open: No conditions. Results ordered Creators, Title. 2024-03-29T00:07:12ZEPrintshttp://crdd.osdd.net/images/sitelogo.gifhttp://crdd.osdd.net/open/2012-02-14T10:30:22Z2012-02-14T10:30:22Zhttp://crdd.osdd.net/open/id/eprint/950This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9502012-02-14T10:30:22ZAn observation of non-superimposable stereogeometrical features in a non-chiral one-component β-Ala model peptideThis paper describes the chemical synthesis and crystal molecular conformation of a non-chiral β-Ala containing model peptide Boc-β-Ala-Acc5-OCH3. The analysis revealed the existence of two crystallographically independent molecules A and B, in the asymmetric unit. Unexpectedly, while the magnitudes of the backbone torsion angles in both molecules are remarkably similar, the signs of the corresponding torsion angles are reverse therefore, inclining us to suggest the existence of non-superimposable stereogeometrical features in a non-chiral one-component β-Ala model system. The critical μ torsion angle around CβH2–CαH2 bond of the β-Ala residue represents a typical gauche orientation i.e., μ=67.7° in A and μ=−61.2° in B, providing the molecule an overall crescent shaped topology. The observed conformation contrasts markedly to those determined for the correlated non-chiral model peptides: Boc-β-Ala-Acc6-OCH3 and Boc-β-Ala-Aib-OCH3 signifying the role of stereocontrolling elements since the stereochemically constrained Cα,α-disubstituted glycyl residues (e.g., Acc5, Acc6, and the prototype Aib) are known to strongly restrict the peptide backbone conformations in the 310/α-helical-regions (φ≈±60 ±20°, ψ≈±30 ±20°) of the Ramachandran map. Unpredictably, the preferred, φ,ψ torsion angles of the Acc5 residue fall outside the helical regions of the Ramachandran map and exhibit opposite-handed twists for A and B. The implications of the semi-extended conformation of the Acc5 residue in the construction of backbone-modified novel scaffolds and peptides of biological relevance are highlighted. Taken together, the results indicate that in short linear β-Ala containing peptides specific structural changes can be induced by selective substitution of non-coded linear- or cyclic symmetrically Cα,α-disubstituted glycines, reinstating the hypothesis that in addition to conformational restrictions, the chemical nature of the neighboring side-chain substituents and local environments collectively influences the stabilization of folding–unfolding behavior of the two methylene units of a β-Ala residue.M.Mohan BhadbhadeRaghuvansh Kishore2013-10-18T08:46:36Z2016-03-01T06:10:00Zhttp://crdd.osdd.net/open/id/eprint/1400This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14002013-10-18T08:46:36ZKnowledge based Computational Tools for Prediction of Promiscuous MHC Class I/II Binders and T Cell EpitopesManoj Bhasin2012-01-06T14:55:18Z2012-01-06T14:55:18Zhttp://crdd.osdd.net/open/id/eprint/222This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2222012-01-06T14:55:18ZAnalysis and prediction of affinity of TAP binding peptides using cascade SVM.The generation of cytotoxic T lymphocyte (CTL) epitopes from an antigenic sequence involves number of intracellular processes, including production of peptide fragments by proteasome and transport of peptides to endoplasmic reticulum through transporter associated with antigen processing (TAP). In this study, 409 peptides that bind to human TAP transporter with varying affinity were analyzed to explore the selectivity and specificity of TAP transporter. The abundance of each amino acid from P1 to P9 positions in high-, intermediate-, and low-affinity TAP binders were examined. The rules for predicting TAP binding regions in an antigenic sequence were derived from the above analysis. The quantitative matrix was generated on the basis of contribution of each position and residue in binding affinity. The correlation of r = 0.65 was obtained between experimentally determined and predicted binding affinity by using a quantitative matrix. Further a support vector machine (SVM)-based method has been developed to model the TAP binding affinity of peptides. The correlation (r = 0.80) was obtained between the predicted and experimental measured values by using sequence-based SVM. The reliability of prediction was further improved by cascade SVM that uses features of amino acids along with sequence. An extremely good correlation (r = 0.88) was obtained between measured and predicted values, when the cascade SVM-based method was evaluated through jackknife testing. A Web service, TAPPred (http://www.imtech.res.in/raghava/tappred/ or http://bioinformatics.uams.edu/mirror/tappred/), has been developed based on this approach.Manoj BhasinG.P.S. Raghava2012-01-06T14:54:46Z2012-01-06T15:17:14Zhttp://crdd.osdd.net/open/id/eprint/218This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2182012-01-06T14:54:46ZClassification of nuclear receptors based on amino acid composition and dipeptide composition.Nuclear receptors are key transcription factors that regulate crucial gene networks responsible for cell growth, differentiation, and homeostasis. Nuclear receptors form a superfamily of phylogenetically related proteins and control functions associated with major diseases (e.g. diabetes, osteoporosis, and cancer). In this study, a novel method has been developed for classifying the subfamilies of nuclear receptors. The classification was achieved on the basis of amino acid and dipeptide composition from a sequence of receptors using support vector machines. The training and testing was done on a non-redundant data set of 282 proteins obtained from the NucleaRDB data base (1). The performance of all classifiers was evaluated using a 5-fold cross validation test. In the 5-fold cross-validation, the data set was randomly partitioned into five equal sets and evaluated five times on each distinct set while keeping the remaining four sets for training. It was found that different subfamilies of nuclear receptors were quite closely correlated in terms of amino acid composition as well as dipeptide composition. The overall accuracy of amino acid composition-based and dipeptide composition-based classifiers were 82.6 and 97.5%, respectively. Therefore, our results prove that different subfamilies of nuclear receptors are predictable with considerable accuracy using amino acid or dipeptide composition. Furthermore, based on above approach, an online web service, NRpred, was developed, which is available at www.imtech.res.in/raghava/nrpred.Manoj BhasinG.P.S. Raghava2012-01-06T14:53:16Z2012-01-06T14:53:16Zhttp://crdd.osdd.net/open/id/eprint/208This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2082012-01-06T14:53:16ZESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST.Automated prediction of subcellular localization of proteins is an important step in the functional annotation of genomes. The existing subcellular localization prediction methods are based on either amino acid composition or N-terminal characteristics of the proteins. In this paper, support vector machine (SVM) has been used to predict the subcellular location of eukaryotic proteins from their different features such as amino acid composition, dipeptide composition and physico-chemical properties. The SVM module based on dipeptide composition performed better than the SVM modules based on amino acid composition or physico-chemical properties. In addition, PSI-BLAST was also used to search the query sequence against the dataset of proteins (experimentally annotated proteins) to predict its subcellular location. In order to improve the prediction accuracy, we developed a hybrid module using all features of a protein, which consisted of an input vector of 458 dimensions (400 dipeptide compositions, 33 properties, 20 amino acid compositions of the protein and 5 from PSI-BLAST output). Using this hybrid approach, the prediction accuracies of nuclear, cytoplasmic, mitochondrial and extracellular proteins reached 95.3, 85.2, 68.2 and 88.9%, respectively. The overall prediction accuracy of SVM modules based on amino acid composition, physico-chemical properties, dipeptide composition and the hybrid approach was 78.1, 77.8, 82.9 and 88.0%, respectively. The accuracy of all the modules was evaluated using a 5-fold cross-validation technique. Assigning a reliability index (reliability index > or =3), 73.5% of prediction can be made with an accuracy of 96.4%. Based on the above approach, an online web server ESLpred was developed, which is available at http://www.imtech.res.in/raghava/eslpred/.Manoj BhasinG.P.S. Raghava2012-01-06T14:53:23Z2012-01-06T14:53:23Zhttp://crdd.osdd.net/open/id/eprint/209This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2092012-01-06T14:53:23ZGPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors.G-protein coupled receptors (GPCRs) belong to one of the largest superfamilies of membrane proteins and are important targets for drug design. In this study, a support vector machine (SVM)-based method, GPCRpred, has been developed for predicting families and subfamilies of GPCRs from the dipeptide composition of proteins. The dataset used in this study for training and testing was obtained from http://www.soe.ucsc.edu/research/compbio/gpcr/. The method classified GPCRs and non-GPCRs with an accuracy of 99.5% when evaluated using 5-fold cross-validation. The method is further able to predict five major classes or families of GPCRs with an overall Matthew's correlation coefficient (MCC) and accuracy of 0.81 and 97.5% respectively. In recognizing the subfamilies of the rhodopsin-like family, the method achieved an average MCC and accuracy of 0.97 and 97.3% respectively. The method achieved overall accuracy of 91.3% and 96.4% at family and subfamily level respectively when evaluated on an independent/blind dataset of 650 GPCRs. A server for recognition and classification of GPCRs based on multiclass SVMs has been set up at http://www.imtech.res.in/raghava/gpcrpred/. We have also suggested subfamilies for 42 sequences which were previously identified as unclassified ClassA GPCRs. The supplementary information is available at http://www.imtech.res.in/raghava/gpcrpred/info.html.Manoj BhasinG.P.S. Raghava2012-01-08T05:45:49Z2012-01-08T05:45:49Zhttp://crdd.osdd.net/open/id/eprint/203This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2032012-01-08T05:45:49ZPrediction of CTL epitopes using QM, SVM and ANN techniques.Cytotoxic T lymphocyte (CTL) epitopes are potential candidates for subunit vaccine design for various diseases. Most of the existing T cell epitope prediction methods are indirect methods that predict MHC class I binders instead of CTL epitopes. In this study, a systematic attempt has been made to develop a direct method for predicting CTL epitopes from an antigenic sequence. This method is based on quantitative matrix (QM) and machine learning techniques such as Support Vector Machine (SVM) and Artificial Neural Network (ANN). This method has been trained and tested on non-redundant dataset of T cell epitopes and non-epitopes that includes 1137 experimentally proven MHC class I restricted T cell epitopes. The accuracy of QM-, ANN- and SVM-based methods was 70.0, 72.2 and 75.2%, respectively. The performance of these methods has been evaluated through Leave One Out Cross-Validation (LOOCV) at a cutoff score where sensitivity and specificity was nearly equal. Finally, both machine-learning methods were used for consensus and combined prediction of CTL epitopes. The performances of these methods were evaluated on blind dataset where machine learning-based methods perform better than QM-based method. We also demonstrated through subgroup analysis that our methods can discriminate between T-cell epitopes and MHC binders (non-epitopes). In brief this method allows prediction of CTL epitopes using QM, SVM, ANN approaches. The method also facilitates prediction of MHC restriction in predicted T cell epitopes.Manoj BhasinG.P.S. Raghava2012-01-06T14:55:26Z2012-01-06T14:55:26Zhttp://crdd.osdd.net/open/id/eprint/223This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2232012-01-06T14:55:26ZSVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence.Prediction of peptides binding with MHC class II allele HLA-DRB1(*)0401 can effectively reduce the number of experiments required for identifying helper T cell epitopes. This paper describes support vector machine (SVM) based method developed for identifying HLA-DRB1(*)0401 binding peptides in an antigenic sequence. SVM was trained and tested on large and clean data set consisting of 567 binders and equal number of non-binders. The accuracy of the method was 86% when evaluated through 5-fold cross-validation technique.Manoj BhasinG.P.S. Raghava2012-02-14T10:30:11Z2015-01-08T10:32:01Zhttp://crdd.osdd.net/open/id/eprint/952This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9522012-02-14T10:30:11ZRecent applications of biosurfactants as biological and immunological molecules.The interest in microbial biosurfactants has steadily increased during the past decade. In addition to the classical application as emulsifiers of hydrocarbons, they can be used in environmental protection, crude-oil recovery, food-processing industries and in various fields of biomedicine. Biosurfactants have several advantages over chemical surfactants including lower toxicity and higher biodegradability, and are likely to become molecules of the future in areas such as biomedicine and therapeutics. Here, we discuss the role and applications of biosurfactants (mainly glycolipids and lipopeptides) focusing on medicinal and therapeutic perspectives.Swaranjit Singh CameotraR S Makkar2012-02-14T12:16:24Z2015-01-09T09:44:00Zhttp://crdd.osdd.net/open/id/eprint/965This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9652012-02-14T12:16:24ZEmergence and continued circulation of dengue-2 (genotype IV) virus strains in northern India.Dengue (DEN) is an acute mosquito borne viral disease of mankind. Off late it has become an important public health concern in Southeast Asia. Although, all the four known dengue virus serotypes (DEN-1 to 4) are reported from time to time, in the recent past, DEN-2 has emerged as the predominant type, being the causative agent of several outbreaks of dengue fever (DF) and dengue haemorrhagic fever (DHF) in India. To elucidate the true molecular epidemiology of these viruses, we have sequenced C-prM gene junction (454 nucleotides) of 11 DEN-2 viruses directly from patient serum. The C-prM gene junction was amplified initially by reverse transcription-polymerase chain reaction followed by automated DNA sequencing. These sequences provide unique information with regard to molecular epidemiology when compared to other DEN-2 sequences from diverse geographic origins. The sequence analysis revealed that most of the mutations in this region remained silent, except a few at the carboxy-terminal of the capsid. Reported phylogenetic analysis classifies DEN-2 viruses into five distinct genotypes. The Gwalior DEN-2 viruses, included in the present study were classified into genotype-IV, and were found to be most closely related to Delhi 1996 DEN-2 viruses and FJ 10/11 strains prevalent in the Fujian state of China. However, two earlier Indian isolates of DEN-2 were classified into genotype-V. The present study indicates that genotype V of DEN-2 has been replaced by genotype IV during the past decade, which continues to circulate silently in north India, and have the potential to reemerge and cause major epidemics of DF and DHF.Paban Kumar DashMan Mohan ParidaParag SaxenaManoj KumarArvind RaiS.T PashaAsha Mukul Jana2013-10-18T08:58:21Z2013-10-18T08:58:21Zhttp://crdd.osdd.net/open/id/eprint/1404This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14042013-10-18T08:58:21ZStudies on Process Development for the Production of Recombinant StreptokinaseDeepika Goyal2013-10-18T09:03:32Z2013-10-18T09:03:32Zhttp://crdd.osdd.net/open/id/eprint/1406This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14062013-10-18T09:03:32ZPrediction of Genes and Repetitive Elements in Eukaryotic Genomes Using Artificial Intelligence Techinques.Biju Issac2012-01-08T05:45:18Z2012-01-08T05:45:18Zhttp://crdd.osdd.net/open/id/eprint/199This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1992012-01-08T05:45:18ZEGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches.EGPred is a Web-based server that combines ab initio methods and similarity searches to predict genes, particularly exon regions, with high accuracy. The EGPred program proceeds in the following steps: (1) an initial BLASTX search of genomic sequence against the RefSeq database is used to identify protein hits with an E-value <1; (2) a second BLASTX search of genomic sequence against the hits from the previous run with relaxed parameters (E-values <10) helps to retrieve all probable coding exon regions; (3) a BLASTN search of genomic sequence against the intron database is then used to detect probable intron regions; (4) the probable intron and exon regions are compared to filter/remove wrong exons; (5) the NNSPLICE program is then used to reassign splicing signal site positions in the remaining probable coding exons; and (6) finally ab initio predictions are combined with exons derived from the fifth step based on the relative strength of start/stop and splice signal sites as obtained from ab initio and similarity search. The combination method increases the exon level performance of five different ab initio programs by 4%-10% when evaluated on the HMR195 data set. Similar improvement is observed when ab initio programs are evaluated on the Burset/Guigo data set. Finally, EGPred is demonstrated on an approximately 95-Mbp fragment of human chromosome 13. The list of predicted genes from this analysis are available in the supplementary material. The EGPred program is computationally intensive due to multiple BLAST runs during each analysis. The EGPred server is available at http://www.imtech.res.in/raghava/egpred/.Biju IssacG.P.S. Raghava2012-02-14T10:28:47Z2012-02-14T10:28:47Zhttp://crdd.osdd.net/open/id/eprint/962This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9622012-02-14T10:28:47ZMicrobial Diversity: Exploring the UnexploredManisha KapurR K Jain2012-02-14T10:29:18Z2015-01-09T08:38:35Zhttp://crdd.osdd.net/open/id/eprint/959This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9592012-02-14T10:29:18ZScreening for enantioselective nitrilases: kinetic resolution of racemic mandelonitrile to (R)-(−)-mandelic acid by new bacterial isolatesSeveral new microorganisms have been isolated with high nitrilase activity against (RS)-mandelonitrile using the enrichment culture technique. The organisms were cultivated in liquid culture and the enzyme activity was determined at different phases of growth. The organisms having high enzyme titre were further grown and used as catalysts for the transformation of mandelonitrile to mandelic acid. The percentage conversion was checked with RP-HPLC and the enantiomeric excess was determined on a chiral column. Three isolates gave the desired product, (R)-(−)-mandelic acid with high ee (%) and were identified as Pseudomonas putida, Microbacterium paraoxydans and Microbacterium liquefaciens. All three isolates showed good specific activity (0.33–0.50 U/mg min) with high ee (>93%) and E values. The conversion of racemic mandelonitrile to mandelic acid by these isolates was compared: P. putida was found to be the most suitable biocatalyst for further studies as it showed higher reaction rate (kRxn), lower Km, better growth rate (μ), good yield and ee values and higher stability compared to the other two microorganismsPraveen KaulAnirban BanerjeeShanmugam MayilrajU C Banerjee2012-01-06T14:55:02Z2012-01-06T14:55:02Zhttp://crdd.osdd.net/open/id/eprint/220This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2202012-01-06T14:55:02ZPrediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.In this paper a systematic attempt has been made to develop a better method for predicting alpha-turns in proteins. Most of the commonly used approaches in the field of protein structure prediction have been tried in this study, which includes statistical approach "Sequence Coupled Model" and machine learning approaches; i) artificial neural network (ANN); ii) Weka (Waikato Environment for Knowledge Analysis) Classifiers and iii) Parallel Exemplar Based Learning (PEBLS). We have also used multiple sequence alignment obtained from PSIBLAST and secondary structure information predicted by PSIPRED. The training and testing of all methods has been performed on a data set of 193 non-homologous protein X-ray structures using five-fold cross-validation. It has been observed that ANN with multiple sequence alignment and predicted secondary structure information outperforms other methods. Based on our observations we have developed an ANN-based method for predicting alpha-turns in proteins. The main components of the method are two feed-forward back-propagation networks with a single hidden layer. The first sequence-structure network is trained with the multiple sequence alignment in the form of PSI-BLAST-generated position specific scoring matrices. The initial predictions obtained from the first network and PSIPRED predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. The final network yields an overall prediction accuracy of 78.0% and MCC of 0.16. A web server AlphaPred (http://www.imtech.res.in/raghava/alphapred/) has been developed based on this approach.Harpreet KaurG.P.S. Raghava2012-01-06T14:54:23Z2012-01-06T14:54:23Zhttp://crdd.osdd.net/open/id/eprint/216This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2162012-01-06T14:54:23ZRole of evolutionary information in prediction of aromatic-backbone NH interactions in proteins.In this study, an attempt has been made to develop a neural network-based method for predicting segments in proteins containing aromatic-backbone NH (Ar-NH) interactions using multiple sequence alignment. We have analyzed 3121 segments seven residues long containing Ar-NH interactions, extracted from 2298 non-redundant protein structures where no two proteins have more than 25% sequence identity. Two consecutive feed-forward neural networks with a single hidden layer have been trained with standard back-propagation as learning algorithm. The performance of the method improves from 0.12 to 0.15 in terms of Matthews correlation coefficient (MCC) value when evolutionary information (multiple alignment obtained from PSI-BLAST) is used as input instead of a single sequence. The performance of the method further improves from MCC 0.15 to 0.20 when secondary structure information predicted by PSIPRED is incorporated in the prediction. The final network yields an overall prediction accuracy of 70.1% and an MCC of 0.20 when tested by five-fold cross-validation. Overall the performance is 15.2% higher than the random prediction. The method consists of two neural networks: (i) a sequence-to-structure network which predicts the aromatic residues involved in Ar-NH interaction from multiple alignment of protein sequences and (ii) a structure-to structure network where the input consists of the output obtained from the first network and predicted secondary structure. Further, the actual position of the donor residue within the 'potential' predicted fragment has been predicted using a separate sequence-to-structure neural network. Based on the present study, a server Ar_NHPred has been developed which predicts Ar-NH interaction in a given amino acid sequence. The web server Ar_NHPred is available at and (mirror site).Harpreet KaurG.P.S. Raghava2012-01-06T14:54:01Z2012-01-06T14:54:01Zhttp://crdd.osdd.net/open/id/eprint/214This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2142012-01-06T14:54:01ZA neural network method for prediction of beta-turn types in proteins using evolutionary information.A web server for prediction of beta-turn types I, II, IV and VIII based on above approach is available at http://www.imtech.res.in/raghava/betaturns/ and http://bioinformatics.uams.edu/mirror/betaturns/ (mirror site).Harpreet KaurG.P.S. Raghava2012-02-14T10:30:16Z2012-02-14T10:30:16Zhttp://crdd.osdd.net/open/id/eprint/951This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9512012-02-14T10:30:16ZStrategies for direct attachment of hapten to a polystyrene support for applications in enzyme-linked immunosorbent assay (ELISA)A new method describing direct attachment of carboxylated haptens on a polystyrene support, using 3-aminopropyltriethoxysilane (3-APTES) as a linker, is reported. The hapten coated polystyrene support showed excellent stability as a function of the buffer pH and reaction time, and was successfully used to demonstrate its application in enzyme-linked immunosorbent assay (ELISA).J KaurK.V. SinghManoj RajeGrish C VarshneyC Raman Suri2012-01-08T05:45:26Z2012-01-08T05:45:26Zhttp://crdd.osdd.net/open/id/eprint/200This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2002012-01-08T05:45:26ZAtomic force spectroscopy-based study of antibody pesticide interactions for characterization of immunosensor surface.Development of immunobiosensor detector surfaces involves the immobilization of active antibodies on the capture surface without any significant loss of antigen binding activity. An atomic force microscope (AFM) was used to directly evaluate specific interactions between pesticides and antibodies on a biosensor surface. Oriented immobilization of antibodies against two herbicide molecules 2,4-dichlorophenoxyacetic acid (2,4-D) and atrazine, on gold, was carried out to create the active immunobiosensor surfaces. The adhesive forces between immobilized antibodies and their respective antigens were measured by force spectroscopy using hapten-carrier protein functionalized AFM cantilevers. Relative functional affinity (avidity) measurements of the antibodies carried out prior to immobilization, well correlated with subsequent AFM force measurement observations. Analysis showed that immobilization had not compromised the reactivity of the surface immobilized antibody molecules for antigen nor was there any change in their relative quality with respect to each other. The utility of the immunoreactive surface was further confirmed using a Surface Plasmon Resonance (SPR) based detection system. Our study indicates that AFM can be utilized as a convenient immunobiosensing tool for confirming the presence and also assessing the strength of antibody-hapten interactions on biosensor surfaces under development.Jasdeep KaurKanwar Vikas SinghAshwini Hirlekar SchmidGrish C VarshneyC Raman SuriManoj Raje2012-01-08T05:44:15Z2012-01-08T05:44:15Zhttp://crdd.osdd.net/open/id/eprint/195This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1952012-01-08T05:44:15ZBeta-Ala containing peptides: potentials in design and construction of bioactive peptides and protein secondary structure mimics.In recent years, there has been increasing interest in de novo design and construction of novel synthetic peptides that mimic protein secondary structures, i.e., turns, helices and sheets. The unique structural influences exerted by unsubstituted, non-coded, non-chiral beta-amino acid, i.e., beta-alanine (beta-Ala; 3- or beta- aminopropionic acid) on peptide backbone, when inserted into peptide chain comprised alpha-amino acids, offer an excellent opportunity to design and construct diverse well-defined three-dimensional structures. Our current understanding of folding-unfolding behavior of the beta-Ala residues relies primarily from an examination of conformational preferences of a large number of short cyclic- as well as acyclic beta-Ala containing peptides investigated using single crystal X-ray diffraction analysis. In addition, theoretical conformational energy calculations and different spectroscopic techniques: 1H NMR, FT-IR and CD, have also been employed although, to a lesser extent. The obtainable results tend to reveal overwhelming preferences of the beta-Ala moiety for the folded gauche (mu approximately +/-65+/-10 degrees conformation in cyclic- and for an extended trans (mu approximately +/-165+/-10 degrees) as well as gauche (mu approximately +/-65+/-10 degrees) orientations in acyclic beta-Ala containing peptides. The results also indicate that in short linear beta-Ala containing peptides, the specific influence of selective neighboring side-chain substituents e.g. linear- or cyclic symmetrically C(alpha,alpha)-disubstituted glycines and other conformational constraints, may be significant in controlling the overall folded-unfolded topographical features across the two methylene units (-CbetaH2-CalphaH2-) of the beta-Ala residue. Taking into consideration the wide occurrence of beta-Ala moiety in animal and plant kingdoms and the remarkable structural versatility of the peptides incorporating beta-Ala residue(s), together with appreciable resistance towards enzymatic degradation, hold strong promise for biophysicists and biochemists not only to design molecules that fold to mimic protein secondary structures but also to develop potent peptide analogs and peptidomimetics displaying unique pharmaceutical properties.Raghuvansh Kishore2012-01-08T05:44:41Z2012-01-08T05:44:41Zhttp://crdd.osdd.net/open/id/eprint/197This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1972012-01-08T05:44:41ZA search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoter.We describe a web-based resource to identify, search and analyze sequence patterns conserved in the multiple sequence alignments of orthologous promoters from closely related / distant Saccharomyces spp. The webtool interfaces with a database where conserved sequence patterns (greater than 4 bp) have been previously extracted from genome-wide promoter alignments, allowing one to carry out user-defined genome-wide searches for conserved sequences to assist in the discovery of novel promoter elements based on comparative genomics. The web-based server can be accessed at http://www2.imtech.res.in/ anand/sacch_prom_pat.html.Davinder K KohliChittur V SrikanthAnand K Bachhawat2012-02-14T12:16:18Z2015-01-09T11:38:54Zhttp://crdd.osdd.net/open/id/eprint/966This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9662012-02-14T12:16:18ZUnusual emergence of guate98-like molecular subtype of DEN-3 during 2003 dengue outbreak in DelhiWith a view to identifying the molecular subtype of the circulating dengue virus responsible for a major
outbreak of dengue fever (DF) / dengue haemorrhagic fever (DHF) in and around Delhi during the postmonsoon
period in 2003, 32 serum samples were collected from clinically suspected cases. These were
subjected to reverse transcription/polymerase chain reaction (RT/PCR) for amplification of 511 bp CPreM
gene region of the dengue virus. Seven specimens, yielding a satisfactory quantum of viral RNA,
were subsequently processed for automated nucleotide sequencing. Five of the seven analysed isolates
showed close DNA sequence homology with Guate96-98 strains of DEN-3 virus, whereas two turned out
to be genotype IV of DEN-2. Earlier, DEN-2 (genotype IV) had been identified as the etiological agent
during a major DF/DHF outbreak in Delhi in 1996 and also in 2000. Though DEN-2 continues to prevail,
DEN-3, having a close sequence homology with Guate96-98 strains, seems to have entered India for the
first time in late 2003, resulting in a major DF/DHF outbreak. How the Guate96-98 strain of DEN-3
entered India remains to be linked epidemiologically.Manoj KumarS.T PashaV. MittalS.C. AryaN. AgrawalD. BhattacharyaLal ShivArvind Rai2012-01-08T05:44:22Z2012-01-08T05:44:22Zhttp://crdd.osdd.net/open/id/eprint/196This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1962012-01-08T05:44:22ZExpression and secretion of a prokaryotic protein streptokinase without glycosylation and degradation in Schizosaccharomyces pombe.Streptokinase (SK) is an important thrombolytic protein that is secreted by pathogenic strains of Streptococcus. Expression of streptokinase has been so far attempted in Pichia pastoris, Escherichia coli and Bacillus subtilis and shown to yield protein that was either highly glycosylated or degraded. Since the fission yeast, Schizosaccharomyces pombe, shares several molecular characteristics with higher eukaryotes, we decided to express the streptokinase gene in this yeast. A chimeric gene comprising the signal sequence of the Plus pheromone of Sz. pombe fused in-frame with the mature streptokinase from Streptococcus sp. was constructed and inserted into the expression vector containing the thiamine-regulated promoter. We obtained a high level of expression of streptokinase comparable to that in E. coli and P. pastoris, with 50-100% processing of the signal sequence and secretion of the mature streptokinase into the periplasmic fraction. The mature enzyme co-migrates with the authentic mature SK in SDS gels, lacks any major modification and is functional. Importantly, a higher level of expression under stationary phase conditions and improved extractability of the mature and undegraded streptokinase was achieved in a novel mutant of Sz. pombe defective for a potent extracellular protease activity. We suggest that the unique vector/strain system developed here could be advantageous for large-scale production of prokaryotic proteins without significant modification or degradation in Sz. pombe.Raj KumarJagmohan Singh2012-01-08T05:46:08Z2012-01-08T05:46:08Zhttp://crdd.osdd.net/open/id/eprint/205This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2052012-01-08T05:46:08ZThe excised heat-shock domain of alphaB crystallin is a folded, proteolytically susceptible trimer with significant surface hydrophobicity and a tendency to self-aggregate upon heating.The lens protein, alpha-crystallin, is a molecular chaperone that prevents the thermal aggregation of other proteins. The C-terminal domain of this protein (homologous to domains present in small heat-shock proteins) is implicated in chaperone function, although the domain itself has been reported to show no chaperone activity. Here, we show that the domain can be excised out of the intact alphaB polypeptide and recovered directly in pure form through the transfer of CNBr digests of whole lens homogenates into urea-containing buffer, followed by dialysis-based refolding of digests under acidic conditions and a single gel-filtration purification step. The folded (beta sheet) domain thus obtained is found to be (a) predominantly trimeric, and to display (b) significant surface hydrophobicity, (c) a marked tendency to undergo degradation, and (d) a tendency to aggregate upon heating, and on exposure to UV light. Thus, the twin 'chaperone' features of multimericity and surface hydrophobicity are clearly seen to be insufficient for this domain to function as a chaperone. Since alpha-crystallin interacts with its substrates through hydrophobic interactions, the hydrophobicity of the excised domain indicates that separation of domains may regulate function; at the same time, the fact is also highlighted that surface hydrophobicity is a liability in a chaperone since heating strengthens hydrophobic interactions and can potentially promote self-aggregation. Thus, it would appear that the role of the N-terminal domain in alpha-crystallin is to facilitate the creation of a porous, hollow structural framework of >/=24 subunits in which solubility is effected through increase in the ratio of exposed surface area to buried volume. Trimers of interacting C-terminal domains anchored to this superstructure, and positioned within its interior, might allow hydrophobic surfaces to remain accessible to substrates without compromising solubility.Bishwajit KunduAnshuman ShuklaRachna ChabaPurnananda Guptasarma2012-02-14T12:16:00Z2012-02-14T12:16:00Zhttp://crdd.osdd.net/open/id/eprint/970This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9702012-02-14T12:16:00ZHLA-B27 lacking associated beta2-microglobulin rearranges to auto-display or cross-display residues 169-181: a novel molecular mechanism for spondyloarthropathies.Expression of the MHC class I allele, HLA-B27, is correlated with autoimmune disease. The misfolding and association of B27 heavy chains through non-native disulfide bonds has recently been implicated. Here, we propose that beta2m-free, peptide-free heavy chains support a helix-coil transition in the segment leading from the alpha2 domain to the alpha3 domain, facilitating rotation of backbone angles around residues 167/168, and allowing residues 169-181 (identical to a known B27 ligand) to loop around and occupy the molecule's own peptide-binding cleft. Such 'auto-display', occurring either within B27 molecules, or between B27 molecules, could provoke autoimmune attack.Manni Luthra-GuptasarmaBalvinder Singh2012-02-14T10:31:29Z2015-01-09T08:50:48Zhttp://crdd.osdd.net/open/id/eprint/940This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9402012-02-14T10:31:29ZGeneration and characterization of anti-MUC4 monoclonal antibodies reactive with normal and cancer cells in humans.We have previously cloned the full-length cDNA (approximately 28 Kb) and established the complete genomic organization (25 exons/introns over 100 kb) of the human MUC4 mucin. This large molecule is predicted to protrude over 2 microm above the cell surface, in which MUC4alpha is an extracellular mucin-type glycoprotein subunit and MUC4beta is the transmembrane subunit. Over two thirds of the encoded protein sequence consists of 16-amino-acid tandem repeats (TR), which are flanked by unique sequences. In this study we generated and characterized monoclonal antibodies (MAbs) directed against the TR region of MUC4. Mice were immunized with a KLH-conjugated MUC4 TR peptide, STGDTTPLPVTDTSSV. Several clones were purified by three rounds of limited dilutions and stable clones presenting a sustained antibody production were selected for subsequent characterization. Antibodies were tested for their reactivity and specificity to recognize the MUC4 peptide and further screened by enzyme-linked immunosorbent assay (ELISA) and Western blotting analyses. One of the MAbs (8G7) was strongly reactive against the MUC4 peptide and with native MUC4 from human tissues or pancreatic cancer cells in Western blotting, immunohistochemistry, and confocal analysis. Anti-MUC4 MAb may represent a powerful tool for the study of MUC4 function under normal and pathological conditions and for diagnosis of solid tumors including those in the breast, pancreas, lungs, and ovaries.N MoniauxGrish C VarshneySubhash Chand ChauhanMarie Christine CopinM JainUwe A WittelMahefatiana AndrianifahananaJean-Pierre AubertSurinder K Batra2013-10-18T09:08:27Z2013-10-22T11:12:57Zhttp://crdd.osdd.net/open/id/eprint/1407This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14072013-10-18T09:08:27ZStructure-Function Studies of Staphylokinase. Monika2012-01-06T14:53:54Z2015-01-09T09:16:42Zhttp://crdd.osdd.net/open/id/eprint/213This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2132012-01-06T14:53:54ZPrediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods.This article describes a method developed for predicting transmembrane beta-barrel regions in membrane proteins using machine learning techniques: artificial neural network (ANN) and support vector machine (SVM). The ANN used in this study is a feed-forward neural network with a standard back-propagation training algorithm. The accuracy of the ANN-based method improved significantly, from 70.4% to 80.5%, when evolutionary information was added to a single sequence as a multiple sequence alignment obtained from PSI-BLAST. We have also developed an SVM-based method using a primary sequence as input and achieved an accuracy of 77.4%. The SVM model was modified by adding 36 physicochemical parameters to the amino acid sequence information. Finally, ANN- and SVM-based methods were combined to utilize the full potential of both techniques. The accuracy and Matthews correlation coefficient (MCC) value of SVM, ANN, and combined method are 78.5%, 80.5%, and 81.8%, and 0.55, 0.63, and 0.64, respectively. These methods were trained and tested on a nonredundant data set of 16 proteins, and performance was evaluated using "leave one out cross-validation" (LOOCV). Based on this study, we have developed a Web server, TBBPred, for predicting transmembrane beta-barrel regions in proteins (available at http://www.imtech.res.in/raghava/tbbpred).Navjot K NattHarpreet KaurG.P.S. Raghava2013-10-18T09:00:50Z2013-10-18T09:00:50Zhttp://crdd.osdd.net/open/id/eprint/1405This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14052013-10-18T09:00:50ZBio degradation of Some of the Nitroaromatic Compounds and Bacterial ChemotaxisGunjan Pandey2012-02-14T10:29:45Z2012-02-14T10:29:45Zhttp://crdd.osdd.net/open/id/eprint/956This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9562012-02-14T10:29:45ZHow effective is the extended kalman filter for continuous yeast cultures affected by both inflow and measurement noise?. The usefulness of the extended Kalman filter (EKF) as
an on-line estimator of process variables is known for
monotonic laboratory-scale fermentations. However,
this has not been tested for oscillating cultures under
non-ideal conditions representative of large bioreactors.
So, in this study an EKF was applied for on-line
filtering of simulated data of an oscillating continuous
Saccharomyces cerevisiae culture with inflow and measurement
noise. For better accuracy, the tuning of the
EKF was updated over successive time slices such that
deviations between the noise-affected and noise-free
profiles were minimized during each interval. As shown
by the concentrations of biomass and ethanol, noise disrupted periodicity in both, but oscillations close to
the noise-free behaviour could be restored substantially
by the EKF, thus suggesting its suitability for
large non-ideal bioreactors with either monotonic or
oscillating cultures.P R Patnaik2012-02-14T10:30:05Z2012-02-14T10:30:05Zhttp://crdd.osdd.net/open/id/eprint/953This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9532012-02-14T10:30:05ZInfluence of fluid mixing on oscillations in recombinant fermentations with variable plasmid loss. A preliminary studyP R Patnaik2012-02-14T10:29:52Z2015-01-09T09:49:46Zhttp://crdd.osdd.net/open/id/eprint/955This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9552012-02-14T10:29:52ZLyapunov comparison of noise-filtering methods for oscillating yeast culturesP R Patnaik2012-02-14T10:29:58Z2012-02-14T10:29:58Zhttp://crdd.osdd.net/open/id/eprint/954This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9542012-02-14T10:29:58ZNeural and hybrid neural modelling and control of fed-batch fermentation for streptokinase: Comparative evaluation under nonideal conditions.Fermentations involving competition between two or
more kinds of cells under nonideal conditions show
complex profi les that are sensitive to the extra-cellular
environment. These fermentations therefore require
accurate and rapid on-line data acquisition and control.
However, both on-line measurements and modelling
are diffi cult and expensive for large bioreactors, thus
limiting the usefulness of model-based control. While
neural networks offer an alternative, they require
extensive training and can be diffi cult to optimize
for large arrays. Hybrid networks combining
a few neural networks with some mathematical
equations offer a good compromise. The possibility of
using a hybrid model for simulation-cum-control has
been examined here for the fed-batch production of
streptokinase. Under noideal conditions, hybrid neural
models outperformed both mathematical models
and arrays of neural networks, thus suggesting their
viability for large-scale fermentation monitoring and
control.
Les fermentations provoquant une compétition entre
deux ou plusieurs sortes de cellules dans des conditions
non idéales montrent des profi ls complexes qui
sont sensibles à l’environnement extra-cellulaires. Ces
fermentations nécessitent donc une acquisition et un
contrôle en continu des données qui soient précis et
rapides. Toutefois, les mesures et la modélisation en
continu sont diffi ciles et coûteuses pour les grands
bioréacteurs, ce qui limite l’utilité du contrôle basé sur
des modèles. Les réseaux neuronaux sont une autre
possibilité, mais ceux-ci nécessitent un entraînement
poussé et peuvent être diffi ciles à optimiser pour de
grands dispositifs. Les réseaux hybrides combinant
réseaux neuronaux et équations mathématiques
offrent un bon compromis. La possibilité d’utiliser
un modèle hybride pour la simulation et le contrôle
a été examinée dans ce travail pour la production
à alimentation discontinue de streptokinase. Dans
des conditions non idéales, les modèles neuronaux
hybrides offrent une meilleure performance que les
modèles mathématiques ou les dispositifs de réseaux
neuronaux, et il pourrait donc s’avérer viable pour la
surveillance et le contrôle de fermentation à grande
échelleP R Patnaik2012-02-14T10:28:55Z2012-02-14T10:28:55Zhttp://crdd.osdd.net/open/id/eprint/961This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9612012-02-14T10:28:55ZPathway for the degradation of p-hydroxybenzoate in Arthrobacter protophormiae RKJ100 and Burkholderia cepacia RKJ200Debarati PaulArchana ChauhanGunjan PandeyR K Jain2013-10-22T11:24:42Z2013-10-30T10:59:28Zhttp://crdd.osdd.net/open/id/eprint/1478This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14782013-10-22T11:24:42ZProtein Engineering studies on Thrombolytic Proteins Kammara Rajagopal2012-02-14T12:18:05Z2012-02-14T12:18:05Zhttp://crdd.osdd.net/open/id/eprint/963This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9632012-02-14T12:18:05ZGlomus hyderabadensis, a new species: Its taxonomy and phylogenetic comparison with related speciesAbstract—A novel Glomus species was isolated from rhizosphere soils
supporting Allamanda cathartica from Hyderabad, India. The spores proliferate
and bud out a daughter spore terminally which is connected to the mother spore by
a small connective. Sequence analysis of D1D2 variable domain of 26S ribosomal
RNA gene of this Glomus sp. shows that it is different from other known AM
fungi. The morphological and molecular phylogenetic analyses support the
creation of Glomus hyderabadensis sp. nov.S. RaniI. SwarupaK. KunwarG S PrasadC. Manoharachary2012-02-14T10:30:28Z2020-06-10T10:49:53Zhttp://crdd.osdd.net/open/id/eprint/949This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9492012-02-14T10:30:28ZBcePred: Prediction of Continuous B-cell epitopes in antigenic sequences using physico-chemical propertiesA crucial step in designing of peptide vaccines involves the identification of B-cell epitopes. In past, numerous methods have been developed for predicting continuous B-cell epitopes, most of these methods are based on physico-chemical properties of amino acids. Presently, its difficult to say which residue property or method is better than the others because there is no independent evaluation or benchmarking of existing methods. In this study the performance of various residue properties commonly used in B-cell epitope prediction has been evaluated on a clean dataset. The dataset used in this study consists of 1029 non-redundant B cell epitopes obtained from Bcipep database and equally number of non-epitopes obtained randomly from SWISS-PROT database. The performance of each residue property used in existing methods has been computed at various thresholds on above dataset. The accuracy of prediction based on properties varies between 52.92% and 57.53%. We have also evaluated the combination of two or more properties as combination of parameters enhance the accuracy of prediction. Based on our analysis we have developed a method for predicting B cell epitopes, which combines four residue properties. The accuracy of this method is 58.70%, which is slightly better than any single residue property. A web server has been developed to predict B cell epitopes in an antigen sequence.Sudipto SahaG.P.S. Raghava2013-10-18T06:25:26Z2013-10-18T06:25:26Zhttp://crdd.osdd.net/open/id/eprint/1397This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13972013-10-18T06:25:26ZDevelopment of Bioinformatics Tools for Prediction of Beta- Turns in Proteins and Their role in Bioactive PeptidesHarpreet Kaur Saini2013-10-18T08:43:41Z2013-10-18T08:43:41Zhttp://crdd.osdd.net/open/id/eprint/1399This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13992013-10-18T08:43:41ZCharacterization of a Thioesterase from Alcaligenes faecalis and a Dehydrogenase from Penicillium Funiculasum and Applications of the Dehydrogenase in the Proparation of Pharmaceuticals and Fine ChemicalsPuja Shahi2012-01-10T08:06:16Z2012-01-10T08:06:16Zhttp://crdd.osdd.net/open/id/eprint/87This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/872012-01-10T08:06:16ZSpectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.Motivation: Repetitive DNA sequences, besides having a variety of regulatory functions, are one of the principal causes of genomic instability. Understanding their origin and evolution is of fundamental importance for genome studies. The identification of repeats and their units helps in deducing the intra-genomic dynamics as an important feature of comparative genomics. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length.
Results: The Spectral Repeat Finder program circumvents these problems by using a discrete Fourier transformation to identify significant periodicities present in a sequence. The specific regions of the sequence that contribute to a given periodicity are located through a sliding window analysis, and an exact search method is then used to find the repetitive units. Efficient and complete detection of repeats is provided together with interactive and detailed visualization of the spectral analysis of input sequence. We demonstrate the utility of our method with various examples that contain previously unannotated repeats. A Web server has been developed for convenient access to the automated program
Deepak SharmaBiju IssacG.P.S. RaghavaR Ramaswamy2012-01-06T14:53:31Z2015-01-07T05:24:43Zhttp://crdd.osdd.net/open/id/eprint/210This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2102012-01-06T14:53:31ZPotent role of vaccines prepared from macrophages infected with live bacteria in protection against Mycobacterium tuberculosis and Salmonella typhimurium infections.The present study describes a novel and simple vaccination strategy that involves the culturing of live Mycobacterium tuberculosis and Salmonella typhimurium in syngeneic, allogeneic, and xenogeneic macrophages, followed by drug treatment and gamma irradiation, to kill the bacteria. Notable observations were that the lymphocytes obtained from the vaccinated mice proliferated and secreted mainly interferon- gamma and IgG2a, but not interleukin-4 and IgG1. The enumeration of viability of M. tuberculosis indicated a significant level of protection in the vaccinated mice after challenge with live M. tuberculosis. This vaccination strategy worked successfully for tuberculosis but also showed a significant decrease in mortality of mice challenged with live S. typhimurium.Naresh SharmaJ N Agrewala2013-10-18T08:55:30Z2013-10-18T08:55:30Zhttp://crdd.osdd.net/open/id/eprint/1403This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14032013-10-18T08:55:30ZIsolation and Characterization of PBS2 Homologue From Debaryomyces HenseniiPratima Sharma2012-01-06T14:54:11Z2012-01-06T14:54:11Zhttp://crdd.osdd.net/open/id/eprint/215This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2152012-01-06T14:54:11ZFolding of beta/alpha-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (beta/alpha)8-barrel.The (beta/alpha)(8)-barrel domain consists of eight topologically equivalent supersecondary structural motifs known as beta/alpha-units. Each unit consists of a single beta-strand, an alpha-helix, and two loops. Evidence collected in recent years indicates that the (beta/alpha)(8)-barrel motif may not be a single, autonomously-folding domain, as was previously assumed. Segments of some (beta/alpha)(8)-barrels appear to fold autonomously. However, the extent to which this is true of various (beta/alpha)(8)-barrel domains remains to be explored. In this study, we have scrambled (reshuffled) the native order of beta/alpha-units (1-2-3-4-5-6-7-8) comprising the polypeptide chain of a model (beta/alpha)(8)-barrel from S. cerevisiae, triosephosphate isomerase (TIM). Total scrambling was effected in order to examine whether folding can still occur to yield beta/alpha-structures in spite of a global 'destruction' of native hydrophobic and hydrogen bonding interactions among beta/alpha-units, while still allowing the occurrence of native interactions within individual units. Our results demonstrate that scrambled full-barrel forms (2-4-6-8-1-3-5-7 and 1-3-5-7-2-4-6-8), as well as half-barrel (2-4-6-8) and quarter-barrel (1-3) forms of TIM fold into beta/alpha-structures that sustain tertiary and quaternary structural interactions. In particular, one variant (2-4-6-8-1-3-5-7) was found to fold and form a stable dimer with native-like structural content and other characteristics. Our results demonstrate that (beta/alpha)(8)-barrels can tolerate profound alterations of both strand-strand interactions responsible for the creation of the beta-barrel and the geometry of presentation of nonpolar sidechains into the hydrophobic core of the beta-barrel by individual beta-strands. These findings lend support to our recent proposal1 that a hierarchy of interactions probably regulates structure formation and stability in (beta/alpha)(8)-barrels, where folding proceeds successively through three stages: (i) the tentative formation of individual beta/alpha-units which associate through 'near-neighbor' diffusion-collision interactions into (ii) curved assemblies of multiple beta/alpha-units through sequence-independent hydrogen bonding of strands of neighboring units, leading finally to (iii) the association of curved (quarter/half-barrel) assemblies around a common hydrophobic core through packing interactions that remain plastic and amenable to change.Anshuman ShuklaPurnananda Guptasarma2012-01-08T05:46:15Z2012-04-02T09:19:34Zhttp://crdd.osdd.net/open/id/eprint/206This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2062012-01-08T05:46:15ZA novel UV laser-induced visible blue radiation from protein crystals and aggregates: scattering artifacts or fluorescence transitions of peptide electrons delocalized through hydrogen bonding?Proteins lacking prosthetic groups and/or cofactors are known to undergo electronic excitation transitions only upon exposure to UV-C (< 280 nm) and UV-B (280-320 nm), but not UV-A (320-400 nm) photons. Here, we report the discovery of a novel excitation that peaks at approximately 340 nm and yields visible violet-blue radiation with apparent band maxima at approximately 425, 445, 470, and 500 nm. All proteins and large polypeptides examined in solid form, and in solutions, display this quenchable and photobleachable radiation which can be established not owing to aromatic sidechains. As a note of caution, we wish to state that we have not been able to completely eliminate the possibility that the radiation may be an artifact owing to second order effects such as, e.g., Raman scattering of Raman-scattered photons; however, we assert that all our experiments indicate that the radiation actually owes to some form of fluorescence. We propose that peptide electrons that have been delocalized through intramolecular or intermolecular hydrogen bond formation display these long-wavelength electronic transitions. If confirmed by future studies, this preliminary discovery may turn out to have important implications for biomolecular spectroscopy, protein crystallography, and materials science.Anshuman ShuklaSourav MukherjeeSwati SharmaVishal AgrawalK V Radha KishanPurnananda Guptasarma2012-01-06T14:53:07Z2012-01-06T14:53:07Zhttp://crdd.osdd.net/open/id/eprint/207This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2072012-01-06T14:53:07ZPepBuild: a web server for building structure data of peptides/proteins.PepBuild, a web server, will aid in designing and building a capped or uncapped peptide/protein with known secondary and tertiary structure. The user can build a peptide/protein by choosing the required amino acid residue with regular secondary structure. The torsional angles can be supplied by the user, if desired. The server also allows the user to add relevant protecting groups at the N- and/or C-terminal of the peptide. The amino acid side chains of the designed peptide are optimized using rotameric libraries. Finally, the server provides the option of displaying the result or downloading the complete file in PDB (Protein Data Bank) format. This PDB file can later be used as an input for various molecular simulation programs or for graphical display. The web server is available at http://www.imtech.res.in/bvs/pepbuild/.Balvinder Singh2012-02-14T10:29:28Z2015-01-09T10:50:19Zhttp://crdd.osdd.net/open/id/eprint/958This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9582012-02-14T10:29:28ZEnhanced production of alkaline proteases by Bacillus sphaericus using fed-batch cultureBacillus sphaericus, an obligate alkalophile, overproduces extracellular alkaline proteases. Kinetics of growth and protease production by this organism were analyzed to identify parameters that control protease synthesis. Results showed protease production to be both growth and non-growth associated although a major portion of the enzyme was secreted in post exponential phases. The initial concentration of glucose and nitrogen sources significantly affected cell growth and enzyme secretion. Fed-batch cultures were performed to maximize protease activity in a bioreactor. By using suitable feeding strategies, the protease activity and its productivity in a fed-batch process was increased by 44% over that in batch process, primarily due to the longer maintenance of increased rates of growth and enzyme production by providing continuous and controlled supply of additional substrate and nutrients.Jasvir SinghR M VohraDebendra K Sahoo2012-01-06T14:55:37Z2012-01-07T10:51:50Zhttp://crdd.osdd.net/open/id/eprint/224This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2242012-01-06T14:55:37ZSynthesis and characterization of hapten-protein conjugates for antibody production against small molecules.For the generation of antibodies against small hapten molecules, the hapten is cross-linked with some carrier protein to make it immunogenic. However, the formation of such conjugates is not always reproducible. This may lead to inconsistent hapten-protein stoichiometries, resulting in large variations in the generation of the desired antibodies. In the study described here the hapten (mercaptopropionic acid derivative of atrazine) was coupled to carrier protein at five different molar ratios. The hapten-protein conjugates prepared were characterized thoroughly by spectrophotometric absorption, fluorescence, matrix-assisted laser desorption ionization (MALDI), and gel electrophoresis methods, before being used for the immunization and assay purposes. Electrophoresis and fluorescence methods were very useful in detecting hapten-protein cross-linking while MALDI-MS and spectrophotometric detection provided qualitatively comparable hapten density. The production of specific antibodies was sought following the generation of appropriate hapten-protein conjugates. A high antibody titer with moderate antibody specificity was obtained with hapten density around 15 molecules per carrier protein. The study proved useful for monitoring the course of hapten-protein conjugation for the production of specific antibodies against small molecules.K V SinghJasdeep KaurGrish C VarshneyManoj RajeC Raman Suri2012-01-06T14:53:39Z2012-01-06T14:53:39Zhttp://crdd.osdd.net/open/id/eprint/211This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2112012-01-06T14:53:39ZEnhancement of metal bioremediation by use of microbial surfactants.Metal pollution all around the globe, especially in the mining and plating areas of the world, has been found to have grave consequences. An excellent option for enhanced metal contaminated site bioremediation is the use of microbial products viz. microbial surfactants and extracellular polymers which would increase the efficiency of metal reducing/sequestering organisms for field bioremediation. Important here is the advantage of such compounds at metal and organic compound co-contaminated site since microorganisms have long been found to produce surface-active compounds when grown on hydrocarbons. Other options capable of proving efficient enhancers include exploiting the chemotactic potential and biofilm forming ability of the relevant microorganisms. Chemotaxis towards environmental pollutants has excellent potential to enhance the biodegradation of many contaminants and biofilm offers them a better survival niche even in the presence of high levels of toxic compounds.Pooja SinghSwaranjit Singh Cameotra2012-01-06T14:54:54Z2012-01-06T14:54:54Zhttp://crdd.osdd.net/open/id/eprint/219This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2192012-01-06T14:54:54ZPotential applications of microbial surfactants in biomedical sciences.The main commercial use of biosurfactants is in pollution remediation because of their ability to stabilize emulsions. This enhances the solubility and availability of hydrophobic pollutants, thus increasing their potential for biodegradation. One useful property of many biosurfactants that has not been reviewed extensively is their antimicrobial activity. Several biosurfactants have strong antibacterial, antifungal and antiviral activity. Other medically relevant uses of biosurfactants include their role as anti-adhesive agents to pathogens, making them useful for treating many diseases and as therapeutic and probiotic agents. Here, we discuss some of the new and exciting applications and related developments of various microbial surfactants in the field of biomedical sciences.Pooja SinghSwaranjit Singh Cameotra2012-01-06T14:54:38Z2015-01-07T04:39:25Zhttp://crdd.osdd.net/open/id/eprint/217This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2172012-01-06T14:54:38ZIsolation of a member of Acinetobacter species involved
in atrazine degradationContribution of Acinetobacter genus in the degradation of atrazine and its analogs is reported here. An interesting bacterial isolate capable of degrading atrazine as high as 250 ppm was isolated from a soil heavily contaminated with atrazine. The permissible level of atrazine in drinking water is 3 ppb and hence use of a strain capable of atrazine degradation as high as 250 ppm would be of immense help for rapid environmental cleanup. This isolate was found to be capable of best growth at 37 degrees C and at pH inclined towards the alkaline side. It was found that atrazine was utilized as a carbon and not as a nitrogen source. Acinetobacter species was also active on other triazine pesticides, viz., simazine, terbutryn, cyanazine, and prometon. There are very few reports on the degradation of atrazine by any member of this genus and hence this could lead to new degradation pathways and new metabolites.Pooja SinghC Raman SuriSwaranjit Singh Cameotra2013-10-18T09:18:29Z2013-10-18T09:18:29Zhttp://crdd.osdd.net/open/id/eprint/1410This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14102013-10-18T09:18:29ZIsolation and Characterization of Bioactive Compounds from ActinomycetesArvind Kumar Singla2013-10-18T09:14:38Z2013-10-18T09:14:38Zhttp://crdd.osdd.net/open/id/eprint/1409This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14092013-10-18T09:14:38ZStudies on the Glutathione Transpors of the Yeast S. CerevisiaeC V Srikanth2012-02-14T12:16:06Z2015-01-12T04:31:36Zhttp://crdd.osdd.net/open/id/eprint/968This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9682012-02-14T12:16:06ZBacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, IndiaStrain Sd/3T (=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23° 3′ N 88° 35′ E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genus Bacillus, such as it had A4β murein type (l-orn-d-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3T was identified as a species of the genus Bacillus. It exhibited maximum similarity (95 %) at the 16S rRNA gene level with Bacillus cohnii; however, DNA–DNA similarity with B. cohnii was 60·7 %. Strain Sd/3T also exhibited a number of phenotypic differences from B. cohnii (DSM 6307T). These data suggest that Sd/3T represents a novel species of the genus Bacillus. The name Bacillus indicus sp. nov. is proposed. K. SureshS R PrabagaranS SenguptaS Shivaji2012-02-14T12:16:12Z2015-01-19T05:54:15Zhttp://crdd.osdd.net/open/id/eprint/967This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9672012-02-14T12:16:12ZDeinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, IndiaAn arsenic- and radiation-resistant bacterium, strain Wt/1aT, was isolated from water from an arsenic-contaminated aquifer located in the Chakdah district of West Bengal, India. The bacterium stains Gram-negative and is rod-shaped, non-motile, non-sporulating and red-pigmented. Cell-wall peptidoglycan contains ornithine as the diamino acid, MK-8 is the major menaquinone, C15 : 1 and C16 : 1 are the major fatty acids and the DNA G+C content of the organism is 65·8 mol%. Based on these phenotypic and chemotaxonomic characteristics, strain Wt/1aT was identified as a member of the genus Deinococcus. Strain Wt/1aT exhibited maximum 16S rRNA gene sequence similarity (95 %) with Deinococcus grandis; however, strain Wt/1aT exhibited only 14 % similarity to D. grandis IAM 13005T at the DNA–DNA level. Furthermore, strain Wt/1aT (compared to D. grandis IAM 13005T) is more resistant to arsenate and arsenite, is positive for arginine dihydrolase, utilizes a number of carbon sources and exhibits quantitative differences in fatty acid composition and qualitative differences in lipid composition. Strain Wt/1aT is identified as a novel species of the genus Deinococcus, for which the name Deinococcus indicus sp. nov. is proposed. The type strain of Deinococcus indicus is Wt/1aT (=MTCC 4913T=DSM 15307T). K. SureshG.S.N. ReddyS SenguptaS Shivaji2012-01-06T14:55:56Z2012-03-29T09:41:18Zhttp://crdd.osdd.net/open/id/eprint/225This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2252012-01-06T14:55:56ZComparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of Pichia anomala.Pichia anomala is an emerging nosocomial pathogen and there is a need for methods that distinguish between different P. anomala strains. In the typing of several clinical as well as non-clinical P. anomala strains, the sequence variation of the internal transcribed spacer (ITS) was found to be inadequate for typing purposes. The intergenic spacer 1 (IGS1) region of the rDNA of several P. anomala strains was therefore investigated in detail. The IGS1 region (which varied from 1213 to 1231 bp in length) was interspersed with repeats and had more variation than the ITS regions. Comparative analysis in cases where analysis by the ITS was ambiguous clearly revealed the IGS1 region to be a more discriminatory tool in the typing of P. anomala strains.Rajeshwari SutarJ K DavidK GanesanAnup K GhoshSunit SinghiArunaloke ChakrabartiAnand K Bachhawat2012-01-08T05:45:09Z2012-01-08T05:45:09Zhttp://crdd.osdd.net/open/id/eprint/198This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/1982012-01-08T05:45:09ZDirectional ligation of long-flanking homology regions to selection cassettes for efficient targeted gene-disruption in Candida albicans.PCR-product directed gene disruption with a marker cassette having short homology regions is often used in Candida albicans. However, it is quite inefficient due to the high frequency of non-homologous recombination at non-targeted loci, which necessitates extensive screening to identify the correct disruptants. Thus, many PCR-based methods to introduce long flanking homology regions have been developed to increase the frequency of integration at the targeted loci. However, these methods are not that amenable for use with the widely employed C. albicans marker cassettes having direct repeats, as these repeats tend to recombine during PCR, resulting in shorter amplified products without the selection marker. To circumvent this limitation, we have developed a dinucleotide-sticky-end-ligation strategy to add one flanking homology region to one side of the selection cassette, and the other flanking homology region to the other side of the selection cassette. This method involves release of the selection cassette from the plasmid by digestion with two different restriction enzymes, followed by partial fill-in, to provide a unique two base overhang at each end of the cassette. The flanking homology regions, corresponding to the gene to be disrupted, are individually PCR-amplified, and treated with T4-DNA Polymerase in the presence of appropriate dNTPs to yield two base-5' overhangs. The primers used for the PCR have additional bases at the 5' ends such that after T4 DNA Polymerase treatment, the two flanks will have distinct overhangs compatible with the overhangs of the partially filled-in selection cassette. The selection cassette and the flanks are then ligated together and directly used to transform C. albicans. We have successfully used this method for disruption of several C. albicans genes. We have also used this method to recreate insertion mutations obtained with transposons to reconfirm the mutant phenotypes. This approach can be extended to other organisms like Schizosaccharomyces pombe which also require long flanking regions of homology for targeted gene disruption.Vibha TanejaSanjoy PaulK Ganesan2013-10-18T09:12:03Z2013-10-18T09:12:03Zhttp://crdd.osdd.net/open/id/eprint/1408This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14082013-10-18T09:12:03ZMolecualr and Biochemical Characterization of Mycobacterial Nucleoside Diphosphatekinase A.Sangeeta Tiwari2012-01-08T05:45:42Z2012-03-29T07:09:46Zhttp://crdd.osdd.net/open/id/eprint/202This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2022012-01-08T05:45:42ZAmino acid residues involved in autophosphorylation and phosphotransfer activities are distinct in nucleoside diphosphate kinase from Mycobacterium tuberculosis.Nucleoside diphosphate kinase (NdK) is a ubiquitous enzyme in both prokaryotes and eukaryotes and is primarily involved in the maintenance of cellular nucleotide pools. We have cloned ndk from Mycobacterium tuberculosis strain H37Ra and expressed it in Escherichia coli as a fusion protein with glutathione S-transferase. The purified protein, following thrombin cleavage and gel permeation chromatography, was found to be hexameric with a monomeric unit molecular mass of approximately 16.5 kDa. The protein exhibited nucleotide binding, divalent cation-dependent autophosphorylation, and phosphate transfer ability from nucleoside triphosphate to nucleoside diphosphate. Although UDP inhibited the catalytic activity of the recombinant protein, the classic inhibitors, like cromoglycate, 5'-adenosine 3'-phosphate, and adenosine 3'-phosphate 5'-phosphosulfate, had no effect on the activity. Among three histidine residues in the protein, His-117 was found to be essential for autophosphorylation. However, in subsequent phosphate transfer, we observed that His-53 had a significant contribution. Consistent with this observation, substitution of His-53 with either Ala or Gln affected the ability of the recombinant protein to complement NdK function in Pseudomonas aeruginosa. Furthermore, mutational analysis established critical roles for Tyr-50 and Arg-86 of the M. tuberculosis protein in maintaining phosphotransfer ability.Sangeeta TiwariK V Radha KishanT ChakrabartiPradip K Chakraborti2012-01-06T14:53:46Z2015-01-07T06:14:31Zhttp://crdd.osdd.net/open/id/eprint/212This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2122012-01-06T14:53:46ZProduction of phytase (myo-inositolhexakisphosphate phosphohydrolase) by Aspergillus niger van Teighem in laboratory-scale fermenter.The growth and production pattern of phytase by a filamentous fungus, Aspergillus niger van Teighem, were studied in submerged culture at varying agitation rates and controlled and uncontrolled pH conditions. Allowing the initial culture to grow under neutral condition with subsequent decline in pH resulted in increased phytase productivity. A maximum of 141 nkat/mL phytase was obtained when the broth pH was maintained at pH 2.5 as compared to 17 nkat/mL units at controlled pH 5.5. The culture morphology and rheological properties of the fermentation broth significantly varied with the agitation rate. The volumetric oxygen transfer coefficient was determined at different phases of fungal growth during batch fermentation using static gassing out and dynamic gassing out methods. The oxygen transfer coefficient (k(L)a) of the fermenter was found to be 125 h(-)(1) at 500 rpm as compared to 38 h(-)(1) at 200 rpm. The oxygen transfer rates at different phases of growth were significantly affected by cell mass concentration and fungal morphology. During the course of fermentation there was a gradual decline of k(L)a from 97 h(-)(1) on day 2 to 63 h(-)(1) on day 6 of fermentation, after which no significant change was observed. The degree of agitation considerably influenced the culture morphology where shear thinning of filamentous fungus was observed with the increase in agitation.Purva VatsDebendra K SahooU C Banerjee2012-02-14T10:29:01Z2015-01-07T06:15:34Zhttp://crdd.osdd.net/open/id/eprint/960This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9602012-02-14T10:29:01ZProduction of phytase (myo-inositolhexakisphosphate phosphohydrolase) by Aspergillus niger van Teighem in laboratory-scale fermenter.The growth and production pattern of phytase by a filamentous fungus, Aspergillus niger van Teighem, were studied in submerged culture at varying agitation rates and controlled and uncontrolled pH conditions. Allowing the initial culture to grow under neutral condition with subsequent decline in pH resulted in increased phytase productivity. A maximum of 141 nkat/mL phytase was obtained when the broth pH was maintained at pH 2.5 as compared to 17 nkat/mL units at controlled pH 5.5. The culture morphology and rheological properties of the fermentation broth significantly varied with the agitation rate. The volumetric oxygen transfer coefficient was determined at different phases of fungal growth during batch fermentation using static gassing out and dynamic gassing out methods. The oxygen transfer coefficient (k(L)a) of the fermenter was found to be 125 h(-)(1) at 500 rpm as compared to 38 h(-)(1) at 200 rpm. The oxygen transfer rates at different phases of growth were significantly affected by cell mass concentration and fungal morphology. During the course of fermentation there was a gradual decline of k(L)a from 97 h(-)(1) on day 2 to 63 h(-)(1) on day 6 of fermentation, after which no significant change was observed. The degree of agitation considerably influenced the culture morphology where shear thinning of filamentous fungus was observed with the increase in agitation.Purva VatsDebendra K SahooU C Banerjee2012-02-14T12:17:58Z2012-02-14T12:17:58Zhttp://crdd.osdd.net/open/id/eprint/964This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9642012-02-14T12:17:58ZStructural analysis of Bombyx mori silk fibroin peptides with formic acid treatment using high-resolution solid-state 13C NMR spectroscopy.Bombyx mori silk fibroin fiber is a fibrous protein produced by the silkworm at room temperature and from an aqueous solution whose primary structure is highly repetitive. In this study we analyzed the structural characteristics of native peptides, derived from B. mori silk fibroin, with formic acid treatment using high-resolution solid-state 13C NMR. We establish that the Ser residue bearing a short polar side chain has the ability to stabilize the conformation formed in the model peptides due to its ability to form intermolecular hydrogen bonds involving its hydroxyl group as a donor and the carbonyl groups of other residues as acceptors. On the other hand, insertion of Tyr residue in the basic (AG)n and (AGSGAG)n sequence motifs usually exhibited disruptive effects on the preferred conformations. Moreover, the environmental effect was investigated by mixing the native Cp fraction with the model peptides, showing that there is no significant structural difference on the Ser-containing peptides, while structural transformation was observed on the peptides containing the GAAS unit. This may be attributed to the fact that the Cp fraction promotes the formation of an antiparallel beta-sheet in the Ala-Ala unit. Such periodically disrupted ordered structures in the semicrystalline region of B. mori silk fibroin may be critical not only for facilitating the conformational transformation from silk I to silk II structural form but also for having some correlation with the unique properties of the silk materials.Juming YaoKosuke OhgoRena SuginoRaghuvansh KishoreTetsuo Asakura2012-02-14T10:29:37Z2012-02-14T10:29:37Zhttp://crdd.osdd.net/open/id/eprint/957This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9572012-02-14T10:29:37ZA novel family of transporters mediating the transport of glutathione derivatives in plants.Uptake and compartmentation of reduced glutathione (GSH), oxidized glutathione (GSSG), and glutathione conjugates are important for many functions including sulfur transport, resistance against biotic and abiotic stresses, and developmental processes. Complementation of a yeast (Saccharomyces cerevisiae) mutant (hgt1) deficient in glutathione transport was used to characterize a glutathione transporter cDNA (OsGT1) from rice (Oryza sativa). The 2.58-kb full-length cDNA (AF393848, gi 27497095), which was obtained by screening of a cDNA library and 5'-rapid amplification of cDNA ends-polymerase chain reaction, contains an open reading frame encoding a 766-amino acid protein. Complementation of the hgt1 yeast mutant strain with the OsGT1 cDNA restored growth on a medium containing GSH as the sole sulfur source. The strain expressing OsGT1 mediated [3H]GSH uptake, and this uptake was significantly competed not only by unlabeled GSSG and GS conjugates but also by some amino acids and peptides, suggesting a wide substrate specificity. OsGT1 may be involved in the retrieval of GSSG, GS conjugates, and nitrogen-containing peptides from the cell wall.Ming-Yong ZhangAndrée BourboulouxOlivier CagnacChittur V SrikanthDoris RentschAnand K BachhawatSerge Delrot