1
|
Straniero S, Laskar A, Savva C, Härdfeldt J, Angelin B, Rudling M. Murine bile acids explain species differences in the regulation of bile acid and cholesterol metabolism. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
2
|
Bernasconi SM, Daëron M, Bergmann KD, Bonifacie M, Meckler AN, Affek HP, Anderson N, Bajnai D, Barkan E, Beverly E, Blamart D, Burgener L, Calmels D, Chaduteau C, Clog M, Davidheiser‐Kroll B, Davies A, Dux F, Eiler J, Elliott B, Fetrow AC, Fiebig J, Goldberg S, Hermoso M, Huntington KW, Hyland E, Ingalls M, Jaggi M, John CM, Jost AB, Katz S, Kelson J, Kluge T, Kocken IJ, Laskar A, Leutert TJ, Liang D, Lucarelli J, Mackey TJ, Mangenot X, Meinicke N, Modestou SE, Müller IA, Murray S, Neary A, Packard N, Passey BH, Pelletier E, Petersen S, Piasecki A, Schauer A, Snell KE, Swart PK, Tripati A, Upadhyay D, Vennemann T, Winkelstern I, Yarian D, Yoshida N, Zhang N, Ziegler M. InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards. Geochem Geophys Geosyst 2021; 22:e2020GC009588. [PMID: 34220359 PMCID: PMC8244079 DOI: 10.1029/2020gc009588] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Increased use and improved methodology of carbonate clumped isotope thermometry has greatly enhanced our ability to interrogate a suite of Earth-system processes. However, interlaboratory discrepancies in quantifying carbonate clumped isotope (Δ47) measurements persist, and their specific sources remain unclear. To address interlaboratory differences, we first provide consensus values from the clumped isotope community for four carbonate standards relative to heated and equilibrated gases with 1,819 individual analyses from 10 laboratories. Then we analyzed the four carbonate standards along with three additional standards, spanning a broad range of δ47 and Δ47 values, for a total of 5,329 analyses on 25 individual mass spectrometers from 22 different laboratories. Treating three of the materials as known standards and the other four as unknowns, we find that the use of carbonate reference materials is a robust method for standardization that yields interlaboratory discrepancies entirely consistent with intralaboratory analytical uncertainties. Carbonate reference materials, along with measurement and data processing practices described herein, provide the carbonate clumped isotope community with a robust approach to achieve interlaboratory agreement as we continue to use and improve this powerful geochemical tool. We propose that carbonate clumped isotope data normalized to the carbonate reference materials described in this publication should be reported as Δ47 (I-CDES) values for Intercarb-Carbon Dioxide Equilibrium Scale.
Collapse
Affiliation(s)
| | - M. Daëron
- Laboratoire des Sciences du Climat et de l’EnvironnementLSCE/IPSLCEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - K. D. Bergmann
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Bonifacie
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
| | - A. N. Meckler
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - H. P. Affek
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - N. Anderson
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - D. Bajnai
- Institute of GeosciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - E. Barkan
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - E. Beverly
- Now at Department of Earth and Atmospheric SciencesUniversity of HoustonHoustonTXUSA
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - D. Blamart
- Laboratoire des Sciences du Climat et de l’EnvironnementLSCE/IPSLCEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - L. Burgener
- Department of Marine, Earth and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | - D. Calmels
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Now at Geosciences Paris Sud (GEOPS)Université Paris‐SaclayCNRSOrsayFrance
| | - C. Chaduteau
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
| | - M. Clog
- Scottish Universities Environmental Research Centre (SUERC)ScotlandUK
| | | | - A. Davies
- Now at Stockholm UniversityStockholmSweden
- Imperial CollegeLondonUK
| | - F. Dux
- Now at School of Earth and Life SciencesUniversity of WollongongWollongongAustralia
- School of GeographyUniversity of MelbourneMelbourneAustralia
| | - J. Eiler
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - B. Elliott
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | | | - J. Fiebig
- Institute of GeosciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - S. Goldberg
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Hermoso
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Univ. Littoral Côte d’OpaleUniv. LilleCNRSLaboratoire d’Océanologie et de Géosciences (UMR 8187 LOG)WimereuxFrance
| | | | - E. Hyland
- Department of Marine, Earth and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | - M. Ingalls
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
- Now at Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - M. Jaggi
- Geological InstituteETH ZürichZürichSwitzerland
| | | | - A. B. Jost
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - S. Katz
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - J. Kelson
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - T. Kluge
- Imperial CollegeLondonUK
- Now at Karlsruher Institut für Technologie KITKarlsruheGermany
| | - I. J. Kocken
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| | - A. Laskar
- Institute of Earth SciencesAcademia SinicaTaipeiTaiwan
| | - T. J. Leutert
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
- Now at Max Planck Institute for ChemistryMainzGermany
| | - D. Liang
- Institute of Earth SciencesAcademia SinicaTaipeiTaiwan
| | - J. Lucarelli
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - T. J. Mackey
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Now at Department of Earth and Planetary SciencesUniversity of New MexicoAlbuquerqueNMUSA
| | - X. Mangenot
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - N. Meinicke
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - S. E. Modestou
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - I. A. Müller
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| | | | - A. Neary
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - N. Packard
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - B. H. Passey
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - E. Pelletier
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - S. Petersen
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - A. Piasecki
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
- Now at Department of Earth SciencesDartmouth CollegeHanoverNHUSA
| | | | | | - P. K. Swart
- Department of Marine GeosciencesRostiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFLUSA
| | - A. Tripati
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - D. Upadhyay
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - T. Vennemann
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - I. Winkelstern
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
- Now at Geology DepartmentGrand Valley State UniversityAllendaleMIUSA
| | - D. Yarian
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - N. Yoshida
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
- National Institute of Information and Communications TechnologyTokyoJapan
| | - N. Zhang
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - M. Ziegler
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| |
Collapse
|
3
|
Ghosh A, Bhowmik A, Bhandary S, Putatunda S, Laskar A, Biswas A, Dolui S, Banerjee B, Khan R, Das N, Chakraborty A, Ghosh MK, Sen PC. Formulation and antitumorigenic activities of nanoencapsulated nifetepimine: A promising approach in treating triple negative breast carcinoma. Nanomedicine: Nanotechnology, Biology and Medicine 2016; 12:1973-1985. [DOI: 10.1016/j.nano.2016.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 04/05/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
|
4
|
Ghosh P, Mukherjee N, Ghosh K, Mallick S, Pal C, Laskar A, Ghosh A. Prospective microglia and brain macrophage distribution pattern in normal rat brain shows age sensitive dispersal and stabilization with development. Indian J Exp Biol 2015; 53:561-567. [PMID: 26548075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The monocytic lineage cells in brain, generally speaking brain macrophage and/or microglia show some dissimilar distribution patterns and disagreement regarding their origin and onset in brain. Here, we investigated its onset and distribution/colonization pattern in normal brain with development. Primarily, early and late embryonic stages, neonate and adult brains were sectioned for routine H/E staining; a modified silver-gold staining was used for discriminating monocytic lineage cells in brain; and TEM to deliver ultramicroscopic details of these cells in brain. Immunofluorescence study with CD11b marker revealed the distribution of active microglia/macrophage like cells. Overall, in early embryonic day 12, the band of densely stained cells are found at the margin of developing ventricles and cells sprout from there dispersed towards the outer edge. However, with development, this band shrunk and the dispersion trend decreased. The deeply stained macrophage like cell population migration from outer cortex to ventricle observed highest in late embryonic days, continued with decreased amount in neonates and settled down in adult. In adult, a few blood borne macrophage like cells were observed through the vascular margins. TEM study depicted less distinguishable features of cells in brain in early embryo, whereas from late embryo to adult different neuroglial populations and microglia/macrophages showed distinctive features and organization in brain. CD11b expression showed some similarity, though not fully, with the distribution pattern depending on the differentiation/activation status of these macrophage lineage cells. This study provides some generalized spatial and temporal pattern of macrophage/microglia distribution in rat brain, and further indicates some intrigue areas that need to be addressed.
Collapse
|
5
|
Maity J, Bohr VA, Laskar A, Karmakar P. Transient overexpression of Werner protein rescues starvation induced autophagy in Werner syndrome cells. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2387-94. [PMID: 25257404 DOI: 10.1016/j.bbadis.2014.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/02/2014] [Accepted: 09/17/2014] [Indexed: 01/07/2023]
Abstract
Reduced autophagy may be associated with normal and pathological aging. Here we report a link between autophagy and Werner protein (WRNp), mutated in Werner syndrome, the human premature aging Werner syndrome (WS). WRN mutant fibroblast AG11395 and AG05229 respond weakly to starvation induced autophagy compared to normal cells. While the fusion of phagosomes with lysosome is normal, WS cells contain fewer autophagy vacuoles. Cellular starvation autophagy in WS cells is restored after transfection with full length WRN. Further, siRNA mediated silencing of WRN in the normal fibroblast cell line WI-38 results in decreased autophagy and altered expression of autophagy related proteins. Thus, our observations suggest that WRN may have a role in controlling autophagy and hereby cellular maintenance.
Collapse
Affiliation(s)
- Jyotirindra Maity
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata 700032, India
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Aparna Laskar
- CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata 700032, India.
| |
Collapse
|
6
|
Biswas A, Kurkute P, Jana B, Laskar A, Ghosh S. An amyloid inhibitor octapeptide forms amyloid type fibrous aggregates and affects microtubule motility. Chem Commun (Camb) 2014; 50:2604-7. [DOI: 10.1039/c3cc49396b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide in dual action: an amyloid inhibitor octapeptide spontaneously forms amyloid like fibrillar aggregates in solution and slows down the microtubule gliding speed through strong peptide–tubulin interaction.
Collapse
Affiliation(s)
- Atanu Biswas
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Prashant Kurkute
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Batakrishna Jana
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Aparna Laskar
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Surajit Ghosh
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| |
Collapse
|
7
|
Laha D, Pramanik A, Maity J, Mukherjee A, Pramanik P, Laskar A, Karmakar P. Interplay between autophagy and apoptosis mediated by copper oxide nanoparticles in human breast cancer cells MCF7. Biochim Biophys Acta Gen Subj 2013; 1840:1-9. [PMID: 23962629 DOI: 10.1016/j.bbagen.2013.08.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 08/10/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022]
Abstract
BACKGROUND Metal oxide nanoparticles are well known to generate oxidative stress and deregulate normal cellular activities. Among these, transition metals copper oxide nanoparticles (CuO NPs) are more compelling than others and able to modulate different cellular responses. METHODS In this work, we have synthesized and characterized CuO NPs by various biophysical methods. These CuO NPs (~30nm) induce autophagy in human breast cancer cell line, MCF7 in a time- and dose-dependent manner. Cellular autophagy was tested by MDC staining, induction of green fluorescent protein-light chain 3 (GFP-LC3B) foci by confocal microscopy, transfection of pBABE-puro mCherry-EGFP-LC3B plasmid and Western blotting of autophagy marker proteins LC3B, beclin1 and ATG5. Further, inhibition of autophagy by 3-MA decreased LD50 doses of CuO NPs. Such cell death was associated with the induction of apoptosis as revealed by FACS analysis, cleavage of PARP, de-phosphorylation of Bad and increased cleavage product of caspase 3. siRNA mediated inhibition of autophagy related gene beclin1 also demonstrated similar results. Finally induction of apoptosis by 3-MA in CuO NP treated cells was observed by TEM. RESULTS This study indicates that CuO NPs are a potent inducer of autophagy which may be a cellular defense against the CuO NP mediated toxicity and inhibition of autophagy switches the cellular response into apoptosis. CONCLUSIONS A combination of CuO NPs with the autophagy inhibitor is essential to induce apoptosis in breast cancer cells. GENERAL SIGNIFICANCE CuO NP induced autophagy is a survival strategy of MCF7 cells and inhibition of autophagy renders cellular fate to apoptosis.
Collapse
Affiliation(s)
- Dipranjan Laha
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700 032, India
| | | | | | | | | | | | | |
Collapse
|
8
|
Laskar A, Rodger EJ, Chatterjee A, Mandal C. Modeling and structural analysis of PA clan serine proteases. BMC Res Notes 2012; 5:256. [PMID: 22624962 PMCID: PMC3434108 DOI: 10.1186/1756-0500-5-256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 05/11/2012] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into clans sharing structural homology. The PA clan of endopeptidases is the most abundant and over two thirds of this clan is comprised of the S1 family of serine proteases, which bear the archetypal trypsin fold and have a catalytic triad in the order Histidine, Aspartate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques. RESULTS Our predicted models from protozoa, archaea, fungi and plants were combined with the experimentally determined structures of 16 S1 family members and used for analysis of the catalytic core. Amino acid sequences were submitted to SWISS-MODEL for homology-based structure prediction or the LOOPP server for threading-based structure prediction. Predicted models were refined using INSIGHT II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Some highly conserved residues potentially contributing to the stability of the structural core were identified. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. CONCLUSIONS Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on S1 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, this analysis is beneficial for future molecular modeling strategies and structural analysis of serine protease models.
Collapse
Affiliation(s)
- Aparna Laskar
- Indian Institute of Chemical Biology (CSIR Unit, Government of India), Kolkata, West Bengal, India.
| | | | | | | |
Collapse
|
9
|
Laskar A, Rodger EJ, Chatterjee A, Mandal C. Modeling and structural analysis of evolutionarily diverse S8 family serine proteases. Bioinformation 2011; 7:239-45. [PMID: 22125392 PMCID: PMC3218418 DOI: 10.6026/97320630007239] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 10/18/2011] [Indexed: 11/23/2022] Open
Abstract
Serine proteases are an abundant class of enzymes that are involved in a wide range of physiological processes and are classified into clans sharing structural homology. The active site of the subtilisin-like clan contains a catalytic triad in the order Asp, His, Ser (S8 family) or a catalytic tetrad in the order Glu, Asp and Ser (S53 family). The core structure and active site geometry of these proteases is of interest for many applications. The aim of this study was to investigate the structural properties of different S8 family serine proteases from a diverse range of taxa using molecular modeling techniques. In conjunction with 12 experimentally determined three-dimensional structures of S8 family members, our predicted structures from an archaeon, protozoan and a plant were used for analysis of the catalytic core. Amino acid sequences were obtained from the MEROPS database and submitted to the LOOPP server for threading based structure prediction. The predicted structures were refined and validated using PROCHECK, SCRWL and MODELYN. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on S8 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, the analysis presented here is beneficial for future molecular modeling strategies and structure-based rational drug design.
Collapse
Affiliation(s)
- Aparna Laskar
- Indian Institute of Chemical Biology (CSIR Unit, Government of India), Kolkata-700032, West Bengal, India
| | - Euan James Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin-9054, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin-9054, New Zealand
- National Research Centre for Growth and Development, New Zealand
| | - Chhabinath Mandal
- Indian Institute of Chemical Biology (CSIR Unit, Government of India), Kolkata-700032, West Bengal, India
| |
Collapse
|
10
|
Sarkar J, Ray S, Chattopadhyay D, Laskar A, Acharya K. Mycogenesis of gold nanoparticles using a phytopathogen Alternaria alternata. Bioprocess Biosyst Eng 2011; 35:637-43. [DOI: 10.1007/s00449-011-0646-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
|
11
|
Ghorai A, Gayen A, Kulsi G, Padmanaban E, Laskar A, Achari B, Mukhopadhyay C, Chattopadhyay P. Simultaneous Parallel and Antiparallel Self-Assembly in a Triazole/Amide Macrocycle Conformationally Homologous to d-,l-α-Amino Acid Based Cyclic Peptides: NMR and Molecular Modeling Study. Org Lett 2011; 13:5512-5. [DOI: 10.1021/ol2022356] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abhijit Ghorai
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - Anindita Gayen
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - Goutam Kulsi
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - E. Padmanaban
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - Aparna Laskar
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - Basudeb Achari
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - Chaitali Mukhopadhyay
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| | - Partha Chattopadhyay
- Chemistry Division, Indian Institute of Chemical Biology (CSIR), Kolkata, 700032, India, and Department of Chemistry, University College of Science, University of Calcutta, Kolkata, 700009, India
| |
Collapse
|
12
|
Laskar A, Chatterjee S, Roy A, Kumar Dey S, Mandal C. Molecular Modeling and Structural Analysis of Five SE Clan (S12 Family) Serine Proteases. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/ajbkr.2011.435.448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
13
|
Bera I, Laskar A, Ghoshal N. Exploring the structure of opioid receptors with homology modeling based on single and multiple templates and subsequent docking: A comparative study. J Mol Model 2010; 17:1207-21. [DOI: 10.1007/s00894-010-0803-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/06/2010] [Indexed: 01/09/2023]
|
14
|
Bandyopadhyay A, Arora A, Jain S, Laskar A, Mandal C, Ivanisenko VA, Fomin ES, Pintus SS, Kolchanov NA, Maiti S, Ramachandran S. Expression and molecular characterization of the Mycobacterium tuberculosis PII protein. J Biochem 2009; 147:279-89. [PMID: 19884192 DOI: 10.1093/jb/mvp174] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The signal transduction protein PII plays an important role in cellular nitrogen assimilation and regulation. The molecular characteristics of the Mycobacterium tuberculosis PII (Mtb PII) were investigated using biophysical experiments. The Mtb PII coding ORF Rv2919c was cloned and expressed in Escherichia coli. The binding characteristics of the purified protein with ATP and ADP were investigated using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). Mtb PII binds to ATP strongly with K(d) in the range 1.93-6.44 microM. This binding strength was not significantly affected by the presence of 2-ketoglutarate even in molar concentrations of 66 (ITC) or 636 (SPR) fold excess of protein concentration. However, an additional enthalpy of 0.3 kcal/mol was released in presence of 2-ketoglutarate. Binding of Mtb PII to ADP was weaker by an order of magnitude. Binding of ATP and 2-ketoglutarate were analysed by docking studies on the Mtb PII crystal structure (PDB id 3BZQ). We observed that hydrogen bonds involving the gamma-phosphate of ATP contribute to enhanced binding of ATP compared with ADP. Glutaraldehyde crosslinking showed that Mtb PII exists in homotrimeric state which is consistent with other PII proteins. Phylogenetic analysis showed that Mtb PII consistently grouped with other actinobacterial PII proteins.
Collapse
Affiliation(s)
- Anannya Bandyopadhyay
- Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), Delhi 110 007, India
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|