Publications
2023 - 2021
Majumdar S, Emmerich A, Krakovka S, Mandava CS, Svärd SG, Sanyal S.1 Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis. Nucleic Acids Res. 2023 Mar 13:gkad176. doi: 10.1093/nar/gkad176. Epub ahead of print. PMID: 36912103.
Parajuli NP, Emmerich A, Mandava CS, Pavlov MY, Sanyal S.1 Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria. Nat Commun. 2023 Feb 17;14(1):918. doi: 10.1038/s41467-023-36528-7. PMID: 36806263; PMCID: PMC9938272.
Zhao L, Sanyal S.1 p53 Isoforms as Cancer Biomarkers and Therapeutic Targets. Cancers (Basel). 2022 Jun 27;14(13):3145. doi: 10.3390/cancers14133145. PMID: 35804915; PMCID: PMC9264937.
Albers S, Beckert B, Matthies MC, Mandava CS, Schuster R, Seuring C, Riedner M, Sanyal S, Torda AE, Wilson DN, Ignatova Z. Repurposing tRNAs for nonsense suppression. Nat Commun. 2021 Jun 22;12(1):3850. doi: 10.1038/s41467-021-24076-x. PMID: 34158503; PMCID: PMC8219837.
Parajuli NP, Mandava CS, Pavlov MY, and Sanyal S.1, Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin. Nucleic Acids Research 2021 Jul 9;49(12):6880-6892. doi: 10.1093/nar/gkab495. PMID: 34125898; PMCID: PMC8266624.
Eaglesfield R, Madsen MA, and Sanyal S, Reboud J, Amtmann A, Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis. iScience 2021 May 21, https://doi.org/10.1016/ j.isci.2021.102429.
Kim C, Holm M, Mandava CS, and Sanyal S.1, Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation. RNA Biol. 2021 May 3:1-12. doi: 10.1080/15476286.2021.1913312.
Pundir S, Ge X, and Sanyal S.1 , GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors. J Biol Chem. 2021 Apr 19:100681. doi: 10.1016/j.jbc.2021.100681.
De Tarafder A, Parajuli NP, Majumdar S, Kaçar B, and Sanyal S.1 , Kinetic Analysis Suggests Evolution of Ribosome Specificity in Modern Elongation Factor-Tus from 'Generalist' Ancestors. Mol Biol Evol. 2021 Apr 19:msab114. doi: 10.1093/molbev/msab114
Rivera JA., Larsson J., Volkov IJK., Seedfeldt CA., Sanyal S., and Johansson M., Real-time measurements of aminoglycoside effects on protein synthesis in live cells. Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):e2013315118. doi: 10.1073/pnas.2013315118.
2019 - 2020
Pang Y., Kovachev P., Sanyal S., Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s. Int J Mol Sci. 2020;21(17):E6340. doi: 10.3390/ijms21176340
Chen Y.X., Xu Z.Y., Ge X., Sanyal S., Lu Z.J., Javid B., Selective translation by alternative bacterial ribosomes. Proc Natl Acad Sci U S A. 2020;117(32):19487-19496. doi: 10.1073/pnas.2009607117. [Pubmed]
Wang W, Li W, Ge X, Yan K, Mandava CS, Sanyal S and Gao N, Loss of a single methylation in 23S rRNA delyas 50S assembly at multiple late stages and impairs translation initiation and elongation. Proc Natl Acad Sci USA, 2020; 117(27):15609-15619. doi: 10.1073/pnas.1914323117. [Pubmed]
Abdalaal H, Pu. ndir S, Ge X, Sanyal S, Näsvall J, Collateral Toxicity Limits the Evolution of Bacterial Release Factor 2 Towards Total Omnipotence. Molecular Biology and Evolution 2020, msaa129, doi: 10.1093/molbev/msaa129. Online ahead of print. [Pubmed]
Ge X, Oliveira A, Hjort K, Bergfors T, de Teran HG, Andersson DI, Sanyal S, Åqvist J, Inhibition of translation termination by small molecules targeting ribosomal release factors. Scientific Reports 2019, Oct 28; 9;15424, doi: 10.1038/s41598-019-51977-1 [PubMed]
Kovachev PS, Gomes MPB, Cordeiro Y, Ferreira NC, VAladao LPF, Ascari LM, Rangel LP, Silvia JL, Sanyal S, RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction. Scientific Reports 2019, Aug 27; 9(1):12406, doi: 10.1038/s41598-019-48883-x, [PubMed]
Holm M, Mandava CS, Ehrenberg M and Sanyal S, The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation, eLIFE, 2019 Jun, doi:10.7554/eLife.46124 [PubMed]
Cordeiro Y., Vieira T., Kovachev P., Sanyal S. and Silv J.L..Modulation of p53 and prion protein aggreation by RNA, BBA - Proteins and Proteomics, 2019 Feb, doi: 10.1016/j.bbapap.2019.02.006
Liljas A and Sanyal S, The enigmatic ribosomal stalk, Quarterly Reviews of Biophysics, Cambridge Press, 2019, doi: 10.1017/S0033483518000100
2018-2017
Vovusha H., Banerjee D., Yadav M. K., Perrozzi F., Ottaviano L., Sanyal S. and Sanyal B., Binding Characteristics of Anticancer Drug Doxorubicin with Two-Dimensional graphene and Graphene Oxide: Insights from Density functional Theory Calculations and Fluorescence Spectroscopy. J. Phys. Chem, 2018 August, doi: 10.1021/acs.jpcc.8b04496
Vieler M. and Sanyal S., p53 Isoforms and Their Implications in Cancer (Review). Cancers, 2018, 10, 288
Fislage M., Zhang J., Brown ZP., Mandava CS. Sanyal S., Ehrenberg. and Frank J., Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA complex with GTP and the GTPase-deficient EF-TuH84A. Nucleic Acids Research, 2018 May 4. doi: 10.1093/nar/gky346. [Epub ahead of print] [PubMed]
Ge X., Mandava CS., Lind C., Åqvist J. and Sanyal S., Complementary charge based interaction between the ribosomal stalk protein L7/L12 and IF2 is the key to rapid subunit association. Proc Natl Acad Sci USA, 2018. 115(18) 4649-4654, [PubMed]
Qiang X, Liotta AS, Shiloach J, Gutierrez JC, Wang H, Ochani M, Ochani K, Yang H, Rabin A, LeRoith D, Lesniak MA, Böhm M, Maaser C, Kannengiesser K, Donowitz M, Rabizadeh S, Czura CJ, Tracey KJ, Westlake M, Zarfeshani A, Mehdi SF, Danoff A, Ge X, Sanyal S, Schwartz GJ, Roth J. New melanocortin-like peptide of <i>E. coli</i> can suppress inflammation via the mammalian melanocortin-1 receptor (MC1R): possible endocrine-like function for microbes of the gut. NPJ Biofilms Microbiomes. 2017 Nov 13;3:31. doi: 10.1038/s41522-017-0039-9. eCollection 2017. PMID: 29152323 [PubMed]
Li Z, Ge X, Zhang Y, Zheng L, Sanyal S, Gao N. Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers. Protein Cell. 2017 Sep 5. doi: 10.1007/s13238-017-0456-9. [Epub ahead of print] PMID: 28875450 [PubMed]
Korkmaz G, Sanyal S. R213I mutation in release factor 2 (RF2) is one step forward for engineering an omnipotent release factor in bacteria Escherichia coli. J Biol Chem. 2017 Sep 8;292(36):15134-15142. doi: 10.1074/jbc.M117.785238. Epub 2017 Jul 25. PMID: 28743745 [PubMed]
Mohapatra S., Choi H., Ge X., Sanyal S., Weisshaar JC. Spatial distribution and ribosome-binding dynamics of EF-P in live Escherichia coli. mBio 2017 8:e00300-17. [PubMed] (mBio Editor's pick)
Kovachev PS, Banerjee D, Rangel LP, Eriksson J, Pedrote MM, Martins-Dinis MMDC, Edwards K, Cordeiro Y, Silva JL, Sanyal S. Distinct modulatory role of RNA in the aggregation of the tumor suppressor protein p53 core domain. J Biol Chem 2017 292, 9345-9357. [PubMed] (JBC Editor's pick )
Chan S., Frasch A., Mandava CS., Chong JH., Quintana MP., Vesterlund M., Ghorbal M., Joannin N., Franzen O., Lopez-Rubio JJ., Barbiere S., Lanzavecchia A., Sanyal S., and Wahlgren M*. Regulation of PfEMP1–VAR2CSA translation by a Plasmodium translation-enhancing factor. Nature Microbiology, 2017 10.1038/nmicrobiol.2017.68. [PubMed]
Kacar B., Ge X., Sanyal S., and Gaucher E. Experimental evolution of Escherichia coli harbouring an ancient translation protein. J Mol Evol, 2017 DOI:10.1007/s00239-017-9781-0. [PubMed] (Journal cover and research news)
Masuda I., Igarasgi T., Sakaguchi R., Nitharwal RG., Takase R., Han Kyu Y., Leslie B., Liu C., Gamper Jr. H., Ha T., Sanyal S., and Hou YM. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. Nucleic Acids Research, 2017; 45(7):4081-4093.
2016 - 2015
Holm M., Borg A., Ehrenberg M., Sanyal S. Molecular mechanism of viomycin inhibition of peptide elongation in bacteria. Proc Natl Acad Sci U S A. 2016 Jan 11. pii: 201517541. [PubMed]
Degiacomi G., Personne Y., Mondésert G., Ge X., Mandava CS., Hartkoorn RC., Boldrin F., Goel P., Peisker K., Benjak A., Barrio MB., Ventura M., Brown AC., Leblanc V., Bauer A., Sanyal S., Cole ST., Lagrange S., Parish T., Manganelli R., Micrococcin P1 - A bactericidal thiopeptide active against Mycobacterium tuberculosis. Tuberculosis (Edinb). 2016 Sep;100:95-101. doi: 10.1016/j.tube.2016.07.011. [PubMed]
Zhang Y., Mandava CS., Cao W., Li X., Zhang, D., Li N., Zhang Y., Zhang X., Qin Y., Mi K., Lei J., Sanyal S.*, Gao N. HflX is an alternative ribosome recycling factor rescuing stalled ribosomes under stress conditions, Nature Structure Molecular Biology, 2015 Sep 04. doi:10.1038/nsmb.3103 [PubMed]
Koripella RK., Holm M., Dourado D., Mandava CS., Flores S., and Sanyal S. A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate. Scientific Reports, 2015 Aug 12;5:12970. doi: 10.1038/srep12970. [PubMed]
Li W., Liu Z., Koripella RK., Langlois R., Sanyal S., and Frank J. Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor G. Science Advances, 2015 (1) 4, e1500169 [PubMed]
Vovusha H., Banerjee D., Oumata N., Sanyal B., and Sanyal S. Electronic Structure and Spectroscopic Properties of 6-Aminophenanthridine and Its Derivatives: Insights from Density Functional Theory. International Journal of Quantum Chemistry, 2015, 115, 846-852
Borg A., Holm M., Shiroyama I., Hauryliuk V., Pavlov M., Sanyal S. and Ehrenberg M. Fusidic acid targets elongation factor G in several stages of translocation on the bacterial ribosome. J. Biol. Chem., 2015, 290, 3440-3454 [PubMed]
2014 - 2013
Banerjee D. and Sanyal S. Protein Folding Activity of the Ribosome (PFAR) - A Target for Antiprion Compounds. Viruses. 2014, 6, 3907-3924. [PubMed]
Nguyen P h. et al. Structure - Activity Relationship Study around Guanabenz Identifies Two Derivatives Retaining Antiprion Activity but Having List alpha2-Adrenergic Receptor Agonistic Activity. ACS Chemical Neuroscience 2014, 5, 1075-1082 [PubMed]
Korkmaz G., Holm M., Wiens T. and Sanyal S. Comprehensive Analysis of Stop Codon Usage in bacteria and its Correlation with Release Factor Abundance. J. Biol. Chem., 2014, 289, 30334-3042 [PubMed]
Feng, B., Mandava CS., Guo Q., Wang J., Cao W., Li N., Zhang Yi., Zhang Ya., Wang Z., Wu J., Sanyal S., Lei J., and Gao N. Structural and Functional Insights into the Mode of Action of a Universally Conserved Obg GTPase, PLOS Biology, 2014, 12(5). [PubMed]
Chai Q., Singh B., Peisker K., Metzendorf N., Ge X., Dasgupta S. and Sanyal S. Organization of Ribosomes and Nucleoids in Escherichia coli Cells During Growth and in Quiescence, J. Biol. Chem., 2014, 289, 11342-11352. [PubMed]
Banerjee, D., Vovusha H., Pang Y., Oumata N., Sanyal B. and Sanyal S. Spectroscopic and DFT studies on 6-Aminophenanthridine and its derivatives provide insights in their activity towards ribosomal RNA. Biochimie, 2014, 97, 194-199 [PubMed]
Vovusha H., Sanyal S., Sanyal B. Interaction of Nucleobases and Aromatic Amino Acids with Graphene Oxide and Graphene Flakes. J. Phys. Chem. Lett., 2013, 4 (21), 3710-3718
Oumata N. et al. The Toll-Like Receptor Agonist Imiquimod Is Active against Prions. PLoS ONE, 2013 8, e72112. [PubMed]
Pang Y., Kurella S., Voisset C., Samanta D., Banerjee D., Schabe A., Das Gupta C., Galons H., Blondel M. and Sanyal S. The antiprion compound 6-Aminophenanthridine inhibits protein folding activity of the ribosome by direct competition 2013. J. Biol. Chem., 2013, 288: 19081-19089 [PubMed]
Pallesen J., Hashem Y., Korkmaz G., Koripella RK., Huang C., Ehrenberg M., Sanyal S. and Frank J. Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1. eLIFE 2013, 2. [PubMed]
2012 - 2011
Koripella RK., Chen Y., Peisker K., Koh CS., Selmer M. and Sanyal S. Mechanism of elongation factor-G mediated fusidic acid resistance and fitness compensation in Staphylococcus aureus, J. Biol. Chem., 2012; 287(36):30257-30267 [PubMed]
Deroo S., Hyung SJ., Marcoux J., Gordiyenko Y., Koripella RK., Sanyal S. and Robinson CV. Mechanism and Rates of Exchange of L7/L12 between Ribosomes and the Effects of Binding EF-G, ACS Chem. Biol., 2012, 7 (6), pp 1120–1127 [PubMed]
Kåhrstrom Tobin C., Andersson DI. and Sanyal S. Comprehending a molecular conundrum: functional studies of ribosomal protein mutants from Salmonella typhimurium, 2012; Ed. Annous BA. InTech Open Access Publisher. ISBN 979-953-307-690-3.
Guo X., Peisker K., Bäckbro K., Chen Y., Koripella RK., Mandava CS., Sanyal S. and Selmer M. Structure and function of FusB: an elongation factor G-binding fusidic acid resistance protein active on ribosomal translocation and recycling Open Biol, 2012; 2: 120016. [PubMed]
Mandava CS., Peisker K., Ederth J., Kumar R., Ge X., Szaflarski W. and Sanyal S. Bacterial ribosome requires multiple L12 dimers for efficient initiation and elongation of protein synthesis involving IF2 and EF-G, Nucleic Acids Research, 2012; 40(5): 1969-1983. [PubMed]
Sridhara S. and Sanyal S. RNA-RNA ligation: Methods, Prospects and Applications, GERF Bulletin of Biosciences 2011; 2(2):32-35.
Kumar R. and Sanyal S. Mycobacterium tuberculosis: Dormancy, Persistence and Survival in the Light of Protein Synthesis in Mycobacterium tuberculosis, 2011; Ed. Cardona P. InTech Open Access Publisher. ISBN 979-953-307-699-6.
Dos-Reis S., Pang Y., Vishnu N., Voisset C., Galon H., Blondel M. and Sanyal S. Mode of action of the antiprion drugs 6AP and GA on ribosome assisted protein folding. Biochimie, 2011; 93(6):1047-54. [PubMed]
Abraham E.J., Slater K.A., Sanyal S, Linehan K., Flaherty P.M., and Qian S. Scale-up of Mammalian Cell culture using a New Multilayered Flask. Journal of Visulaized Experiments. 2011, DOI: 10.3791/3418 [PubMed]
2010 - 2009
Pavlov M., Sanyal S. and Ehrenberg M. Initiation of bacterial protein synthesis with wild type and novel mutants of initiation factor 2 in Ribosomes: Structure, Function and Dynamics eds. Rodnina M., Wintermeyer W., Green R., Springer Verlag GmbH
Yang C., Koripella RK., Sanyal S. and Selmer S. Staphylococcus aureus elongation factor G - structure and analysis of a target for fusidic acid. FEBS Jour, 2010; 277(18):3789-803. [PubMed]
Huang C., Mandava CS. and Sanyal S. The ribosomal stalk plays a key role in IF2 mediated association of the ribosomal subunits. J. Mol. Biol., 2010; 399(1):145-53. [PubMed]
Tobin C., Mandava CS., Ehrenberg M., Andersson DI., and Sanyal S. Ribosomes Lacking Protein S20 Are Defective in mRNA Binding and Subunit Association. J. Mol. Biol., 2010, 397(3):767-776. [PubMed]
Ederth J., Mandava CS., Bouakaz L., Dasgupta S. and Sanyal S. A high-throughput one-step purification method of affinity tagged active 70S ribosome from Escherichia coli. Nucleic Acids Res., 2009, 37(2):e15 [PubMed]
2008 - 2007
Li W., Agirrezabala X., Lei J., Brunelle J., Ortiz-Meoz J., Green R., Sanyal S., Ehrenberg M. and Frank J. Recognition of Phe-tRNAPhe, Trp-tRNATrp and Leu-tRNALeuI: a common molecular mechanism for aminoacyl-tRNA selection revealed by cryo-EM. EMBO J, 2008, Dec 17;27(24):3322-31. [PubMed]
Das D., Das A., Samanta D., Ghosh J, Dasgupta S., Bhattacharya A., Basu A, Sanyal S. and Das Gupta C. Role of the ribosome in protein folding. Biotechnol J., 2008 Aug 13;3(8):999-1009. [PubMed]
Tribouillard-Tanvier D. et al Protein folding activity of ribosomal RNA is a selective target of two unrelated antiprion drugs. PLOS One, 2008, May 14;3(5):e2174. [PubMed]
Gao H., Zhou Z., Rawat U., Huang C., Bouakaz L., Wang C., Cheng Z., Liu Y., Zavialov A., Gursky R., Sanyal S., Ehrenberg M., Frank J. and Song H. RF3 induces ribosomal conformational changes responsible for the dissociation of class-I release factors. Cell 2007; 129, 929-941. [PubMed]
Helgstrand M., Mandava CS., Mulder FAA., Liljas A., Sanyal S. and Akke M. The Ribosomal Stalk Binds to Translation Factors IF2, EF-Tu, EF-G and RF3 via a Conserved Region of the L12 C-terminal Domain, J. Mol. Biol., 2007; 365(2):468-79. [PubMed]
2006 -
Riber D., Venkataramana M., Sanyal S. and Duvold T. Synthesis and biological evaluation of photoaffinity labeled fusidic acid analogues. J Med Chem., 2006;49(5):1503-5 [PubMed]
Bouakaz L., Bouakaz E., Murgola EJ., Ehrenberg M. and Sanyal S. The Role of Ribosomal Protein L11 in Class I Release Factor-mediated Translation Termination and Translational Accuracy. J Biol Chem. 2006 Feb 17;281(7):4548-56. [PubMed]
Li JJ., Venkataramana M., Sanyal S., Janson JC. and Su ZG. Immobilized beta-cyclodextrin polymer coupled to agarose gel properly refolding recombinant Staphylococcus aureus elongation factor-G in combination with detergent micelle. Protein Expr Purif. 2006 Jan;45(1):72-9. [PubMed]
Vestergaard B., Sanyal S., Roessle M., Mora L., Buckingham RH., Kastrup JS., Gajhede M., Svergun DI. and Ehrenberg M. The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Mol Cell. 2005 Dec 22;20(6):929-38. [PubMed]
Sörensen M., Elf J., Bouakaz E., Tenson T., Sanyal S., Björk GR. and Ehrenberg, M. Over Expression of a tRNALeu Isoacceptor Changes Charging Pattern of Leucine tRNAs and Reveals New Codon Reading J Mol Biol. 2005 Nov 18;354(1):16-24. Epub 2005 Oct 5. [PubMed]
Li JJ., Venkataramana M., Wang AQ., Sanyal S., Janson JC. and Su ZG. A mild hydrophobic interaction chromatography involving polyethylene glycol immobilized to agarose media refolding recombinant Staphylococcus aureus elongation factor G. Protein Expr Purif. 2005 Apr;40(2):327-35. [PubMed]
Mulder FA., Bouakaz L., Lundell A., Venkataramana M., Liljas A., Akke M. and Sanyal S. Conformation and dynamics of ribosomal stalk protein L12 in solution and on the ribosome. Biochemistry. 2004 May 25;43(20):5930-6. [PubMed]
Sanyal SC., Bhattacharyya D. and Das Gupta C. The folding of dimeric cytoplasmic malate dehydrogenase. Equilibrium and kinetic studies. Eur J Biochem. 2002 Aug;269(15):3856-66. [PubMed]
Sanyal SC., Pal S., Chaudhuri S. and DasGupta C. 23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding. Nucleic Acids Res. 2002 June. 1;30(11):2390-7. [PubMed]
Chandra Sanyal S. and Liljas A. The end of the beginning: structural studies of ribosomal proteins. Curr Opin Struct Biol. 2000 Dec;10(6):633-6. Review. [PubMed]
Chattopadhyay S., Pal S., Pal D., Sarkar D., Chandra S. and Das Gupta C. Protein folding in Escherichia coli: role of 23S ribosomal RNA. Biochim Biophys Acta. 1999 Jan 11;1429(2):293-8. [PubMed]
Pal D., Chattopadhyay S., Chandra S., Sarkar D., Chakraborty A. and Das Gupta C. Reactivation of denatured proteins by domain V of bacterial 23S rRNA. Nucleic Acids Res. 1997 Dec 15;25(24):5047-51. [PubMed]
Pal S., Chandra S., Chowdhury S., Sarkar D., Ghosh AN. and Gupta CD. Complementary role of two fragments of domain V of 23 S ribosomal RNA in protein folding. J Biol Chem. 1999 Nov 12;274(46):32771-7. [PubMed]
Basusarkar P., Chandra S. and Bhattacharyya B. The colchicine-binding and pyrene-excimer-formation activities of tubulin involve a common cysteine residue in the beta subunit. Eur J Biochem. 1997 Mar 1;244(2):378-83. [PubMed]