http://nopr.niscair.res.in/handle/123456789/71 Search the Channel search http://nopr.niscair.res.in/simple-search http://nopr.niscair.res.in/handle/123456789/102 Title: Purification of protein from a crude mixture through SDS-PAGE transfer method <br/> <br/>Authors: Bhattacharyya, Dipankar; Basu, Arindam; Sen, Parimal C <br/> <br/>Abstract: SDS-polyacrylamide gel electrophoresis (SDS-PAGE) transfer method was used for purification and enrichment of the protein from crude sample. Coomassie blue/ZnSO₄ stained protein band(s) containing intact polyacrylamide gel were loaded on to another polyacrylamide gel either alone or as pooled gel bands. Two/three bands were combined together and arranged tightly over one another, sealed with stacking gel and ran in another gel, which was quite useful for enrichment and purification of a particular protein from a complex mixture. Recovery of protein by gel transfer method was found to be 70% in case of ZnSO₄ staining, whereas around 30% recovery was possible, following Coomassie blue staining. The method described here for purification of protein(s) from a complex mixture, following gel transfer procedure could be useful for further characterization of the desired protein. <br/> <br/>Page(s): 122-125 Thu, 29 Mar 2007 22:58:59 GMT http://nopr.niscair.res.in/handle/123456789/101 Title: Exploring QSAR of peripheral benzodiazepine receptor binding affinity of N,N-dialkyl-2-phenylindol -3-yl-glyoxylamides using physico-chemical descriptors <br/> <br/>Authors: Roy, Kunal; Dalai, Manoj Kumar <br/> <br/>Abstract: The present QSAR study has attempted to explore the structural and physicochemical requirements of ligands N,N-dialkyl-2-phenylindol-3-yl-glyoxylamides for binding with peripheral benzodiazepine receptor (PBR). The calcu¬lated partition coefficient values show parabolic relations with the PBR binding affinity, suggesting that the binding affinity increases with increase in the partition coefficient of the compounds until it reaches the critical value after which the affinity decreases. The critical value of logP is within range of 6.052-6.410. Furthermore, positive Wang-Ford charge values of carbonyl oxygens of the glyoxamide moiety and negative Wang-Ford charge value of the glyoxamide nitrogen are conducive for the binding affinity. Again, the indole moiety should have favorable charge distribution. Higher values of the parameters dipole moment (Dipole) and moment of inertia (I_z) of the ligands are conducive for the binding affinity. The presence of hydrogen atom at R₂ and cyclic moiety at R₁ and R₂ positions are detrimental to the binding affinity. <br/> <br/>Page(s): 114-121 Thu, 29 Mar 2007 22:58:59 GMT http://nopr.niscair.res.in/handle/123456789/100 Title: Construction and design of single stranded collagen-like structure <br/> <br/>Authors: Nandel, Fateh Singh; Saini, Avneet <br/> <br/>Abstract: Polytheonamide B, a 48 residue long highly cytotoxic polypeptide extracted from marine sponges contains amino acids of alternate chirality and the N-terminal region is rich in t-Leu residues. The aim of this study is to analyze the effect of these alternate chiralities and conformational behavior of various model peptides containing t-Leu, in order to explore their role in designing bioactive peptides that shall offer advantages comparable to polytheonamide B, while circumventing its limitations. The conformational behavior of various peptides constructed from t-Leu of the form Ac-(L/D-X-L/D-Y)n-NHMe, where X = Gly/Ala/Leu and Y = t-Leu has been studied and compared with the corresponding peptides containing Leu residue. The results show that the helix driving capacity of L and D forms of t-Leu is less than that of Leu residue. In poly t-Leu peptides, the population of collagen/inverse collagen-type structures or right/left handed-helical structures for L and D forms respectively is found to be chain length-dependent. The stability of the helical structures is increased by ~2 kcal per residue over the collagen-type structure in poly t-Leu peptides with chain length greater than five residues. Molecular view of peptides in collagen-type structure shows that the bulky side chains of t-Leu residues mask the NH moieties of the peptide bond, while the carbonyl groups lying along the helical groove are accessible to the small solvent molecules. Molecular model building suggests that one ethylene glycol molecule interacts by forming hydrogen bonds with carbonyl groups of two adjacent t-Leu residues. To the best of our knowledge, this is the first study of its own kind on the construction of a single-strand collagen/inverse collagen-type structure using unusual amino acid residues. Such synthetic collagen mimetic peptides shall exhibit specific affinity to natural collagen under controlled thermal conditions (heat or laser treatment) and hence can be explored as a new targeting method to attach therapeutic drugs to collagens in the living tissues and to biomaterials that incorporate natural collagens. <br/> <br/>Page(s): 106-113 Thu, 29 Mar 2007 22:58:59 GMT http://nopr.niscair.res.in/handle/123456789/99 Title: Studies on interactions between plant secondary metabolites and glutathione transferase using fluorescence quenching method <br/> <br/>Authors: Zhang, Xian; Cheng, Xinsheng; Wang, Chuanqin; Xue, Zechun; Yang, Liwen; Xi, Zheng <br/> <br/>Abstract: The interactions between plant secondary metabolites (tannic acid, rutin, cinnamic acid and catechin) and glutathione transferase (GST) were investigated by fluorescence and UV-Vis absorption spectroscopy. Intrinsic fluorescence of GST was measured by selectively exciting their tryptophan (Trp) residues and quenching constants were determined using the Stern-Volmer equation. The binding affinity was found to be strongest for tannic acid and ranked in the order tannic acid>rutin>cinnamic acid>catechin. The pH values in the range of 6.7-7.9, except for tannic acid, did not affect significantly the affinity of rutin, cinnamic acid and catechin with GST. Results showed that the fluorescence quenching of GST was a static quenching. Fluorescence quenching and UV-Vis absorption spectroscopy suggested that only the tannic acid changed the microenvironment of the Trp residues. Furthermore, the number of binding sites and binding constants at different pH values showed that tannic acid had strongest affinity towards GST and hydrogen bonding played an important role in the affinity between GST and the metabolites. <br/> <br/>Page(s): 101-105 Thu, 29 Mar 2007 22:58:59 GMT