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Subramanian E, Elewa A, Brito G, Kumar A, Segerstolpe Å, Karampelias C, Björklund Å, Sandberg R, Echeverri K, Lui WO, Andersson O, Simon A. A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration. Dev Cell 2023; 58:450-460.e6. [PMID: 36893754 DOI: 10.1016/j.devcel.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/15/2021] [Revised: 08/11/2022] [Accepted: 02/09/2023] [Indexed: 03/11/2023]
Abstract
Building a blastema from the stump is a key step of salamander limb regeneration. Stump-derived cells temporarily suspend their identity as they contribute to the blastema by a process generally referred to as dedifferentiation. Here, we provide evidence for a mechanism that involves an active inhibition of protein synthesis during blastema formation and growth. Relieving this inhibition results in a higher number of cycling cells and enhances the pace of limb regeneration. By small RNA profiling and fate mapping of skeletal muscle progeny as a cellular model for dedifferentiation, we find that the downregulation of miR-10b-5p is critical for rebooting the translation machinery. miR-10b-5p targets ribosomal mRNAs, and its artificial upregulation causes decreased blastema cell proliferation, reduction in transcripts that encode ribosomal subunits, diminished nascent protein synthesis, and retardation of limb regeneration. Taken together, our data identify a link between miRNA regulation, ribosome biogenesis, and protein synthesis during newt limb regeneration.
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Affiliation(s)
| | - Ahmed Elewa
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Gonçalo Brito
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anoop Kumar
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christos Karampelias
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Åsa Björklund
- Department of Cell and Molecular Biology, National Infrastructure of Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Echeverri
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, University of Chicago, Woods Hole, MA, USA
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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Oliveira CR, Knapp D, Elewa A, Gerber T, Gonzalez Malagon SG, Gates PB, Walters HE, Petzold A, Arce H, Cordoba RC, Subramanian E, Chara O, Tanaka EM, Simon A, Yun MH. Tig1 regulates proximo-distal identity during salamander limb regeneration. Nat Commun 2022; 13:1141. [PMID: 35241664 PMCID: PMC8894484 DOI: 10.1038/s41467-022-28755-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/06/2021] [Accepted: 02/10/2022] [Indexed: 12/22/2022] Open
Abstract
Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed positional identity. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/Rarres1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting Hoxa13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb. The mechanisms by which cells determine their position within the 3D space are poorly understood. Research in salamanders offers fresh insights into this question, uncovering Tig1 as a central determinant of proximo-distal identity in regeneration.
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Affiliation(s)
- Catarina R Oliveira
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Dunja Knapp
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany.
| | - Ahmed Elewa
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Tobias Gerber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sandra G Gonzalez Malagon
- Institute of Structural and Molecular Biology, University College London, London, UK.,Biomedical Research Institute, Foundation for Research and Technology, University of Ioannina Campus, 45115, Ioannina, Greece
| | - Phillip B Gates
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Hannah E Walters
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Andreas Petzold
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Hernan Arce
- Systems Biology Group, Institute of Physics of Liquids and Biological Systems, National Scientific and Technical Research Council (CONICET) and University of La Plata, La Plata, Argentina.,Instituto de Tecnología, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Rodrigo C Cordoba
- Systems Biology Group, Institute of Physics of Liquids and Biological Systems, National Scientific and Technical Research Council (CONICET) and University of La Plata, La Plata, Argentina
| | | | - Osvaldo Chara
- Systems Biology Group, Institute of Physics of Liquids and Biological Systems, National Scientific and Technical Research Council (CONICET) and University of La Plata, La Plata, Argentina.,Instituto de Tecnología, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina.,Technische Universität Dresden, Center for Information Services and High Performance Computing ZIH, Dresden, Germany
| | - Elly M Tanaka
- Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Maximina H Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany. .,Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany.
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Ahila M, Malligavathy M, Subramanian E, Pathinettam Padiyan D. Effect of anodization time on the growth of twinned pyramid crystals of bismite from polyhedral bismuth particle by facile electrolysis-based oxidation. Particulate Science and Technology 2017. [DOI: 10.1080/02726351.2017.1287793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M. Ahila
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - M. Malligavathy
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - E. Subramanian
- Department of Chemistry, Manonmaniam Sundaranar University, Tirunelveli, India
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Nishanthi S, Iyyapushpam S, Sundarakannan B, Subramanian E, Pathinettam Padiyan D. Inter-relationship between extent of anatase crystalline phase and photocatalytic activity of TiO2 nanotubes prepared by anodization and annealing method. Sep Purif Technol 2014. [DOI: 10.1016/j.seppur.2014.04.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Nishanthi S, Henry Raja D, Subramanian E, Pathinettam Padiyan D. Remarkable role of annealing time on anatase phase titania nanotubes and its photoelectrochemical response. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2012.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Vijayakumar N, Subramanian E, Padiyan DP. Conducting Polyaniline Blends with the Soft Template Poly(Vinyl Pyrrolidone) and their Chemosensor Application. INT J POLYM MATER PO 2012. [DOI: 10.1080/00914037.2011.610054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vijayakumar N, Subramanian E, Padiyan DP. Single/Double Soft-Templates Involved Synthesis of Polyaniline Blends: Interfacial Polymerization and Characterization by AC Impedance Analysis. J MACROMOL SCI B 2012. [DOI: 10.1080/00222348.2012.657121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- N. Vijayakumar
- a Department of Physics , Sri K.G.S. Arts College, Srivaikuntam , Thoothukudi , Tamil Nadu , India
| | - E. Subramanian
- b Department of Chemistry , Manonmaniam Sundaranar University , Tirunelveli , Tamil Nadu , India
| | - D. Pathinettam Padiyan
- c Department of Physics , Manonmaniam Sundaranar University , Tirunelveli , Tamil Nadu , India
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Subramanian S, Balaji M, Chithra lekha P, Sanjeev G, Subramanian E, Pathinettam Padiyan D. Electron beam induced modifications of bismuth sulphide (Bi2S3) thin films: Structural and optical properties. Radiat Phys Chem Oxf Engl 1993 2010. [DOI: 10.1016/j.radphyschem.2010.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Subramanian E, Anitha G, Vijayakumar N. Constructive modification of conducting polyaniline characteristics in unusual proportion through nanomaterial blend formation with the neutral polymer poly(vinyl pyrrolidone). J Appl Polym Sci 2007. [DOI: 10.1002/app.26566] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Murugan M, Subramanian E. Studies on defluoridation of water by tamarind seed, an unconventional biosorbent. J Water Health 2006; 4:453-61. [PMID: 17176816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Tamarind seed, a household waste from the kitchen is used for the sorptive removal of fluoride from synthetic aqueous solution as well as from field water samples. Batch sorptive defluoridation was conducted under variable experimental conditions such as pH, agitation time, initial fluoride concentration, particle size and sorbent dose. Maximum defluoridation was achieved at pH 7.0. Defluoridation capacity decreases with increase in temperature and particle size. Further, defluoridation follows first order kinetics and Langmuir adsorption isotherm. Desorption was carried out with 0.1 N HCl and is 90 per cent. The surface and sorption characteristics were analysed using FTIR and SEM techniques. All these results indicate the involvement of energetic forces such as coulombic interaction in sorption. For domestic and industrial applications, defluoridation with 100% achievement and subsequent regeneration of adsorbent was performed with a household water filter and fixed bed column respectively.
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Affiliation(s)
- M Murugan
- Department of Chemistry, S.K.G.S. College, Srivaikuntam, Tuticorin 628 619, Tamil Nadu, India.
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Mehlin C, Boni E, Buckner FS, Engel L, Feist T, Gelb MH, Haji L, Kim D, Liu C, Mueller N, Myler PJ, Reddy JT, Sampson JN, Subramanian E, Van Voorhis WC, Worthey E, Zucker F, Hol WGJ. Heterologous expression of proteins from Plasmodium falciparum: results from 1000 genes. Mol Biochem Parasitol 2006; 148:144-60. [PMID: 16644028 DOI: 10.1016/j.molbiopara.2006.03.011] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 03/16/2006] [Accepted: 03/21/2006] [Indexed: 11/19/2022]
Abstract
As part of a structural genomics initiative, 1000 open reading frames from Plasmodium falciparum, the causative agent of the most deadly form of malaria, were tested in an E. coli protein expression system. Three hundred and thirty-seven of these targets were observed to express, although typically the protein was insoluble. Sixty-three of the targets provided soluble protein in yields ranging from 0.9 to 406.6 mg from one liter of rich media. Higher molecular weight, greater protein disorder (segmental analysis, SEG), more basic isoelectric point (pI), and a lack of homology to E. coli proteins were all highly and independently correlated with difficulties in expression. Surprisingly, codon usage and the percentage of adenosines and thymidines (%AT) did not appear to play a significant role. Of those proteins which expressed, high pI and a hypothetical annotation were both strongly and independently correlated with insolubility. The overwhelmingly important role of pI in both expression and solubility appears to be a surprising and fundamental issue in the heterologous expression of P. falciparum proteins in E. coli. Twelve targets which did not express in E. coli from the native gene sequence were codon-optimized through whole gene synthesis, resulting in the (insoluble) expression of three of these proteins. Seventeen targets which were expressed insolubly in E. coli were moved into a baculovirus/Sf-21 system, resulting in the soluble expression of one protein at a high level and six others at a low level. A variety of factors conspire to make the heterologous expression of P. falciparum proteins challenging, and these observations lay the groundwork for a rational approach to prioritizing and, ultimately, eliminating these impediments.
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Affiliation(s)
- Christopher Mehlin
- Structural Genomics of Pathogenic Protozoa, Box 357350, University of Washington, Seattle, WA 98195, USA.
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Anitha G, Subramanian E. Intricate relation between the content and interactive roles of β-cyclodextrin in fixing the characteristics of conducting polyaniline composites. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/pola.21133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Srivastava A, Srivastava V, Verma SM, Subramanian E. Restricted Inversion of Pyramidal Nitrogen through .pi.-Electronic Interaction in an Acyclic System. J Org Chem 2002. [DOI: 10.1021/jo00092a012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rosati RL, Kapili LV, Morrissey P, Bordner J, Subramanian E. Photochemical transformation of cephalosporins into carbapenems. J Am Chem Soc 2002. [DOI: 10.1021/ja00379a044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Affiliation(s)
- E Subramanian
- Department of Crystallography and Biophysics, University of Madras, H 21/8 Vaigai Street, Chennai - 600 090, India.
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Gopalan R, Kulkarni G, Subramanian E, Renganayaki S. Molecular geometry versus crystal packing in N -methyl- N -(2-nitrophenyl) cinnamanilide: an experimental charge density study. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(99)00454-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Renganayaki S, Subramanian E, Shanmuga Sundara Raj S, Fun HK. N-Benzyl-2′-iodocinnamanilide and N-benzyl-2′-iodo-4′-methyl-2-phenylcinnamanilide. Acta Crystallogr C 2000. [DOI: 10.1107/s0108270199015243] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Renganayaki S, Subramanian E, Raj SS, Fun HK. N-benzyl-2'-iodocinnamanilide and N-benzyl-2'-iodo-4'-methyl-2-phenylcinnamanilide. Acta Crystallogr C 2000; 56 ( Pt 3):349-50. [PMID: 10777947 DOI: 10.1107/s0108768199015244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Affiliation(s)
- S Renganayaki
- Department of Crystallography and Biophysics, University of Madras, Chennai, India
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Shanmuga Sundara Raj S, Renganayaki S, Subramanian E, Fun HK. N-Benzyl- N-(2-iodo-4-methylphenyl)cinnamamide and N-benzyl- N-( p-tolyl)cinnamamide. Acta Crystallogr C 1999. [DOI: 10.1107/s0108270199011749] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Renganayaki S, Subramanian E, Shanmuga Sundara Raj S, Fun HK. N-(4-Chloro-2-iodophenyl)- N-methylcinnamamide. Acta Crystallogr C 1999. [DOI: 10.1107/s010827019900791x] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Renganayaki S, Govindasamy L, Subramanian E. Crystal and Molecular Structure of 4-methoxy-carbonyl methyl-2,9-bis(phenylsulfonyl)-1,2,3,4-tetrahydro β-carboline : benzene solvate. Cryst Res Technol 1998. [DOI: 10.1002/(sici)1521-4079(1998)33:6<963::aid-crat963>3.0.co;2-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Subramanian E, Govindasamy L, Ravichandran K. trans-Methyl 2,9-Bis(phenylsulfonyl)-1,2,3,4-tetrahydro-4-β-carbolinylideneacetate. Acta Crystallogr C 1997. [DOI: 10.1107/s010827019700228x] [Citation(s) in RCA: 3] [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: 11/11/2022] Open
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Seetharaman J, Shanmugasundaram P. X-ray structure of 5-[2-chlorophenyl]-10-[4-methylphenyl] 1,2,5,8,9,10 hexahydro 4,6[3H,6H] acridinedione and its interaction with calf thymus DNA by spectroscopic methods. J Mol Struct 1996. [DOI: 10.1016/s0022-2860(96)09355-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Shanmugasundram PS. 3,3,6,6-Tetramethyl-10-(4-methylphenyl)-3,4,6,7,9,10-hexahydro-1,8(2H,5H)-acridinedione. Acta Crystallogr C 1996. [DOI: 10.1107/s0108270195010171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Padha N, Subramanian E, Dass AK, Mazumdar SK, Goswami KN. Crystal structure of a furo-[3,2-g]-[1]-benzopyran-7-one derivative. Cryst Res Technol 1995. [DOI: 10.1002/crat.2170300213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Ramakrishnan VT. 9-Methyl-10-(4-methylphenyl)-3,4,6,7,9,10-hexahydro-1,8(2H,5H)-acridinedione. Acta Crystallogr C 1994. [DOI: 10.1107/s0108270194002805] [Citation(s) in RCA: 2] [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: 11/10/2022] Open
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Shanmuga Sundara Raj S, Velmurugan D, Subramanian E, Kandaswamy M. 4-tert-Butyl-2,6-bis[(4-methyl-1-piperazinyl)methyl]phenol. Acta Crystallogr C 1994. [DOI: 10.1107/s010827019400034x] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Shanmuga Sundara Raj S, Velmurugan D, Subramanian E, Kandaswamy M. 4-Chloro-2,6-bis(morpholinomethyl)phenol. Acta Crystallogr C 1994. [DOI: 10.1107/s0108270194000351] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mitra SN, Subramanian E. Observation of a sterically unfavorable side-chain conformation in a leucyl residue: crystal and molecular structure of L-leucyl-L-leucine.DMSO solvate. Biopolymers 1994; 34:1139-43. [PMID: 7948727 DOI: 10.1002/bip.360340903] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The crystal structure of a dipeptide L-leucyl-L-leucine (C12H24N2O3) has been determined. The crystals are monoclinic, space group P2(1), with a = 5.434(4) A, b = 15.712(7) A, c = 11.275(2) A, beta = 100.41(1) degrees, and Z = 2. The crystals contain one molecule of dimethyl sulfoxide (DMSO) as solvent of crystallization for each dipeptide molecule. The structure has been solved by direct methods and refined to a final R index of 0.059 for 920 reflections (sin theta/lambda < or = 0.60 A-1) with I > or = 2 sigma (I). The trans peptide unit shows substantial degree of non-planarity (delta omega = 14 degrees). The peptide backbone adopts an extended conformation with torsion angles of psi 1 = 138(1) degrees, omega 1 = 166(1) degrees, phi 2 = -149.3(7) degrees, psi 21 = 164.2(7) degrees, and psi 22 = -15(1) degrees. For the first leucyl residue, the side-chain conformation is specified by the torsion angles 1 chi 1 = 176.7(7) degrees, 1 chi 21 = 62(1) degrees, 1 chi 22 = -177.4(8) degrees; the second leucyl residue adopts a sterically unfavorable conformation with 2 chi 1 = 61(1) degrees, 2 chi 21 = 97(1) degrees, and 2 chi 22 = -151(1) degrees. The packing involves head-to-tail interaction of peptide molecules and segregation of polar and nonpolar regions. The DMSO molecule is strongly hydrogen bonded to the terminal NH3+ group.
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Affiliation(s)
- S N Mitra
- Department of Crystallography and Biophysics, University of Madras, India
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Velmurugan D, Govindasamy L, Subramanian E, Rajendran TM, Kandaswamy M. 2,6-Bis[(4-methyl-1-piperazinyl)methyl]-4-nitrophenol. Acta Crystallogr C 1994. [DOI: 10.1107/s0108270193010273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Sadanandan EV. [2-(3,4-Methylenedioxyphenyl)-1-(phenylsulfonyl)vinyl]-3-(phenylthio)indole. Acta Crystallogr C 1994. [DOI: 10.1107/s0108270193008285] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Sadanandan EV. 2-[1-Phenylsulfonyl-2-(3,4,5-trimethoxyphenyl)vinyl]-3-(phenylthio)indole. Acta Crystallogr C 1994. [DOI: 10.1107/s0108270193009977] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Sadanandan EV. 2-[2-(4-Methoxyphenyl)-1-(phenylsulfonyl)vinyl]-3-(phenylthio)indole. Acta Crystallogr C 1994. [DOI: 10.1107/s0108270193001817] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Prasad S, Mitra S, Subramanian E, Velmurugan D, Rao RB, Balaram P. Coexistence of folded and extended conformations of a tripeptide containing alpha, alpha -di-n-propylglycine in crystals. Biochem Biophys Res Commun 1994; 198:424-30. [PMID: 8297351 DOI: 10.1006/bbrc.1994.1062] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The crystal structure of the tripeptide Boc-Leu-Dpg-Val-OMe (Dpg, alpha, alpha -di-n-propylglycine) reveals the coexistence of two distinct backbone conformations. In molecule A the Dpg residue adopts a fully extended conformation (phi = 76.0 degrees, psi = 180.0 degrees) while in molecule B a left handed helical conformation (phi = 62.8 degrees, psi = 39.6 degrees) is observed. Molecule B adopts a folded structure corresponding to a highly distorted Type II beta-turn conformation, which lacks an intramolecular 4 -> 1 hydrogen bond. In contrast, molecule A has an open, extended conformation. The results demonstrate that both fully extended and helical conformations are energetically accessible to the Dpg residue.
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Affiliation(s)
- S Prasad
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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Subramanian E, Rajan SS, Jayashree V. Peptide models for understanding packing interactions in the interior of globular proteins: crystal structure of leucyl-leucyl-leucine HCl. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378096348] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sivaraman J, Subramanian K, Velmurugan D, Subramanian E, Ramakrishnan VT. Crystal and molecular structures of some acridine diones. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378094623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sundara Raj SS, Velmurugan D, Subramanian E. Crystal structure of 2,6-bis-( N-methylene morpholino)-4-chlorophenyl. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378094635] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Subramanian E, Sahayamary JJ. Structure and conformation of linear peptides. XIV. Structure of tert-butyloxycarbonyl-L-alanylglycine monohydrate. Int J Pept Protein Res 1993; 41:319-22. [PMID: 8496012 DOI: 10.1111/j.1399-3011.1993.tb00445.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The crystal structure of a dipeptide tert-butyloxycarbonyl-L-alanylglycine monohydrate (C10H18N2O5.H2O), molecular weight 264, has been determined. The crystals are monoclinic, space group P2(1), with a = 10.767(1), b = 6.317(1), c = 10.981(2)A, beta = 109.15(2) degrees, and Z = 2, Dc = 1.24 g cm-3. The structure was solved by direct methods and refined to a final R-index of 0.045 for 856 reflections (sin theta/lambda < 0.55 A-1) with I > 2 sigma. The N-terminus of the molecule blocked with the t-Boc group is uncharged and the C-terminus exists in an unionized state. The peptide unit is trans and shows slight deviations from planarity. (delta omega = 3.1 degrees). The peptide backbone is folded, with torsion angles of phi 1 = -76.0(5), psi 1 = 164.3(4), omega 1 = 176.9(5), phi 2 = 116.1(5), psi 21 = -2.8(7) and psi 22 = 177.8(4) degrees. The conformation about the urethane bond (C5-N1) is trans. The urethane group is essential planar. The conformation of the boc group is trans-trans.
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Affiliation(s)
- E Subramanian
- Department of Crystallography and Biophysics, University of Madras, India
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Ananthanarayanan VS, Boulay G, Mary JS, Subramanian E, Michel AG. Crystal structure of tert.-butyloxycarbonyl-L-prolyl-D-alanyl-D-alanyl-N-methylamide. Dimeric beta-sheet formation. Int J Pept Protein Res 1992; 39:458-63. [PMID: 1428534 DOI: 10.1111/j.1399-3011.1992.tb01450.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The crystal structure of the tripeptide t-Boc-L-Pro-D-Ala-D-Ala-NHCH3, monohydrate, (C17H30N4O5.H2O, molecular weight = 404.44) has been determined by single crystal X-ray diffraction. The crystals are monoclinic, space group P2(1), a = 9.2585(4), b = 9.3541(5), c = 12.4529(4)A, beta = 96.449(3) degrees, Z = 2. The peptide units are in the trans and the tBoc-Pro bond in the cis orientation. The first and third peptide units show significant deviations from planarity (delta omega = 5.2 degrees and delta omega = 3.7 degrees, respectively). The backbone torsion angles are: phi 1 = -60 degrees, psi 1 = 143.3 degrees, omega 1 = -174.8 degrees, phi 2 = 148.4 degrees, psi 2 = -143.1 degrees, omega 2 = -179.7 degrees, phi 3 = 151.4 degrees, psi 3 = -151.9 degrees, omega 3 = -176.3 degrees. The pyrrolidine ring of the proline residue adopts the C2-C gamma conformation. The molecular packing gives rise to an antiparallel beta-sheet structure formed of dimeric repeating units of the peptide. The surface of the dimeric beta-sheet is hydrophobic. Water molecules are found systematically at the edges of the sheets interacting with the urethane oxygen and terminal amino groups. Surface catalysis of an L-Ala to D-Ala epimerization process by water molecules adsorbed on to an incipient beta-sheet is suggested as a mechanism whereby crystals of the title peptide were obtained from a solution of tBoc-Pro-D-Ala-Ala-NHCH3.
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Abstract
The crystal structure of a tripeptide, L-phenylalanyl-glycyl-glycine (C13H17N3O4), molecular weight = 279.3, has been determined. The crystals are orthorhombic, space group P2(1)2(1)2(1), with a = 5.462(1) A, b = 15.285(5), c = 16.056(4), Z = 4, and P (calc) = 1.384 g.cm-3. The final R-index is 0.052 for 866 reflections with sin theta/lambda less than or equal to 0.55 A-1 and I greater than 1 sigma. The molecule exists as a zwitterion, with the N-terminus protonated and the C-terminus in an ionized form. Both the peptide units are in the trans configuration and planar, though one of them shows significant deviations from planarity ([delta w[ = 5.1 degrees). The peptide backbone is folded, with the torsion angles of: psi 1 = 116.2(5) degrees, omega 1 = 178.8(4), phi 2 = -89.7(5). psi 2 = -28.9(6), omega 2 = -174.9(4), phi 3 = 134.9(5), psi 31 = 7.8(6), psi 32 = -172.6(4). The terminal glycine adopts a "D-residue" conformation. For the sidechain of phenylalanine, chi 1 = 175.5(4), chi 2 = -127.0(6).
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Affiliation(s)
- E Subramanian
- Department of Crystallography and Biophysics, University of Madras, India
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Subramanian E, Sahayamary JJ. Structure and conformation of linear peptides. XII. Structure of tryptophanyl-glycyl-glycine dihydrate. Int J Pept Protein Res 1989; 34:134-8. [PMID: 2807731 DOI: 10.1111/j.1399-3011.1989.tb01502.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The crystal structure of a tripeptide, tryptophanyl-glycyl-glycine dihydrate (C15H18N4O4.2H2O, molecular weight = 354) has been determined. The crystals are orthorhombic, space group P2(1)2(1)2(1), with a = 7.875 (1) A, b = 9.009(1), c = 24.307(1) and Z = 4. The final R-index is 0.058 for 1488 reflections [sin theta)/lambda less than or equal to 0.6 A-1) with I greater than 2 sigma (I). The molecule exists as a zwitterion, with terminal NH3+ and COO- groups. The peptide units are trans and nearly perpendicular to the plane of the carboxyl group. The backbone torsion angles are: psi 1 = 132.7 degrees, omega 1 = 174.2 degrees, phi 2 = 88.2 degrees, psi 2 = 8.6 degrees, omega 2 = -179.8 degrees, phi 3 = -85.2 degrees, psi 31 = -178.1 degrees, psi 32 = 5.0 degrees. For the sidechain of tryptophan, chi 1 = -171.6 degrees, chi 2 = 101.0 degrees.
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Affiliation(s)
- E Subramanian
- Department of Crystallography and Biophysics, University of Madras, India
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Maruthamuthu M, Subramanian E. pH-Dependent interaction of sulfamethoxazole with crosslinked poly(N-vinyl-2-pyrrolidone). Polym Bull (Berl) 1989. [DOI: 10.1007/bf00271974] [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] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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