@article {46383, title = {Engineering of the tat pathway and chaperons}, journal = {Acta Crystallographica A-Foundation and Advances}, volume = {70}, year = {2014}, month = {APR}, pages = {C273}, type = {Meeting Abstract}, keywords = {Protein transport, Signal sequence, Tat Pathway}, issn = {2053-2733}, author = {Ghosh, Deepanjan and Ramasamy, Sureshkumar} } @article {44422, title = {Analysis of tail-anchored protein translocation pathway in plants}, journal = {Biochemistry and Biophysics Reports }, volume = {14}, year = {2018}, month = {JUL}, pages = {161-167}, abstract = {Tail-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. }, doi = {10.1016/j.bbrep.2018.05.001}, author = {Manu, M. S. and Ghosh, Deepanjan and Chaudhari, Bhushan P. and Ramasamy, Sureshkumar} } @article {46445, title = {Core-composite mediated separation of diverse nanoparticles to purity}, journal = {Soft Matter}, volume = {15}, year = {2019}, month = {OCT}, pages = {7787-7794}, type = {Article}, abstract = {

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.

}, issn = {1744-683X}, doi = {10.1039/c9sm01571j}, author = {Bhatt, Chandra S. and Nagaraj, Bharathkumar and Ghosh, Deepanjan and Ramasamy, Sureshkumar and Thapa, Ranjit and Marpu, Sreekar B. and Suresh, Anil K.} } @article {45551, title = {Investigation of structural and saccharide binding transitions of Bauhinia purpurea and Wisteria floribunda lectins}, journal = {Archives of Biochemistry and Biophysics}, volume = {662}, year = {2019}, month = {FEB }, pages = {134-142}, type = {Article}, abstract = {

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.

}, keywords = {Conformation, Homology model, Lectin, Molten globule, saccharide binding, Thermal aggregation}, issn = {0003-9861}, doi = {10.1016/j.abb.2018.12.003}, author = {Agrawal, Sanskruthi B. and Ghosh, Deepanjan and Gaikwad, Sushama M.} } @article {46693, title = {Structural and enzymatic analysis of a dimeric cholylglycine hydrolase like acylase active on N-acyl homoserine lactones}, journal = {Biochimie}, volume = {177}, year = {2020}, month = {OCT}, pages = {108-116}, type = {Article}, abstract = {

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.

}, keywords = {AHL acylase, Cholyolglycine hydrolase, Homodimer, Ntn-fold, Shewanella loihica-PV4}, issn = {0300-9084}, doi = {10.1016/j.biochi.2020.07.017}, author = {Philem, Pushparani D. and Yadav, Yashpal and Sunder, Avinash Vellore and Ghosh, Deepanjan and Prabhune, Asmita and Ramasamy, Sureshkumar} }