00541nas a2200181 4500008004100000022001400041245004900055210004900104260000800153300000900161490000700170653002200177653002000199653001600219100002100235700002600256856007700282 2014 eng d a2053-273300aEngineering of the tat pathway and chaperons0 aEngineering of the tat pathway and chaperons cAPR aC2730 v7010aProtein transport10aSignal sequence10aTat Pathway1 aGhosh, Deepanjan1 aRamasamy, Sureshkumar uhttps://library.ncl.res.in/content/engineering-tat-pathway-and-chaperons02238nas a2200169 4500008004100000245007000041210006900111260000800180300001200188490000700200520167100207100001701878700002101895700002701916700002601943856009901969 2018 eng d00aAnalysis of tail-anchored protein translocation pathway in plants0 aAnalysis of tailanchored protein translocation pathway in plants cJUL a161-1670 v143 aTail-anchored (TA) proteins are a special class of membrane proteins that carry out vital functions in all living cells. Targeting mechanisms of TA proteins are investigated as the best example for post-translational protein targeting in yeast. Of the several mechanisms, Guided Entry of Tail-anchored protein (GET) pathway plays a major role in TA protein targeting. Many in silico and in vivo analyses are geared to identify TA proteins and their targeting mechanisms in different systems including Arabidopsis thaliana. Yet, crop plants that grow in specific and/or different conditions are not investigated for the presence of TA proteins and GET pathway. This study majorly investigates GET pathway in two crop plants, Oryza sativa subsp. Indica and Solanum tuberosum, through detailed in silico analysis. 508 and 912 TA proteins are identified in Oryza sativa subsp. Indica and Solanum tuberosum respectively and their localization with respect to endoplasmic reticulum (ER), mitochondria, and chloroplast has been delineated. Similarly, the associated GET proteins are identified (Get1, Get3 and Get4) and their structural inferences are elucidated using homology modelling. Get3 models are based on yeast Get3. The cytoplasmic Get3 from O. sativa is identified to be very similar to yeast Get3 with conserved P-loop and TA binding groove. Three cytoplasmic Get3s are identified for S. tuberosum. Taken together, this is the first study to identify TA proteins and GET components in Oryza sativa subsp. Indica and Solanum tuberosum, forming the basis for any further experimental characterization of TA targeting and GET pathway mechanisms in crop plants. 1 aManu, M., S.1 aGhosh, Deepanjan1 aChaudhari, Bhushan, P.1 aRamasamy, Sureshkumar uhttps://library.ncl.res.in/content/analysis-tail-anchored-protein-translocation-pathway-plants02295nas a2200217 4500008004100000022001400041245007400055210006900129260000800198300001400206490000700220520158900227100002301816700002601839700002101865700002601886700001801912700002301930700002101953856010301974 2019 eng d a1744-683X00aCore-composite mediated separation of diverse nanoparticles to purity0 aCorecomposite mediated separation of diverse nanoparticles to pu cOCT a7787-77940 v153 a

A generalized method for sorting nanoparticles based on their cores does not exist; it is an immediate necessity, and an approach incorporating cost-effectiveness and biocompatibility is in demand. Therefore, an efficient method for the separation of various mixed core-compositions or dissimilar metallic nanoparticles to their pure forms at the nano-bio interface was developed. Various simple core-combinations of monodispersed nanoparticles with dual cores, including silver plus gold, iron oxide plus gold and platinum plus gold, to the complex three-set core-combinations of platinum plus gold plus silver and platinum plus iron plus gold were sorted using step-gradient centrifugation in a sucrose suspension. Viscosity mediated differential terminal velocities of the nanoparticles permitted diversified dragging at different gradients allowing separation. Stability, purity and properties of the nanoparticles during separation were evaluated based on visual confirmation and by employing advanced instrumentations. Moreover, theoretical studies validated our experimental observations, revealing the roles of various parameters, such as the viscosity of sucrose, the density of the particles and the velocity and duration of centrifugation, involved during the separation process. This remarkably rapid, cost-efficient and sustainable strategy can be adapted to separate other cores of nanoparticles for various biomedical research purposes, primarily to understand nanoparticle induced toxicity and particle fate and transformations in natural biotic environments.

1 aBhatt, Chandra, S.1 aNagaraj, Bharathkumar1 aGhosh, Deepanjan1 aRamasamy, Sureshkumar1 aThapa, Ranjit1 aMarpu, Sreekar, B.1 aSuresh, Anil, K. uhttps://library.ncl.res.in/content/core-composite-mediated-separation-diverse-nanoparticles-purity02220nas a2200241 4500008004100000022001400041245012000055210006900175260000900244300001200253490000800265520138800273653001701661653001901678653001101697653001901708653002301727653002401750100002801774700002101802700002501823856013001848 2019 eng d a0003-986100aInvestigation of structural and saccharide binding transitions of Bauhinia purpurea and Wisteria floribunda lectins0 aInvestigation of structural and saccharide binding transitions o cFEB  a134-1420 v6623 a

Two novel medicinally important legume lectins from Bauhinia purpurea (BPL) and Wisteria floribunda (WFL) possessing extended sugar binding site were investigated for functional and conformational transitions using biochemical and biophysical techniques as well as bioinformatical tools. Homology model of BPL was constructed using the Schrodinger suite and docked with N-acetyl galactosamine and T-antigen disaccharide (Gal beta 1-3GalNAc alpha O-Me). The longer loop D in the structure of WFL compared to that in BPL was found to be responsible for its specificity to LacdiNac (beta-D-GalNAc-[1 -> 4]-DGlcNAc) over Gal beta 1-3GalNAc. BPL remained functionally stable up to 40 degrees C whereas WFL remained stable upto 70 degrees C indicating the strength of the sugar binding site geometry. Both the lectins showed intense but non-specific secondary structure in the range of 65-90 degrees C. WFL showed rapid aggregation above 80 degrees C as indicated by light scattering intensity. The lectins showed simultaneous dissociation and multistate unfolding in the vicinity of GdnHCl. At pH 1.0, both the lectins exhibited molten globule like structures, which were characterized further and were found to respond in a different way towards denaturants. The results have provided valuable insights into the molecular basis of the activity and stability of the two lectins.

10aConformation10aHomology model10aLectin10aMolten globule10asaccharide binding10aThermal aggregation1 aAgrawal, Sanskruthi, B.1 aGhosh, Deepanjan1 aGaikwad, Sushama, M. uhttps://library.ncl.res.in/content/investigation-structural-and-saccharide-binding-transitions-bauhinia-purpurea-and-wisteria02161nas a2200265 4500008004100000022001400041245012500055210006900180260000800249300001200257490000800269520124900277653001601526653002901542653001401571653001301585653002701598100002701625700001901652700002901671700002101700700002101721700002601742856012701768 2020 eng d a0300-908400aStructural and enzymatic analysis of a dimeric cholylglycine hydrolase like acylase active on N-acyl homoserine lactones0 aStructural and enzymatic analysis of a dimeric cholylglycine hyd cOCT a108-1160 v1773 a

The prevalence of substrate cross-reactivity between AHL acylases and beta-lactam acylases provides a glimpse of probable links between quorum sensing and antibiotic resistance in bacteria. Both these enzyme classes belong to the N-terminal nucleophile (Ntn)-hydrolase superfamily. Penicillin V acylases alongside bile salt hydrolases constitute the cholylglycine hydrolase (CGH) group of the Ntn-hydrolase superfamily. Here we report the ability of two acylases, Slac1 and Slac2, from the marine bacterium Shewanella loihica PV4 to hydrolyze AHLs. Three-dimensional structure of Slac1 reveals the conservation of the Ntn hydrolase fold and CGH active site, making it a unique CGH exclusively active on AHLs. Slac1homologs phylogenetically cluster separate from reported CGHs and AHL acylases, thereby representing a functionally distinct sub-class of CGH that might have evolved as an adaptation to the marine environment. We hypothesize that Slac1 could provide the structural framework for understanding this subclass, and further our understanding of the evolutionary link between AHL acylases and beta-lactam acylases. (C) 2020 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.

10aAHL acylase10aCholyolglycine hydrolase10aHomodimer10aNtn-fold10aShewanella loihica-PV41 aPhilem, Pushparani, D.1 aYadav, Yashpal1 aSunder, Avinash, Vellore1 aGhosh, Deepanjan1 aPrabhune, Asmita1 aRamasamy, Sureshkumar uhttps://library.ncl.res.in/content/structural-and-enzymatic-analysis-dimeric-cholylglycine-hydrolase-acylase-active-n-acyl