how Ser(119) in sNDK is phosphorylated. Furthermore, our findings illustrate for the first time that the intermolecular phosphotransfer is mandatory for the efficient NTP synthesis in any NDK.
Haider Hussain Dar
Pradip K Chakraborti
2012-02-28T16:08:13Z
2012-02-28T16:08:13Z
http://crdd.osdd.net/open/id/eprint/1114
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1114
2012-02-28T16:08:13Z
A single-amino-acid substitution in the C terminus of PhoP determines DNA-binding specificity of the virulence-associated response regulator from Mycobacterium tuberculosis.
The Mycobacterium tuberculosis PhoP-PhoR two-component system is essential for virulence in animal models of tuberculosis. Genetic and biochemical studies indicate that PhoP regulates the expression of more than 110 genes in M. tuberculosis. The C-terminal effector domain of PhoP exhibits a winged helix-turn-helix motif with the molecular surfaces around the recognition helix (alpha 8) displaying strong positive electrostatic potential, suggesting its role in DNA binding and nucleotide sequence recognition. Here, the relative importance of interfacial alpha 8-DNA contacts has been tested through rational mutagenesis coupled with in vitro binding-affinity studies. Most PhoP mutants, each with a potential DNA contacting residue replaced with Ala, had significantly reduced DNA binding affinity. However, substitution of nonconserved Glu215 had a major effect on the specificity of recognition. Although lack of specificity does not necessarily correlate with gross change in the overall DNA binding properties of PhoP, structural superposition of the PhoP C-domain on the Escherichia coli PhoB C-domain-DNA complex suggests a base-specific interaction between Glu215 of PhoP and the ninth base of the DR1 repeat motif. Biochemical experiments corroborate these results, showing that DNA recognition specificity can be altered by as little as a single residue change of the protein or a single base change of the DNA. The results have implications for the mechanism of sequence-specific DNA binding by PhoP.
Arijit Kumar Das
Anuj Pathak
Akesh Sinha
Manish Datt
Balvinder Singh
Subramanian Karthikeyan
Dibyendu Sarkar
2012-09-11T04:21:59Z
2012-09-11T04:21:59Z
http://crdd.osdd.net/open/id/eprint/1175
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1175
2012-09-11T04:21:59Z
Modeling protein-DNA recognition -an in Silico approach.
Manish Datt
2011-12-08T19:31:41Z
2011-12-08T19:31:41Z
http://crdd.osdd.net/open/id/eprint/535
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/535
2011-12-08T19:31:41Z
Hexafluoroisopropanol-induced helix-sheet transition of stem bromelain: correlation to function.
Stem bromelain is a proteolytic phytoprotein with a variety of therapeutic effects. Understanding its structural properties could provide insight into the mechanisms underlying its clinical utility. Stem bromelain was evaluated for its conformational and folding properties at the pH conditions it encounters when administered orally. It exists as a partially folded intermediate at pH 2.0. The conformational changes to this intermediate state were evaluated using fluorinated alcohols known to induce changes similar to those seen in vivo. Studies using circular dichroism, fluorescence emission spectroscopy, binding of the hydrophobic dye 1-anilino-8-naphthalene sulfonic acid and mass spectrometry indicate that treatment with 10-30% hexafluoroisopropanol induces the partially folded intermediate to adopt much of the native protein's secondary structure, but only a rudimentary tertiary structure, characteristic of the molten globule state. Addition of slightly higher concentrations of hexafluoroisopropanol caused transformation from an alpha-helix to a beta-sheet and induced formation of a compact nonnative structure. This nonnative form was more inhibitory of cell survival than either the native or the partially folded intermediate forms, as measured by enhanced suppression of proliferative cues (e.g., extracellular-signal-regulated kinase) and initiation of apoptotic events. The nonnative form also showed better antitumorigenic properties, as evaluated using an induced two-stage mouse skin papilloma model. In contrast, the nonnative state showed only a fraction of the proteolytic activity of the native form. This study demonstrates that hexafluoroisopropanol can induce a conformational change in stem bromelain to a form with potentially useful therapeutic properties different from those of the native protein.
Sandeep Dave
H Kitdorlang Dkhar
Manvendra Pratap Singh
Garima Gupta
Vemika Chandra
Sahil Mahajan
Pawan Gupta
2011-12-08T19:18:04Z
2011-12-08T19:18:04Z
http://crdd.osdd.net/open/id/eprint/515
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/515
2011-12-08T19:18:04Z
Specific molten globule conformation of stem bromelain at alkaline pH.
Stem bromelain (SBM), a therapeutic protein, is rapidly absorbed across the gut epithelium. Because SBM encounters an alkaline pH at its principal site of absorption, we investigated the alkaline-induced denaturation of SBM. From pH 7 to 10, the protein's secondary structure remained the same, although a slight loss of tertiary structure was observed. Above pH 10, there was a significant and irreversible loss of secondary and tertiary structure. At pH 10, SBM showed enhanced tryptophan fluorescence, however, the number of accessible tryptophans remained the same. The thermodynamics of temperature transition at pH 7 and 10 were strikingly different, with the former showing a two-phase transition endotherm, and the latter a broad non-two-state transition. At pH 10, SBM showed a significant increase in 8-anilino-1-naphthalene-sulfonate binding relative to the native state, suggestive of a specific molten globule (SMG) state. These studies suggest a distinct conformational rearrangement in SBM, at the protein's isoelectric point.
Sandeep Dave
Sahil Mahajan
Vemika Chandra
H Kitdorlang Dkhar
- Sambhavi
Pawan Gupta
2012-09-11T06:40:16Z
2012-09-11T06:40:16Z
http://crdd.osdd.net/open/id/eprint/1193
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1193
2012-09-11T06:40:16Z
Studies on Bioremediation by metal tolerant bacteria with special emphasis on selenium.
Soniya Dhanjal
2011-12-08T19:00:24Z
2011-12-08T19:00:24Z
http://crdd.osdd.net/open/id/eprint/507
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/507
2011-12-08T19:00:24Z
Aerobic biogenesis of selenium nanospheres by Bacillus cereus isolated from coalmine soil.
This bacterial isolate has the potential to be used as a bionanofactory for the synthesis of stable, nearly monodisperse Se 0 nanoparticles as well as for detoxification of the toxic selenite anions in the environment. A hypothetical mechanism for the biogenesis of selenium nanoparticles (SNs) involving membrane associated reductase enzyme(s) that reduces selenite (SeO3(2-)) to Se 0 through electron shuttle enzymatic metal reduction process has been proposed.
Soniya Dhanjal
Swaranjit Singh Cameotra
2011-12-08T19:22:58Z
2011-12-08T19:22:58Z
http://crdd.osdd.net/open/id/eprint/522
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/522
2011-12-08T19:22:58Z
Structures of differently aggregated and precipitated forms of gamma B crystallin: an FTIR spectroscopic and EM study.
The lens protein, gamma B-crystallin, precipitates during cataract formation. As a recombinant protein, in aqueous solution, gamma B aggregates and precipitates upon heating, cooling, exposure to ultraviolet light, or refolding from a denatured state. We have studied soluble gamma B crystallin, as well as each of the above aggregated forms, to determine whether gamma B's polypeptide chain is differently organized in each form. For this purpose, we used : (a) Fourier Transform Infra Red (FTIR) spectroscopy in the horizontal attenuated total reflectance (HATR) mode, to examine changes in secondary structural content, and (b) transmission electron microscopy (TEM) to examine gross morphological differences. The peak of the gamma B FTIR amide I band shifts from approximately 1633 cm(-1) to approximately 1618 cm(-1) in heat-, UV- and refolding-induced gamma B precipitates, indicating that narrow beta sheets with fewer strands and higher strand twist angles are becoming reorganized into wider, more planar sheets containing larger numbers of shorter strands, with smaller twist angles. In contrast, in cold-induced precipitates, a loss of anti-parallel beta sheet content is observed. This difference is partly explained by the differential effects of temperature on different non-covalent interactions stabilizing protein structures. The native beta sheet content of gamma B crystallin (approximately 50%) is raised in heat- (approximately 60%) and refolding-induced (approximately 58%) precipitates, but lowered in cold- (approximately 41%), and UV-induced (approximately 44%) precipitates. Cold precipitates also display approximately 26% helical content. All four aggregates have distinctively different morphological characteristics; this appears to be in keeping with their distinctively different secondary structural contents.
Uzma Fatima
Swati Sharma
Purnananda Guptasarma
2011-12-08T18:58:40Z
2011-12-08T18:58:40Z
http://crdd.osdd.net/open/id/eprint/499
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/499
2011-12-08T18:58:40Z
Pentoxifylline augments TRAIL/Apo2L mediated apoptosis in cutaneous T cell lymphoma (HuT-78 and MyLa) by modulating the expression of antiapoptotic proteins and death receptors.
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL/Apo2L) is a promising anticancer agent but cutaneous T lymphoma cells (CTCL) are less sensitive to TRAIL-induced apoptosis. Here, we report that pentoxifylline (PTX), a phosphodiesterase inhibitor, augments TRAIL-mediated apoptosis in HuT-78 and MyLa cells through modulating extrinsic death receptors and intrinsic mitochondria dependent pathways. Our results clearly show that PTX augments TRAIL-mediated activation of caspase-8 and induces cleavage of Bid, although PTX alone cannot activate caspase-8. This is followed by cytochrome c release and subsequent, activation of caspase-9 and caspase-3 and cleavage of poly (ADP ribose) polymerase (PARP). Combined treatment downregulates the expression of various antiapoptotic proteins including c-FLIP, Bcl-xl, cIAP-1, cIAP-2 and XIAP. PTX induces the expression of death receptors DR4 and DR5 on cell surface of both the cell types where c-Jun NH2-terminal kinase (JNK) pathway plays an important role. Moreover, combined silencing of DR4 and DR5 by small interfering RNA abrogates the ability of PTX to induce TRAIL-mediated apoptosis. Thus, this is the first demonstration that PTX can potentiate TRAIL-mediated apoptosis through downregulation of cell survival gene products and upregulation of death receptors.
Satindra Gahlot
Mohammad Aslam Khan
Loveena Rishi
Sekhar Majumdar
2011-12-08T19:32:18Z
2015-07-22T03:56:12Z
http://crdd.osdd.net/open/id/eprint/541
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/541
2011-12-08T19:32:18Z
Global structure of HIV-1 neutralizing antibody IgG1 b12 is asymmetric.
Human antibody IgG1 b12 is one of the four antibodies known to neutralize a broad range of human immunodeficiency virus-1. The crystal structure of this antibody displayed an asymmetric disposition of the Fab arms relative to its Fc portion. Comparison of structures solved for other IgG1 antibodies led to a notion that crystal packing forces entrapped a "snap-shot" of different conformations accessible to this antibody. To elucidate global structure of this unique antibody, we acquired small-angle X-ray scattering data from its dilute solution. Data analysis indicated that b12 adopts a bilobal globular structure in solution with a radius of gyration and a maximum linear dimension of approximately 54 and approximately 180A, respectively. Extreme similarity between its solution and crystal structure concludes that non-flexible, asymmetric shape is an inherent property of this rare antibody.
Ashish Ganguly
Ashish K Solanki
Christopher D Boone
Joanna K Krueger
2011-12-08T19:30:46Z
2011-12-08T19:30:46Z
http://crdd.osdd.net/open/id/eprint/528
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/528
2011-12-08T19:30:46Z
KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials.
Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed http://crdd.osdd.net/raghava/kidoq, which allows the prediction of Ki value of a new ligand molecule against DHDPS.
Aarti Garg
Rupinder Tewari
G.P.S. Raghava
2011-12-08T19:31:07Z
2011-12-08T19:31:07Z
http://crdd.osdd.net/open/id/eprint/530
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/530
2011-12-08T19:31:07Z
Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis.
The above-mentioned virtual screening procedures helped in the identification of several potent candidates that possess inhibitory activity against Mtb DHDPS. Therefore, these novel scaffolds/candidates which could have the potential to inhibit Mtb DHDPS enzyme would represent promising starting points as lead compounds and certainly aid the experimental designing of antituberculars in lesser time.
Aarti Garg
Rupinder Tewari
G.P.S. Raghava
2012-02-28T16:08:03Z
2012-04-03T07:05:38Z
http://crdd.osdd.net/open/id/eprint/1115
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1115
2012-02-28T16:08:03Z
Degradation of 4-nitrophenol, 2-chloro-4-nitrophenol, and 2,4-dinitrophenol by Rhodococcus imtechensis strain RKJ300.
A bacterial strain Rhodococcus imtechensis RKJ300 (= MTCC 7085(T) = JCM 13270(T)) was isolated from pesticide-contaminated soil of Punjab by the enrichment technique on minimal medium containing 4-nitrophenol. Strain RKJ300 is capable of utilizing 4-nitrophenol, 2-chloro-4-nitrophenol, and 2,4-dinitrophenol as sole sources of carbon and energy. The strain involved both oxidative and reductive catabolic mechanisms for initial transformation of these compounds. In the case of 2-chloro-4-nitrophenol, colorimetric analysis indicated that nitrite release was followed by stoichiometric elimination of chloride ions. Experiments using whole cells and cell-free extracts showed chlorohydroquinone and hydroquinone as the intermediates of 2-chloro-4-nitrophenol degradation. This is the first report of degradation on 2-chloro-4-nitrophenol by a bacterium under aerobic condition to the best of our knowledge. However, pathways for degradation of 4-nitrophenol and 2,4-dinitrophenol were similar to those reported in other strains of Rhodococcus. Laboratory-scale soil microcosm studies demonstrated that the organism was capable of degrading a mixture of nitrophenols simultaneously, indicating its applicability toward in situ bioremediation of contaminated sites. The fate of the augmented strain as monitored by the plate-counting method and hybridization technique was found to be fairly stable throughout the period of microcosm experiments.
Anuradha Ghosh
Meenu Khurana
Archana Chauhan
Masahiro Takeo
Asit K Chakraborti
R K Jain
2011-12-08T18:59:42Z
2015-01-07T04:57:41Z
http://crdd.osdd.net/open/id/eprint/505
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/505
2011-12-08T18:59:42Z
T cell help to B cells in germinal centers: putting the jigsaw together.
The germinal center (GC) reaction supports the processes of affinity maturation and class switching in B cells that result in long-lasting humoral immunity. CD4(+) T follicular helper cells (Tfh) participate in the GC reaction to help B cells. However, recent studies highlight the heterogeneity of CD4(+) T cells in GCs, which confounds the understanding of Tfh cells. Based on many recent studies, we have tried to form a working model on the niche of Tfh cells in GCs. We have also addressed whether Tfh cells are a distinct lineage and how they may be generated to help B cells.
Uthaman Gowthaman
Sathi Babu Chodisetti
J N Agrewala
2011-12-08T19:23:13Z
2015-01-07T04:56:33Z
http://crdd.osdd.net/open/id/eprint/524
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/524
2011-12-08T19:23:13Z
Evaluation of different generic in silico methods for predicting HLA class I binding peptide vaccine candidates using a reverse approach.
Since CD8+ T cell response is crucial to combat intracellular infections and cancer, identification of class I HLA binding peptides is of immense clinical value. The experimental identification of such peptides is protracted and laborious. Exploiting in silico tools to discover such peptides is an attractive alternative. However, this approach needs a thorough assessment before its elaborate application. We have adopted a reverse approach to evaluate the reliability of eight different servers (inclusive of 55 predictors) by exploiting experimentally proven data. A comprehensive data set of more than 960 peptides was employed to test the efficacy of the programs. We have validated commonly used strategies to predict peptides that bind to seven most prevalent HLA class I alleles. We conclude that four of the eight servers are more adept in predictions. Although the overall predictions for class I MHC binders were superior to class II MHC binders, individual predictors for different alleles belonging to the same program were highly variable in their efficiencies. We have also addressed whether a consensus approach can yield better prediction efficiency. We observed that combining the results from different in silico programs could not increase the efficiency significantly.
Uthaman Gowthaman
Sathi Babu Chodisetti
Pankaj Parihar
J N Agrewala
2012-09-11T04:32:32Z
2012-09-11T04:36:35Z
http://crdd.osdd.net/open/id/eprint/1178
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1178
2012-09-11T04:32:32Z
Multiple Functionalities of chromodomain protein Swi6 in Heterochromatin Structure and Function in Fission Yeast.
Swati Haldar
2012-09-11T04:46:33Z
2012-09-11T04:46:33Z
http://crdd.osdd.net/open/id/eprint/1182
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1182
2012-09-11T04:46:33Z
Influences of Toll like receptors and Costimulatory Molecules in B Cell Activation and Antigen Presentation.
Shweta Jain
2012-02-28T16:08:57Z
2012-02-28T16:08:57Z
http://crdd.osdd.net/open/id/eprint/1109
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1109
2012-02-28T16:08:57Z
Molecular cloning, expression, purification and characterization of truncated forms of human plasminogen in Pichia pastoris expression system
Human plasminogen (HPG), which contains a catalytic domain together with five kringle domains, can be readily purified from blood plasma by chromatography on lysine-agarose. However, its truncated derivatives are needed for various important therapeutic applications. The proteolytic digestion of plasminogen in vitro yields several low molecular weight variants viz. the kringle-less catalytic domain, known as micro-plasminogen (microPG), or miniplasminogen (miniPG), which consists of microPG with an intact kringle-5 domain. However, this method is extremely cumbersome due to a requirement of stringent control on the limited proteolysis process, which often leads to very poor recoveries of the desired product/s, apart from the potentially serious safety-regulatory issues associated with blood-derived therapeutic products. Here, we describe the high-level secretory expression of these important plasminogen derivatives employing Pichia pastoris as the expression host with an engineered alpha-mating factor signal sequence. The purified proteins were found to be functionally comparable with human blood plasminogen-derived ‘native’ forms in terms of their N-terminal amino acid sequences and molecular mass, as well as functional properties. This study paves the way for the facile large-scale production of recombinant human plasminogen derivatives required for thrombolytic and other life-saver therapies
Kishore K. Joshi
Girish Sahni
2012-09-11T06:22:55Z
2012-09-11T06:22:55Z
http://crdd.osdd.net/open/id/eprint/1188
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1188
2012-09-11T06:22:55Z
Elucidation of N-terminal methionine excision pathway in mycobacteria.
Pavitra Kanudia
2012-02-28T16:07:18Z
2012-02-28T16:07:18Z
http://crdd.osdd.net/open/id/eprint/1120
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1120
2012-02-28T16:07:18Z
A functional comparison of the TET aminopeptidases of P. furiosus and B. subtilis with a protein-engineered variant recombining the former's structure with the latter's active site
We have produced and characterized three microbial tetrahedral (TET) aminopeptidases: the previously uncharacterized Bacillus subtilis aminopeptidase (BsuAP), a Pyrococcus furiosus aminopeptidase (PfuAP), and a protein-engineered PfuAP-derived ‘designer’ aminopeptidase (MutAP) in which the entire active site of PfuAP is replaced with that of BsuAP through the making of 9 non-contiguous structure-guided mutations. The temperature/pH values of optimal function of MutAP (60 °C/pH 7.0) were found to be comparable to those of its progenitors, BsuAP (70 °C/pH 7.5) and PfuAP (80 °C/pH 8.0). The Km of MutAP (3.8 mM) was similar to that of PfuAP (5.0 mM) and unlike that of BsuAP (20.8 mM); however, unlike PfuAP, MutAP showed severe substrate-based inhibition like BsuAP, at substrate exceeding 5 mM concentration. MutAP thus inherits certain characteristics from each of its progenitors. At the same time, the Kcat of MutAP was ∼185-fold lower than that of PfuAP and ∼300-fold lower than that of BsuAP, indicating an unanticipated slowing down of activity. The results provide tentative evidence that ‘structure-guided transplantation’ of active sites between proteins can help in recombining enzyme characteristics in interesting and unanticipated ways, to help create novel enzymes.
Divya Kapoor
Balvinder Singh
Subramanian Karthikeyan
Purnananda Guptasarma
2011-12-08T19:31:52Z
2012-04-03T07:03:59Z
http://crdd.osdd.net/open/id/eprint/536
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/536
2011-12-08T19:31:52Z
A case study for assessment of microbial community dynamics in genetically modified Bt cotton crop fields.
Bt cotton was the first genetically modified crop approved for use in India. However, only a few studies have been conducted to assess the feasibility of its commercial application. Bt cotton is genetically modified to express a proteinaceous endotoxin (Cry) encoded by cry gene of Bacillus thuringiensis that has specific insecticidal activity against bollworms. Therefore, the amount of pesticides used for growing Bt cotton is postulated to be considerably low as compared to their non-Bt counterparts. Alternatively, it is also speculated that application of a genetically modified crop may alter the bio-geochemical balance of the agriculture field(s). Microbial community composition and dynamics is an important descriptor for assessment of such alterations. In the present study, we have assessed the culturable and non-culturable microbial diversities in Bt cotton and non-Bt cotton soils to determine the ecological consequences of application of Bt cotton. The analyses of microbial community structures indicated that cropping of Bt cotton did not adversely affect the diversity of the microbial communities.
Manisha Kapur
Ranjana Bhatia
Gunjan Pandey
Janmejay Pandey
Debarati Paul
R K Jain
2012-09-11T06:35:57Z
2012-09-11T06:35:57Z
http://crdd.osdd.net/open/id/eprint/1192
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1192
2012-09-11T06:35:57Z
Studies on the Dug 1p, Dug 2p and Dug 3p Proteins involved in the alternative pathway of glutathione degradation in S. cerevisae.
Hardeep Kaur
2011-12-08T19:34:15Z
2011-12-08T19:34:15Z
http://crdd.osdd.net/open/id/eprint/554
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/554
2011-12-08T19:34:15Z
Salt-assisted religation of proteolyzed Glutathione-S-transferase follows Hofmeister series.
Proteases have been used not only for proteolysis but also in organic solvent-assisted religation processes. Here, we demonstrated the effect of salts on peptide bond resynthesis in Glutathione-S-transferase (GST) and have found it to be in the purview of the Hofmeister phenomena. Our results show that the efficiency and ease of religation increases with an increase in the surface charge densities of the cations used in the study. Thus, the yield of religated GST follows the order: Mg2(+)>Li(+)>Na(+)>K(+). Characteristics of the salt-religated GST were studied using size exclusion chromatography, CD spectroscopy, mass spectrometry and CDNB activity assay. Results show that the properties of salt-religated GST are in close agreement with those of the native GST. Additionally, we also assessed the specific activity of the protease, Subtilisin Carlsberg, used in this study. Contrary, to aqueous-organic systems, wherein there is a remarkable decrease in the proteolytic activity, the activity in the presence of salts is only minimally changed. Our studies suggest that salt-assisted peptide bond formation is favoured primarily due to changes in the ionic environment of the nicked termini of GST, and that there is no role played by the protease.
K V Radha Kishan
Amit Sharma
2011-12-08T18:59:17Z
2015-01-12T04:37:31Z
http://crdd.osdd.net/open/id/eprint/503
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/503
2011-12-08T18:59:17Z
Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov.
The taxonomic status of three Bacillus species, Bacillus insolitus, B. psychrodurans and B. psychrotolerans was reexamined using a polyphasic approach. In our analysis, these three Bacillus species formed a cluster separate from other members of Bacillus rRNA group 2 [5] and from Bacillus sensu stricto. These three species shared high 16S rRNA gene sequence similarities between them (97.8-99.7%) and showed closest sequence similarity (95.3-96.3%) to Paenisporosarcina quisquiliarum gen. nov., sp. nov. [18]. Sequence similarities with other related genera ranged between 90.9% and 94.5%. Phylogenetic coherence of the three species was supported by phenotypic characteristics, such as growth at low temperatures, negative oxidation and assimilation of many carbohydrates, MK8 as the major isoprenoid quinine and broadly similar polar lipid profiles. All three species had a similar peptidoglycan type of the variation A4β and similar genomic G+C contents (35.7-36.6 mol% [1]). Genomic relatedness among them was shown to be less than 70% and justified their separate species status [1]. These three species could be differentiated from each other and from related taxa on the basis of phenotypic, including chemotaxonomic, characteristics and ribotype patterns. On the basis of our analysis, we propose a new genus Psychrobacillus gen. nov. and to transfer B. insolitus, B. psychrodurans and B. psychrotolerans to the new genus as Psychrobacillus insolitus comb. nov. (type species of the genus; type strain W16B(T)=DSM 5(T)), P. psychrodurans comb. nov. (type strain 68E3(T)=DSM 11713(T)) and P. psychrotolerans comb. nov. (type strain 3H1(T)=DSM 11706(T)).
S Krishnamurthi
Arunachalam Ruckmani
Rüdiger Pukall
T Chakrabarti
2016-10-04T06:07:05Z
2016-10-04T06:07:05Z
http://crdd.osdd.net/open/id/eprint/1922
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1922
2016-10-04T06:07:05Z
Continued persistence of a single genotype of dengue virus type-3 (DENV-3) in Delhi, India since its re-emergence over the last decade.
The re-emergence of an epidemic strain of dengue virus type-3 (DENV-3) in Delhi in 2003 and its persistence in subsequent years marked a changing trend in dengue virus circulation in this part of India. Its evolving phylogeny over the past decade has not been studied in detail as yet.
Himani Kukreti
Veena Mittal
Artee Chaudhary
Rajendra Singh Rautela
Manoj Kumar
Sheetal Chauhan
Sunil Bhat
Mala Chhabra
Dipesh Bhattacharya
Syed Tazeen Pasha
Devinder Kumar
Sunil Gomber
Shiv Lal
Arvind Rai
2011-12-08T19:22:32Z
2012-03-28T09:30:18Z
http://crdd.osdd.net/open/id/eprint/520
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/520
2011-12-08T19:22:32Z
OXP1/YKL215c encodes an ATP-dependent 5-oxoprolinase in Saccharomyces cerevisiae: functional characterization, domain structure and identification of actin-like ATP-binding motifs in eukaryotic 5-oxoprolinases.
OXP1/YKL215c, an uncharacterized ORF of Saccharomyces cerevisiae, encodes a functional ATP-dependent 5-oxoprolinase of 1286 amino acids. The yeast 5-oxoprolinase activity was demonstrated in vivo by utilization of 5-oxoproline as a source of glutamate and OTC, a 5-oxoproline sulfur analogue, as a source of sulfur in cells overexpressing OXP1. In vitro characterization by expression and purification of the recombinant protein in S. cerevisiae revealed that the enzyme exists and functions as a dimer, and has a K(m) of 159 microM and a V(max) of 3.5 nmol h(-1) microg(-1) protein. The enzyme was found to be functionally separable in two distinct domains. An 'actin-like ATPase motif' could be identified in 5-oxprolinases, and mutation of key residues within this motif led to complete loss in ATPase and 5-oxoprolinase activity of the enzyme. The results are discussed in the light of the previously postulated truncated gamma-glutamyl cycle of yeasts.
Akhilesh Kumar
Anand K Bachhawat
2011-12-08T19:21:41Z
2012-03-28T09:31:10Z
http://crdd.osdd.net/open/id/eprint/519
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/519
2011-12-08T19:21:41Z
A futile cycle, formed between two ATP-dependant gamma-glutamyl cycle enzymes, gamma-glutamyl cysteine synthetase and 5-oxoprolinase: the cause of cellular ATP depletion in nephrotic cystinosis?
Cystinosis, an inherited disease caused by a defect in the lysosomal cystine transporter (CTNS), is characterized by renal proximal tubular dysfunction. Adenosine triphosphate (ATP) depletion appears to be a key event in the pathophysiology of the disease, even though the manner in which ATP depletion occurs is still a puzzle. We present a model that explains how a futile cycle that is generated between two ATP-utilizing enzymes of the gamma-glutamyl cycle leads to ATP depletion. The enzyme gamma-glutamyl cysteine synthetase (gamma-GCS), in the absence of cysteine, forms 5-oxoproline (instead of the normal substrate, gamma-glutamyl cysteine) and the 5-oxoproline is converted into glutamate by the ATP-dependant enzyme, 5-oxoprolinase. Thus, in cysteine-limiting conditions, glutamate is cycled back into glutamate via 5-oxoproline at the cost of two ATP molecules without production of glutathione and is the cause of the decreased levels of glutathione synthesis, as well as the ATP depletion observed in these cells. The model is also compatible with the differences seen in the human patients and the mouse model of cystinosis, where renal failure is not observed.
Akhilesh Kumar
Anand K Bachhawat
2012-09-11T04:50:04Z
2012-09-11T04:50:04Z
http://crdd.osdd.net/open/id/eprint/1183
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1183
2012-09-11T04:50:04Z
Chemical Syntheses, Conformational Analysis and Bioactivity Evaluation of two Immunodulating Tetrapeptides Tuftsin and Rigin Analogs.
Nigam Kumar
2011-12-08T19:00:05Z
2011-12-08T19:00:05Z
http://crdd.osdd.net/open/id/eprint/506
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/506
2011-12-08T19:00:05Z
Determination of an unusual secondary structural element in the immunostimulating tetrapeptide rigin in aqueous environments: insights via MD simulations, (1)H NMR and CD spectroscopic studies.
An immunomodulating tetrapeptide, rigin (H-Gly-Gln-Pro-Arg-OH), has been examined for its secondary structure preferences through combined use of high-temperature unrestrained MD simulations in implicit water and 1D and 2D 1H NMR spectroscopy.The distribution of backbone torsion angles revealed the predominance of trans conformers across the Xaa-Pro peptide bond. The results of MD simulations revealed that of the five predicted families A-E, the predominant families, family A (92 structures), family C (63 structures) and family D (31 structures), could be complemented by extensive 1D and 2D 1H NMR parameters acquired in aqueous PBS solution. A survey of specific inter- and intraresidue NOEs substantiated the predominance of an unusual type VII beta-turn structure, defined by two torsion angles, i.e. psiGln approximately 155 degrees and psiPro approximately -65 degrees across the Gln-Pro segment. The proposed semi-folded kinked topology precluded formation of any intramolecular interaction, i.e. hydrogen bond or electrostatic interaction. Far-UV CD spectral characteristics of rigin in aqueous PBS solution and non-aqueous structure promoting organic solvents, TFE and TMP, revealed its strong solvent dependence. However, in aqueous PBS solution, the presence of a weak negative shoulder at approximately 234 nm could be ascribed to a small population with ordered, semi-folded topology.We propose that the plausible structural attributes may be exploited for design and rigidification of the bioactive conformation of this immunomodulator toward improved immunopharmacological properties.
Nigam Kumar
Raghuvansh Kishore
2011-12-08T19:17:05Z
2015-01-09T10:43:48Z
http://crdd.osdd.net/open/id/eprint/513
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/513
2011-12-08T19:17:05Z
Crystallographically observed folded topology of an unsubstituted γ-aminobutyric acid incorporated in a model peptide: importance of a C--H···O interaction.
To validate the existing hypothesis put forward by Navarro et al., we performed single crystal X-ray diffraction structural analysis of a designed model peptide incorporating an unsubstituted achiral γ-aminobutyric acid: Boc-Pro-γ-Abu-OH (1) lacking C-terminal amide group. The analysis established existence of an overall unusual tightly folded topology stabilized by a conventional N(i)···H--N(i + 1) and an unconventional C(i)--H···O(i) type intramolecular hydrogen bonding interactions, encompassing a five-membered and a six-membered ring motifs, respectively. Moreover, in conjunction with Fourier transform infrared (FT-IR) absorption study in solid KBr, the results provided evidence that two conventional and one unconventional noncovalent intermolecular interaction stabilize a right-handed helical architecture generated via molecular self-assembly by translating the symmetry related molecules along the crystallographic b axis. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 927-931, 2010.
Nigam Kumar
P Venugopalan
Raghuvansh Kishore
2012-09-11T04:40:47Z
2012-09-11T04:40:47Z
http://crdd.osdd.net/open/id/eprint/1180
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1180
2012-09-11T04:40:47Z
Structure-function studies of enzymes involved in FAD biosynthesis pathway of salmonella typhimurium.
Pankaj Kumar
2011-12-08T18:58:26Z
2011-12-08T18:58:26Z
http://crdd.osdd.net/open/id/eprint/498
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/498
2011-12-08T18:58:26Z
Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2.
3,4-Dihydroxy-2-butanone-4-phosphate synthase (DHBPS) encoded by ribB gene is one of the first enzymes in riboflavin biosynthesis pathway and catalyzes the conversion of ribulose-5-phosphate (Ru5P) to 3,4-dihydroxy-2-butanone-4-phosphate and formate. DHBPS is an attractive target for developing anti-bacterial drugs as this enzyme is essential for pathogens, but absent in humans. The recombinant DHBPS enzyme of Salmonella requires magnesium ion for its activity and catalyzes the formation of 3,4-dihydroxy-2-butanone-4-phosphate from Ru5P at a rate of 199 nmol min(-1) mg(-1) with K(m) value of 116 μM at 37°C. Further, we have determined the crystal structures of Salmonella DHBPS in complex with sulfate, Ru5P and sulfate-zinc ion at a resolution of 2.80, 2.52, and 1.86 Å, respectively. Analysis of these crystal structures reveals that the acidic loop (residues 34-39) responsible for the acid-base catalysis is disordered in the absence of substrate or metal ion at the active site. Upon binding either substrate or sulfate and metal ions, the acidic loop becomes stabilized, adopts a closed conformation and interacts with the substrate. Our structure for the first time reveals that binding of substrate Ru5P alone is sufficient for the stabilization of the acidic active site loop into a closed conformation. In addition, the Glu38 residue from the acidic active site loop undergoes a conformational change upon Ru5P binding, which helps in positioning the second metal ion that stabilizes the Ru5P and the reaction intermediates. This is the first structural report of DHBPS in complex with either substrate or metal ion from any eubacteria.
Pankaj Kumar
Mirage Singh
Ruchi Gautam
Subramanian Karthikeyan
2012-02-28T16:08:45Z
2012-02-28T16:08:45Z
http://crdd.osdd.net/open/id/eprint/1111
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1111
2012-02-28T16:08:45Z
Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207).
Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus Dethiosulfovibrio of the family Synergistaceae in the recently created phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids. It was isolated from an offshore oil well where it was been reported to be involved in pitting corrosion of mild steel. Initially, this bacterium was described as a distant relative of the genus Thermoanaerobacter, but was not assigned to a genus, it was subsequently placed into the novel phylum Synergistetes. A large number of repeats in the genome sequence prevented an economically justifiable closure of the last gaps. This is only the third published genome from a member of the phylum Synergistetes. The 2,576,359 bp long genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Kurt Labutti
Shanmugam Mayilraj
Alicia Clum
Susan Lucas
Tijana Glavina Del Rio
Matt Nolan
Hope Tice
Jan-Fang Cheng
Sam Pitluck
Konstantinos Liolios
Natalia Ivanova
Konstantinos Mavromatis
Natalia Mikhailova
Amrita Pati
Lynne Goodwin
Amy Chen
Krishna Palaniappan
Miriam Land
Loren Hauser
Yun-Juan Chang
Cynthia D Jeffries
Manfred Rohde
Stefan Spring
Markus Göker
Tanja Woyke
James Bristow
Jonathan A Eisen
Victor Markowitz
Philip Hugenholtz
Nikos C Kyrpides
Hans-Peter Klenk
Alla Lapidus
2011-12-08T19:31:21Z
2011-12-08T19:31:21Z
http://crdd.osdd.net/open/id/eprint/532
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/532
2011-12-08T19:31:21Z
AntiBP2: improved version of antibacterial peptide prediction.
Among antibacterial peptides, there is preference for certain residues at N and C terminus, which helps to discriminate them from non-antibacterial peptides. Amino acid composition of antibacterial peptides helps to demarcate them from non-antibacterial peptide and their further classification in source and family. Antibp2 will be helpful in discovering efficacious antibacterial peptide, which we hope will be helpful against antibiotics resistant bacteria. We also developed user friendly web server for the biological community.
Sneh Lata
Nitish K Mishra
G.P.S. Raghava
2012-02-28T16:08:31Z
2012-02-28T16:08:31Z
http://crdd.osdd.net/open/id/eprint/1113
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1113
2012-02-28T16:08:31Z
Metal-catalyzed proteolysis, conformational antigenicity, photosensitized oxidation, and electrical dysfunction explain the pathogenicity of protein aggregates.
It is widely accepted that protein aggregates tend to be pathologic, although little is known about why they are pathologic. Here, we summarize published findings about protein aggregates which have implications for pathology, but which have not yet been covered in any review or hypothesis on the subject, to the best of our knowledge. These findings suggest that protein aggregates can: (i) act as proteases, using exposed surface serines, (ii) function as immunogens, using novel conformational epitopes, (iii) behave as photosensitization-aids, using a novel peptide-based fluorescence, and (iv) act as electrical conductors, using electrons tunneling through hydrogen-bonded networks of peptide bonds. The potential pathological consequences of each finding are speculated upon.
Manni Luthra-Guptasarma
Purnananda Guptasarma
2012-02-28T16:09:09Z
2015-01-09T09:45:57Z
http://crdd.osdd.net/open/id/eprint/1107
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1107
2012-02-28T16:09:09Z
Metabolic profiles and phylogenetic diversity of microbial communities from chlorinated pesticides contaminated sites of different geographical habitats of India.
This study provides insights to evaluate the presence of catabolic genes and assessing the bioremediation potential of the industrial soils contaminated by chlorinated pesticides.
N Manickam
Anuj Pathak
H S Saini
Shanmugam Mayilraj
R Shanker
2012-02-28T16:07:25Z
2012-02-28T16:07:25Z
http://crdd.osdd.net/open/id/eprint/1119
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1119
2012-02-28T16:07:25Z
Emulsification and Hydrolysis of Oil by Syncephalastrum racemosum.
A fungal strain, Syncephalastrum racemosum, was isolated from oil-leak contaminated soils from Kanpur, India. The strain was examined for potential to emulsify soybean oil using a 18 per cent oil supplement as carbon source in minimal salt medium. On 72 h growth of the fungus in oil and salt medium, the cellfree supernatant (CFS) showed presence of mono- and di-glycerides indicating degradation of oils to free fatty acids (FFAs). Increasing concentration of oil resulted in enhanced formation of FFAs. The degradation process was observed to be related to the emulsification activity in CFS which was observed to increase with time. The study reports the emulsification and hydrolytic activity of S. racemosum, an activity that can be exploited for increasing the accessibility and treatment of hazardous substance including hydrophobic explosives
Chandni Mathur
Ranjana Prakash
Amjad Ali
Jasminder Kaur
Swaranjit Singh Cameotra
N. Tejo Prakash
2011-12-08T19:31:34Z
2011-12-08T19:31:34Z
http://crdd.osdd.net/open/id/eprint/534
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/534
2011-12-08T19:31:34Z
Interactions among HAMP domain repeats act as an osmosensing molecular switch in group III hybrid histidine kinases from fungi.
The members of group III hybrid histidine kinases (HHK) are ubiquitous in fungi. Group III HHK have been implicated to function as osmosensors in the high osmolarity glycerol (HOG) pathway that is essential for fungal survival under high osmolarity stress. Recent literature suggests that group III HHK are also involved in conidia formation, virulence in several filamentous fungi, and are an excellent molecular target for antifungal agents. Thus, group III HHK constitute a very important group of sensor kinases. Structurally, group III HHK are distinct from Sln1p, the osmosensing HHK that regulates the HOG pathway in Saccharomyces cerevisiae. Group III HHK lack any transmembrane domain and typically contain HAMP domain repeats at the N terminus. Until now, it is not clear how group III HHK function as an osmosensor to regulate the HOG pathway. To investigate this, we undertook molecular characterization of DhNIK1, an ortholog from osmotolerant yeast Debaryomyces hansenii. We show here that DhNIK1 could complement sln1 mutation in S. cerevisiae thereby confirming its role as a bona fide osmosensor. We further investigated the role of HAMP domains by deleting them systematically. Our results clearly indicate that the HAMP4 domain is crucial for osmosensing by DhNik1p. Most importantly, we also show that the alternative interaction among the HAMP domains regulates the activity of DhNik1p like an "on-off switch" and thus provides, for the first time, an insight into the molecular mechanism of osmosensing by this group of HHKs.
Netrapal Meena
Harsimran Kaur
Alok K Mondal
2012-09-11T04:55:58Z
2015-01-09T08:45:10Z
http://crdd.osdd.net/open/id/eprint/1185
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1185
2012-09-11T04:55:58Z
Development of in-Silico methods for searching of potential drug molecules ad targets.
Nitish K Mishra
2011-12-08T18:59:26Z
2011-12-13T17:14:09Z
http://crdd.osdd.net/open/id/eprint/504
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/504
2011-12-08T18:59:26Z
Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule.
This study demonstrates that SVM based QSAR model can predict substrate specificity of major CYP isoforms with high accuracy. These models can be used to predict isoform responsible for metabolizing a drug molecule. Thus these models can used to understand whether a molecule will be metabolized or not. This is possible to develop highly accurate models for predicting substrate specificity of major isoforms using CDK descriptors. A web server MetaPred has been developed for predicting metabolizing isoform of a drug molecule http://crdd.osdd.net/raghava/metapred/.
Nitish K Mishra
Sandhya Agarwal
G.P.S. Raghava
2011-12-08T19:31:14Z
2011-12-08T19:31:14Z
http://crdd.osdd.net/open/id/eprint/531
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/531
2011-12-08T19:31:14Z
Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information.
This study suggests that evolutionary information of 17 amino acid patterns perform best for FAD interacting residues prediction. We also developed a web server which predicts FAD interacting residues in a protein which is freely available for academics.
Nitish K Mishra
G.P.S. Raghava
2011-12-08T18:59:08Z
2012-04-02T09:47:32Z
http://crdd.osdd.net/open/id/eprint/502
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/502
2011-12-08T18:59:08Z
Chiral solvating agents for cyanohydrins and carboxylic acids.
We have shown that a structure as simple as an ion pair of (R)- or (S)-mandelate and dimethylamminopyridinium ions possesses structural features that are sufficient for NMR enantiodiscrimination of cyanohydrins. Moreover, (1)H NMR data of cyanohydrins of known configuration obtained in the presence of the mandelate-dimethylaminopyridinium ion pair point to the existence of a correlation between chemical shifts and absolute configuration of cyanohydrins. Mandelate-DMAPH(+) ion pair and mandelonitrile form a 1:1 complex with an association constant of 338 M(-1) (DeltaG(0), -3.4 kcal/mol) for the (R)-mandelonitrile/(R)-mandelate-DMAPH(+) and 139 M(-1) (DeltaG(0), -2.9 kcal/mol) for the (R)-mandelonitrile/(S)-mandelate-DMAPH(+) complex. To understand the origin of enantiodiscrimination, the geometry optimization and energy minimization of the models of ternary complexes of (S)-mandelonitrile/(R)-mandelate/DMAPH(+) and (S)-mandelonitrile/(S)-mandelate/DMAPH(+) complexes was performed using DFT methodology (B3LYP) with the 6-31+G(d) basis set in Gaussian 3.0. Further, analysis of optimized molecular model obtained from theoretical studies suggested that (i) DMAP may be replaced with other amines, (ii) the hydroxyl group of mandelic acid is not necessary for stabilization of ternary complex and may be replaced with other groups such as methyl, (iii) the ion pair should form a stable ternary complex with any hydrogen-bond donor, provided its OH bond is sufficiently polarized, and (iv) alpha-H of racemic mandelic acid should also get resolved with optically pure mandelonitrile. These inferences were experimentally verified, which not only validated the proposed model but also led to development of a new chiral solvating agent for determination of ee of carboxylic acids and absolute configuration of aryl but not alkyl carboxylic acids.
Lomary S Moon
Mohan Pal
Yoganjaneyulu Kasetti
Prasad V Bharatam
R S Jolly
2012-02-28T16:07:39Z
2012-03-28T10:11:57Z
http://crdd.osdd.net/open/id/eprint/1117
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1117
2012-02-28T16:07:39Z
Leishmania donovani Isolates with Antimony-Resistant but Not -Sensitive Phenotype Inhibit Sodium Antimony Gluconate-Induced Dendritic Cell Activation
The inability of sodium antimony gluconate (SAG)-unresponsive kala-azar patients to clear Leishmania donovani (LD) infection despite SAG therapy is partly due to an ill-defined immune-dysfunction. Since dendritic cells (DCs) typically initiate anti-leishmanial immunity, a role for DCs in aberrant LD clearance was investigated. Accordingly, regulation of SAG-induced activation of murine DCs following infection with LD isolates exhibiting two distinct phenotypes such as antimony-resistant (SbRLD) and antimony-sensitive (SbSLD) was compared in vitro. Unlike SbSLD, infection of DCs with SbRLD induced more IL-10 production and inhibited SAG-induced secretion of proinflammatory cytokines, up-regulation of co-stimulatory molecules and leishmanicidal effects. SbRLD inhibited these effects of SAG by blocking activation of PI3K/AKT and NF-κB pathways. In contrast, SbSLD failed to block activation of SAG (20 µg/ml)-induced PI3K/AKT pathway; which continued to stimulate NF-κB signaling, induce leishmanicidal effects and promote DC activation. Notably, prolonged incubation of DCs with SbSLD also inhibited SAG (20 µg/ml)-induced activation of PI3K/AKT and NF-κB pathways and leishmanicidal effects, which was restored by increasing the dose of SAG to 40 µg/ml. In contrast, SbRLD inhibited these SAG-induced events regardless of duration of DC exposure to SbRLD or dose of SAG. Interestingly, the inhibitory effects of isogenic SbSLD expressing ATP-binding cassette (ABC) transporter MRPA on SAG-induced leishmanicidal effects mimicked that of SbRLD to some extent, although antimony resistance in clinical LD isolates is known to be multifactorial. Furthermore, NF-κB was found to transcriptionally regulate expression of murine γglutamylcysteine synthetase heavy-chain (mγGCShc) gene, presumably an important regulator of antimony resistance. Importantly, SbRLD but not SbSLD blocked SAG-induced mγGCS expression in DCs by preventing NF-κB binding to the mγGCShc promoter. Our findings demonstrate that SbRLD but not SbSLD prevents SAG-induced DC activation by suppressing a PI3K-dependent NF-κB pathway and provide the evidence for differential host-pathogen interaction mediated by SbRLD and SbSLD.
Ingrid Müller
Arun Kumar Haldar
Vinod Yadav
Eshu Singhal
Kamlesh Kumar Bisht
Alpana Singh
Suniti Bhaumik
R Basu
Pradip Sen
Syamal Roy
2012-02-28T16:08:38Z
2012-04-02T07:21:35Z
http://crdd.osdd.net/open/id/eprint/1112
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1112
2012-02-28T16:08:38Z
Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity.
The open reading frame Rv1326c of Mycobacterium tuberculosis (Mtb) H37Rv encodes for an alpha-1,4-glucan branching enzyme (MtbGlgB, EC 2.4.1.18, Uniprot entry Q10625). This enzyme belongs to glycoside hydrolase (GH) family 13 and catalyzes the branching of a linear glucose chain during glycogenesis by cleaving a 1-->4 bond and making a new 1-->6 bond. Here, we show the crystal structure of full-length MtbGlgB (MtbGlgBWT) at 2.33-A resolution. MtbGlgBWT contains four domains: N1 beta-sandwich, N2 beta-sandwich, a central (beta/alpha)(8) domain that houses the catalytic site, and a C-terminal beta-sandwich. We have assayed the amylase activity with amylose and starch as substrates and the glycogen branching activity using amylose as a substrate for MtbGlgBWT and the N1 domain-deleted (the first 108 residues deleted) MtbDelta108GlgB protein. The N1 beta-sandwich, which is formed by the first 105 amino acids and superimposes well with the N2 beta-sandwich, is shown to have an influence in substrate binding in the amylase assay. Also, we have checked and shown that several GH13 family inhibitors are ineffective against MtbGlgBWT and MtbDelta108GlgB. We propose a two-step reaction mechanism, for the amylase activity (1-->4 bond breakage) and isomerization (1-->6 bond formation), which occurs in the same catalytic pocket. The structural and functional properties of MtbGlgB and MtbDelta108GlgB are compared with those of the N-terminal 112-amino acid-deleted Escherichia coli GlgB (ECDelta112GlgB).
Kuntal Pal
Shiva Kumar
Shikha Sharma
Saurabh K Garg
Md Suhail Alam
H Eric Xu
Pushpa Agrawal
Kunchithapadam Swaminathan
2011-12-08T19:09:33Z
2011-12-08T19:09:33Z
http://crdd.osdd.net/open/id/eprint/494
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/494
2011-12-08T19:09:33Z
Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains.
We have analyzed protein sequences of aaRSs (class-1 and class-2) and non-aaRSs and identified interesting patterns. The high accuracy achieved by our SVM models using selected dipeptide composition demonstrates that certain types of dipeptide are preferred in aaRSs. We were able to identify PROSITE domains that are preferred in aaRSs and their classes, providing interesting insights into tRNA synthetases. The method developed in this study will be useful for researchers studying aaRS enzymes and tRNA biology. The web-server based on the above study, is available at http://www.imtech.res.in/raghava/icaars/.
Bharat Panwar
G.P.S. Raghava
2012-01-10T08:04:45Z
2015-01-09T08:52:06Z
http://crdd.osdd.net/open/id/eprint/24
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24
2012-01-10T08:04:45Z
Bridging innate and adaptive antitumor immunity targeting glycans.
Effective immunotherapy for cancer depends on cellular responses to tumor antigens. The role of major histocompatibility complex (MHC) in T-cell recognition and T-cell receptor repertoire selection has become a central tenet in immunology. Structurally, this does not contradict earlier findings that T-cells can differentiate between small hapten structures like simple glycans. Understanding T-cell recognition of antigens as defined genetically by MHC and combinatorially by T cell receptors led to the "altered self" hypothesis. This notion reflects a more fundamental principle underlying immune surveillance and integrating evolutionarily and mechanistically diverse elements of the immune system. Danger associated molecular patterns, including those generated by glycan remodeling, represent an instance of altered self. A prominent example is the modification of the tumor-associated antigen MUC1. Similar examples emphasize glycan reactivity patterns of antigen receptors as a phenomenon bridging innate and adaptive but also humoral and cellular immunity and providing templates for immunotherapies.
Anastas Pashov
Behjatolah Monzavi-Karbassi
G.P.S. Raghava
Thomas Kieber-Emmons
2012-09-11T04:52:57Z
2012-09-11T04:52:57Z
http://crdd.osdd.net/open/id/eprint/1184
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1184
2012-09-11T04:52:57Z
Studies on Mechanism of Transcription Regulation by Mycobacterium Tuberculosis PhoP.
Anuj Pathak
2011-12-08T18:58:10Z
2011-12-08T18:58:10Z
http://crdd.osdd.net/open/id/eprint/497
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/497
2011-12-08T18:58:10Z
Domain structure of virulence-associated response regulator PhoP of Mycobacterium tuberculosis: role of the linker region in regulator-promoter interaction(s).
The PhoP and PhoR proteins from Mycobacterium tuberculosis form a highly specific two-component system that controls expression of genes involved in complex lipid biosynthesis and regulation of unknown virulence determinants. The several functions of PhoP are apportioned between a C-terminal effector domain (PhoPC) and an N-terminal receiver domain (PhoPN), phosphorylation of which regulates activation of the effector domain. Here we show that PhoPN, on its own, demonstrates PhoR-dependent phosphorylation. PhoPC, the truncated variant bearing the DNA binding domain, binds in vitro to the target site with affinity similar to that of the full-length protein. To complement the finding that residues spanning Met(1) to Arg(138) of PhoP constitute the minimal functional PhoPN, we identified Arg(150) as the first residue of the distal PhoPC domain capable of DNA binding on its own, thereby identifying an interdomain linker. However, coupling of two functional domains together in a single polypeptide chain is essential for phosphorylation-coupled DNA binding by PhoP. We discuss consequences of tethering of two domains on DNA binding and demonstrate that linker length and not individual residues of the newly identified linker plays a critical role in regulating interdomain interactions. Together, these results have implications for the molecular mechanism of transmission of conformation change associated with phosphorylation of PhoP that results in the altered DNA recognition by the C-terminal domain.
Anuj Pathak
Rajni Goyal
Akesh Sinha
Dibyendu Sarkar
2011-12-08T19:30:40Z
2012-04-03T07:04:46Z
http://crdd.osdd.net/open/id/eprint/527
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/527
2011-12-08T19:30:40Z
Physiological adaptations and tolerance towards higher concentration of selenite (Se(+4)) in Enterobacter sp. AR-4, Bacillus sp. AR-6 and Delftia tsuruhatensis AR-7.
Environmental contamination with selenium is a major health concern. A few bacterial strains have been isolated that can transform toxic selenite to non-toxic elemental selenium only at low concentrations (0.001-150 mM) in recent past. We have previously reported isolation and characterization of few selenite-tolerant bacterial strains. These strains were found to be resistant to selenite at (300-600 mM) concentrations. In the present study we have characterized some physiological adaptations of strains Enterobacter sp. AR-4, Bacillus sp. AR-6 and Delftia tsuruhatensis AR-7 during exposure to higher concentration of selenite under aerobic and anaerobic environments. Adaptive responses are largely associated with alteration of cell morphology and change in total cellular fatty acid composition. Interestingly, electron microscopy studies revealed substantial decrease in cell size and intracellular deposition of Se(0) crystals when reduction is carried out under aerobic conditions. On the other hand, cell size increased with adhesion of Se(0) on cell surface during anaerobic reduction. Fatty acid composition analysis demonstrated selective increase in saturated and cyclic fatty acids and decrease in unsaturated ones during aerobic transformation. Changes observed during anaerobic transformation were in surprising contrast as indicated by total absence of saturated and cyclic fatty acids. Results presented here provide evidences for putative occurrence of two distinct mechanisms involved in tolerance towards higher concentrations of selenite utilization under aerobic and anaerobic conditions. Further, prior exposure to higher concentration of Se(+4) enabled rapid adaptation indicating role of inducible system in adaptation.
Dhan Prakash
Janmejay Pandey
B N Tiwary
R K Jain
2011-12-08T19:16:05Z
2012-04-03T07:06:48Z
http://crdd.osdd.net/open/id/eprint/509
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/509
2011-12-08T19:16:05Z
A process optimization for bio-catalytic production of substituted catechols (3-nitrocatechol and 3-methylcatechol.
The biocatalytic production of 3-substituted catechols viz. 3-NC and 3-MC depend on some crucial parameters to obtain maximum yields of the product at pilot scale. The process optimized for production of 3-substituted catechols by using the organisms P. putida (F1) and recombinant E. coli expression clone (pDTG602) may be useful for industrial application.
Dhan Prakash
Janmejay Pandey
Bhupendra N Tiwary
R K Jain
2012-02-28T16:07:33Z
2012-02-28T16:07:33Z
http://crdd.osdd.net/open/id/eprint/1118
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1118
2012-02-28T16:07:33Z
Caliciopsis indica sp. nov. from India
Caliciopsis indica sp. nov. is described from leaf lesions of kokum (Garcinia indica, Clusiaceae)
from the Western Ghats, India. Caliciopsis indica is morphologically similar to C. myrticola but
differs in having larger ascomata, longer asci and smaller ascospores. Phylogenetic analysis of
partial 28S rRNA gene sequence data has confirmed its placement within the Coryneliaceae
(Coryneliales, Eurotiomycetes). The ITS/5.8S rRNA gene sequence, however, did not provide any
clarity on the species delineation due to lack of reference sequences in GenBank.
J. Pratibha
K. Amandeep
BD Shenoy
DJ Bhat
2012-02-28T16:09:55Z
2012-02-28T16:09:55Z
http://crdd.osdd.net/open/id/eprint/1100
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1100
2012-02-28T16:09:55Z
Molecular and functional characterization of a novel efflux pump, AmvA, mediating antimicrobial and disinfectant resistance in Acinetobacter baumannii.
This report describes the functions of a novel resistance determinant, a member of the MFS efflux pumps, for the first time in A. baumannii.
Govindan Rajamohan
Vijaya Bharathi Srinivasan
Wondwossen A Gebreyes
2012-02-28T16:09:47Z
2012-02-28T16:09:47Z
http://crdd.osdd.net/open/id/eprint/1101
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1101
2012-02-28T16:09:47Z
Novel role of Acinetobacter baumannii RND efflux transporters in mediating decreased susceptibility to biocides.
This is the first study demonstrating the role of efflux pumps in mediating decreased susceptibility to disinfectants and other chemical substrates in A. baumannii.
Govindan Rajamohan
Vijaya Bharathi Srinivasan
Wondwossen A Gebreyes
2011-12-08T19:30:33Z
2011-12-08T19:30:33Z
http://crdd.osdd.net/open/id/eprint/526
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/526
2011-12-08T19:30:33Z
Efficient ligation and cloning of DNA fragments with 2-bp overhangs.
Various methods of ligation are currently available and routinely used by molecular biologists, such as blunt end ligation, cohesive end (two and four overhangs), and ligation of Taq polymerase-derived products. However, there is no efficient method for the cloning of DNA fragments with 2-bp overhangs. We present a simple method for the efficient ligation of DNA fragments with 2-bp overhanging ends, ranging in size from 0.7 to 2.5 kbp. Our method involves the initial heating and flash freezing of the vector-insert DNA mix, and a subsequent unique ligation reaction. This method provides a new molecular biology tool for researchers.
Rajiv Kumar Ranjan
Kammara Rajagopal
2012-09-11T06:19:37Z
2012-09-11T06:19:37Z
http://crdd.osdd.net/open/id/eprint/1187
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1187
2012-09-11T06:19:37Z
Development of Bioinformatics tools for analysis and prediction of Therapeutic peptides/proteins.
Mamoon Rashid
2011-12-08T18:57:26Z
2011-12-08T18:57:26Z
http://crdd.osdd.net/open/id/eprint/492
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/492
2011-12-08T18:57:26Z
A simple approach for predicting protein-protein interactions.
The availability of an increased number of fully sequenced genomes demands functional interpretation of the genomic information. Despite high throughput experimental techniques and in silico methods of predicting protein-protein interaction (PPI); the interactome of most organisms is far from completion. Thus, predicting the interactome of an organism is one of the major challenges in the post-genomic era. This manuscript describes Support Vector Machine (SVM) based models that have been developed for discriminating interacting and non-interacting pairs of proteins from their amino acid sequence. We have developed SVM models using various types of sequence compositions e.g. amino acid, dipeptide, biochemical property, split amino acid and pseudo amino acid composition. We also developed SVM models using evolutionary information in the form of Position Specific Scoring Matrix (PSSM) composition. We achieved maximum Matthews's correlation coefficient (MCC) of 1.00, 0.52 and 0.74 for Escherichia coli, Saccharomyces cerevisiae, and Helicobacter pylori, using dipeptide based SVM model at default threshold. It was observed that the performance of a prediction model depends on the dataset used for training and testing. In case of E. coli MCC decreased from 1.0 to 0.67 when evaluated on a new dataset. In order to understand PPI in different cellular environment, we developed species-specific and general models. It was observed that species-specific models are more accurate than general models. We conclude that the primary amino acid sequence based descriptors could be used to differentiate interacting from non-interacting protein pairs. Some amino acids tend to be favored in interacting pairs than non-interacting ones. Finally, a web server has been developed for predicting protein-protein interactions.
Mamoon Rashid
Sumathy Ramasamy
G.P.S. Raghava
2011-12-08T19:32:02Z
2015-07-22T05:33:11Z
http://crdd.osdd.net/open/id/eprint/537
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/537
2011-12-08T19:32:02Z
Molecular mechanism of polyethylene glycol mediated stabilization of protein.
The effect of different molar ratios of polyethylene glycol (PEG) on the conformational stability of protein, bovine serum albumin (BSA), was studied. The binding of PEG with BSA was observed by fluorescence spectroscopy by measuring the fluorescence intensity after displacement of PEG with chromophore ANS and had further been confirmed by measuring the intrinsic fluorescence of tryptophan residues of BSA. Co-lyophilization of BSA with PEG at optimum BSA:PEG molar ratio led to the formation of the stable protein particles. Circular dichroism (CD) spectroscopy study suggested that a conformational change had occurred in the protein after PEG interaction and demonstrated the highest stability of protein at the optimum BSA:PEG molar ratio of 1:0.75. Additional differential scanning calorimetry (DSC) study suggested strong binding of PEG to protein leading to thermal stability at optimum molar ratio. Molecular mechanism operating behind the polyethylene glycol (PEG) mediated stabilization of the protein suggested that strong physical adsorption of PEG on the hydrophobic core of the protein (BSA) along with surface adsorption led to the stability of protein.
Sanjay Rawat
C Raman Suri
Debendra K Sahoo
2011-12-08T19:33:51Z
2011-12-08T19:33:51Z
http://crdd.osdd.net/open/id/eprint/551
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/551
2011-12-08T19:33:51Z
Fontibacillus aquaticus gen. nov., sp. nov., isolated from a warm spring.
A novel facultatively anaerobic strain, designated GPTSA 19(T), was isolated from a warm spring and characterized using a polyphasic approach. The strain behaved as Gram-negative in the Gram staining procedure but showed a Gram-positive reaction in the aminopeptidase test. The novel strain was a mesophilic rod with ellipsoidal endospores. On the basis of 16S rRNA gene sequence analysis, the strain showed closest similarity (96.0 %) with Paenibacillus motobuensis MC10(T). The gene sequence similarity of the novel strain with other species of the genus Paenibacillus was <95.8 %. The novel strain also had PAEN 515F and 682F signature sequence stretches in the 16S rRNA gene that are usually found in most species of the genus Paenibacillus. The strain possessed anteiso-C(15 : 0) as the major fatty acid and MK-7 as the predominant menaquinone. Polar lipids included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), six unknown phospholipids (PLs), one aminophospholipid (PN), three glycolipids (GLs), two aminolipids (ALs), one aminophosphoglycolipid (APGL) and three unknown lipids (ULs). The polar lipid profile of the novel strain, especially as regards ALs, GLs and PLs, distinguished it from the recognized type species of the genus Paenibacillus, Paenibacillus polymyxa, as well as from its closest relative P. motobuensis. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the new strain merits the rank of a novel genus for which the name Fontibacillus gen. nov. is proposed. The type species of the new genus is Fontibacillus aquaticus gen. nov., sp. nov. with the type strain GPTSA 19(T) (=MTCC 7155(T)=DSM 17643(T)).
P Saha
S Krishnamurthi
A Bhattacharya
R Sharma
T Chakrabarti
2011-12-08T19:22:46Z
2011-12-08T19:22:46Z
http://crdd.osdd.net/open/id/eprint/521
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/521
2011-12-08T19:22:46Z
Efficient biotransformation of herbicide diuron by bacterial strain Micrococcus sp. PS-1.
A Gram-positive, Micrococcus sp. strain PS-1 capable of utilizing phenylurea herbicide diuron as a sole carbon source at a high concentration (up to 250 ppm) was isolated from diuron storage site by selective enrichment study. The taxonomic characterization with 16S rRNA gene sequencing (1,477 bp) identified PS-1 as a member of Micrococcus sp. It was studied for the degradation of diuron and a range of its analogues (monuron, linuron, monolinuron, chlortoluron and fenuron). The shake flasks experiments demonstrated fast degradation of diuron (up to 96% at 250 ppm within 30 h incubation) with the addition of small quantity (0.01%) of non-ionic detergent. The relative degradation profile by the isolate was in the order of fenuron > monuron > diuron > linuron > monolinuron > chlortoluron. Further, the biochemical characterization of catabolic pathway by spectroscopic and chromatographic techniques demonstrated that the degradation proceeded via formation of dealkylated metabolites to form 3,4-dichloroaniline (3,4-DCA). It was the major metabolite formed, associated with profound increase in degradation kinetics in presence of appropriate additive.
Priyanka Sharma
Adity Chopra
Swaranjit Singh Cameotra
C Raman Suri
2011-12-08T18:58:51Z
2015-07-22T05:32:12Z
http://crdd.osdd.net/open/id/eprint/500
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/500
2011-12-08T18:58:51Z
Fluoroimmunoassay based on suppression of fluorescence self-quenching for ultra-sensitive detection of herbicide diuron.
A highly sensitive heterogeneous fluoroimmunoassay has been developed for monitoring phenylurea herbicide diuron on the basis of suppression of fluorescence self-quenching. Specific antibody against diuron was produced and labeled with rhodamine isothiocyanate at different molar ratios and used as tracer in the developed immunoassay. The analytical sensitivity of immunoassay was enhanced by changing the microenvironment of fluorescence label with glycerin solution after the completion of immunoassay. Enhancer treatment on developed immunoassay showed improvement of fluorescence signal intensity by approximately 4-folds with higher stability compared with the signal determined without enhancer treatment of the wells. The immunoassay has a detection limit of 0.1 ng mL(-1) with good signal precision (approximately 2%) in the optimum working concentration range between 0.01 and 100 ng mL(-1) of diuron. In addition, the use of enhancer improved the stability of fluorescence signal by suppression of self-quenching of fluorescence signal. The proposed method has been applied satisfactorily for the ultra-sensitive detection of herbicide diuron in samples.
Priyanka Sharma
Sonu Gandhi
Adity Chopra
N Sekar
C Raman Suri
2012-09-11T04:14:32Z
2012-09-11T04:14:32Z
http://crdd.osdd.net/open/id/eprint/1173
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1173
2012-09-11T04:14:32Z
Studies on molecular mechanism of amphotericin bresistance in candida.
Sushma Sharma
2012-09-11T06:29:33Z
2012-09-11T06:29:33Z
http://crdd.osdd.net/open/id/eprint/1190
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1190
2012-09-11T06:29:33Z
Characterization of enzymes involved in riboflavin/ FAD biosynthesis pathway of mycobacterium tuberculosis.
Mirage Singh
2012-09-11T04:44:03Z
2012-09-11T04:44:03Z
http://crdd.osdd.net/open/id/eprint/1181
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1181
2012-09-11T04:44:03Z
Induction of generation of Enduring T Cell Memory Response by Vaccine Engendered from Live Mycobacterium Tuberculosis Infected Macrophages.
Vijender Singh
2011-12-08T19:16:32Z
2012-03-22T09:33:32Z
http://crdd.osdd.net/open/id/eprint/512
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/512
2011-12-08T19:16:32Z
Coadministration of interleukins 7 and 15 with bacille Calmette-Guérin mounts enduring T cell memory response against Mycobacterium tuberculosis.
Our results indicate that supplementation of the BCG vaccine with IL-7 and IL-15 would substantially improve its efficacy by enhancing the T cell memory response.
Vijender Singh
Uthaman Gowthaman
Shweta Jain
Pankaj Parihar
Sunil Banskar
Pushpa Gupta
Umesh D Gupta
J N Agrewala
2011-12-08T19:30:59Z
2011-12-08T19:30:59Z
http://crdd.osdd.net/open/id/eprint/529
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/529
2011-12-08T19:30:59Z
BIAdb: a curated database of benzylisoquinoline alkaloids.
A database of benzylisoquinoline compounds has been created, which provides comprehensive information about benzylisoquinoline alkaloids. This database will be very useful for those who are working in the field of drug discovery based on natural products. This database will also serve researchers working in the field of synthetic biology, as developing medicinally important alkaloids using synthetic process are one of important challenges. This database is available from http://crdd.osdd.net/raghava/biadb/.
Deepak Singla
Arun Sharma
Jasjit Kaur
Bharat Panwar
G.P.S. Raghava
2012-09-11T04:25:41Z
2012-09-11T04:25:41Z
http://crdd.osdd.net/open/id/eprint/1176
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1176
2012-09-11T04:25:41Z
Identification of Mycobacterium Tuberculosis PhoP-regulated promoters and characterization of promoter-regulator interactions.
Akesh Sinha
2011-12-08T19:18:15Z
2011-12-08T19:18:15Z
http://crdd.osdd.net/open/id/eprint/516
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/516
2011-12-08T19:18:15Z
The role of transmembrane domain 9 in substrate recognition by the fungal high-affinity glutathione transporters.
Hgt1p, a high-affinity glutathione transporter from Saccharomyces cerevisiae belongs to the recently described family of OPTs (oligopeptide transporters), the majority of whose members still have unknown substrate specificity. To obtain insights into substrate recognition and translocation, we have subjected all 21 residues of TMD9 (transmembrane domain 9) to alanine-scanning mutagenesis. Phe523 was found to be critical for glutathione recognition, since F523A mutants showed a 4-fold increase in Km without affecting expression or localization. Phe523 and the previously identified polar residue Gln526 were on the same face of the helix suggesting a joint participation in glutathione recognition, whereas two other polar residues, Ser519 and Asn522, of TMD9, although also orientated on the same face, did not appear to be involved. The size and hydrophobicity of Phe523 were both key features of its functionality, as seen from mutational analysis. Sequence alignments revealed that Phe523 and Gln526 were conserved in a cluster of OPT homologues from different fungi. A second cluster contained isoleucine and glutamate residues in place of phenylalanine and glutamine residues, residues that are best tolerated in Hgt1p for glutathione transporter activity, when introduced together. The critical nature of the residues at these positions in TMD9 for substrate recognition was exploited to assign substrate specificities of several putative fungal orthologues present in these and other clusters. The presence of either phenylalanine and glutamine or isoleucine and glutamate residues at these positions correlated with their function as high-affinity glutathione transporters based on genetic assays and the Km of these transporters towards glutathione.
Anil Thakur
Anand K Bachhawat
2011-12-08T19:33:14Z
2011-12-08T19:33:14Z
http://crdd.osdd.net/open/id/eprint/548
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/548
2011-12-08T19:33:14Z
VopF, a type III effector protein from a non-O1, non-O139 Vibrio cholerae strain, demonstrates toxicity in a Saccharomyces cerevisiae model.
VopF, a type III effector protein, has been identified as a contributory factor to the intestinal colonization of type III secretion system-positive, non-O1, non-O139 Vibrio cholerae strains. To gain more insight into the function of VopF, a yeast model was developed. Using this model, it was found that ectopic expression of VopF conferred toxicity in yeast.
Ranjana Tripathi
Santa Singh Naorem
Chetna Dureja
Swati Haldar
Alok K Mondal
Saumya Raychaudhuri
2012-09-11T04:29:09Z
2012-09-11T04:29:09Z
http://crdd.osdd.net/open/id/eprint/1177
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1177
2012-09-11T04:29:09Z
Annotation of Plasmodium Falciparum Proteins using Machine Learning Techniques and Evolutionary Information.
Ruchi Verma
2011-12-08T19:32:32Z
2011-12-08T19:32:32Z
http://crdd.osdd.net/open/id/eprint/542
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/542
2011-12-08T19:32:32Z
Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile.
The rate of human death due to malaria is increasing day-by-day. Thus the malaria causing parasite Plasmodium falciparum (PF) remains the cause of concern. With the wealth of data now available, it is imperative to understand protein localization in order to gain deeper insight into their functional roles. In this manuscript, an attempt has been made to develop prediction method for the localization of mitochondrial proteins. In this study, we describe a method for predicting mitochondrial proteins of malaria parasite using machine-learning technique. All models were trained and tested on 175 proteins (40 mitochondrial and 135 non-mitochondrial proteins) and evaluated using five-fold cross validation. We developed a Support Vector Machine (SVM) model for predicting mitochondrial proteins of P. falciparum, using amino acids and dipeptides composition and achieved maximum MCC 0.38 and 0.51, respectively. In this study, split amino acid composition (SAAC) is used where composition of N-termini, C-termini, and rest of protein is computed separately. The performance of SVM model improved significantly from MCC 0.38 to 0.73 when SAAC instead of simple amino acid composition was used as input. In addition, SVM model has been developed using composition of PSSM profile with MCC 0.75 and accuracy 91.38%. We achieved maximum MCC 0.81 with accuracy 92% using a hybrid model, which combines PSSM profile and SAAC. When evaluated on an independent dataset our method performs better than existing methods. A web server PFMpred has been developed for predicting mitochondrial proteins of malaria parasites ( http://www.imtech.res.in/raghava/pfmpred/).
Ruchi Verma
Grish C Varshney
G.P.S. Raghava
2011-12-08T19:16:21Z
2011-12-08T19:16:21Z
http://crdd.osdd.net/open/id/eprint/511
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/511
2011-12-08T19:16:21Z
Zeta potential based colorimetric immunoassay for the direct detection of diabetic marker HbA1c using gold nanoprobes.
A one-step homogeneous colorimetric immunoassay format coupled with zeta potential measurements for determination of specific diabetic biomarker glycated hemoglobin (HbA1c) using functionalised gold nanoparticles as bioprobes is reported. The assay exhibited an excellent sensitivity based on absorbance and zeta potential measurements showing the dynamic response range from 0.001-0.004 mg mL(-1) for HbA1c with a detection limit of 0.0015 mg mL(-1).
Nishima Wangoo
Jyotsna Kaushal
K K Bhasin
S K Mehta
C Raman Suri
2012-02-28T16:08:52Z
2012-02-28T16:08:52Z
http://crdd.osdd.net/open/id/eprint/1110
This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1110
2012-02-28T16:08:52Z
Probing the primary structural determinants of streptokinase inter-domain linkers by site-specific substitution and deletion mutagenesis.
The bacterial protein streptokinase (SK) contains three independently folded domains (alpha, beta and gamma), interconnected by two flexible linkers with noticeable sequence homology. To investigate their primary structure requirements, the linkers were swapped amongst themselves i.e. linker 1 (between alpha and beta domains) was swapped with linker 2 (between beta and gamma domains) and vice versa. The resultant construct exhibited very low activity essentially due to an enhanced proteolytic susceptibility. However, a SK mutant with two linker 1 sequences, which was proteolytically as stable as WT-rSK retained about 10% of the plasminogen activator activity of rSK When the native sequence of each linker was substituted with 9 consecutive glycine sequences, in case of the linker 1 substitution mutant substantial activity was seen to survive, whereas the linker 2 mutant lost nearly all its activity. The optimal length of linkers was then studied through deletion mutagenesis experiments, which showed that deletion beyond three residues in either of the linkers resulted in virtually complete loss of activator activity. The effect of length of the linkers was then also examined by insertion of extraneous pentapeptide sequences having a propensity for adopting either an extended conformation or a relatively rigid conformation. The insertion of poly-Pro sequences into native linker 2 sequence caused up to 10-fold reduction in activity, whereas its effect in linker 1 was relatively minor. Interestingly, most of the linker mutants could form stable 1:1 complexes with human plasminogen. Taken together, these observations suggest that (i) the functioning of the inter-domain linkers of SK requires a critical minimal length, (ii) linker 1 is relatively more tolerant to insertions and sequence alterations, and appears to function primarily as a covalent connector between the alpha and beta domains, and (iii) the native linker 2 sequence is virtually indispensable for the activity of SK probably because of structural and/or flexibility requirements in SK action during catalysis.
Suman Yadav
Girish Sahni