All Publications
*Corresponding author(s)
2024 |
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| Wadsworth GM, Srinivasan S, Datta M, Gopalan V(2024) RNA-driven phase transitions in biomolecular condensates. Mol. Cell, 84: 3692-3705 | |
| Gopalan V and Kirsebom LA (2024) A tribute to Sidney Altman, one of the architects of modern RNA biology. J. Biol. Chem. 300: 107364 | |
| Shen Y, Bosch G, Pino L and Gopalan V (2024) Use of the “double diamond” design framework to nurture creativity in life sciences research. Trends Biochem. Sci.49: 654-657 | |
| He S-L, Li B, Zahurancik WJ, Arthur HC, Sidharthan V, Gopalan V, Wang L, Jang J-C (2024) Overexpression of stress granule protein TZF1 enhances salt stress tolerance by targeting ACA11 mRNA for degradation in Arabidopsis. Front. Plant Sci. 15: 1375478 | |
2023 |
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| Gopalan V and Musier-Forsyth K (2023) Transfer RNAs: A treasure trove that keeps on giving. J. Biol. Chem., 299(10):105170. | |
| Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V, Banerjee P. (2023) RNAs undergo phase transitions with lower critical solution temperatures. Nat. Chem., 15(12):1693-1704. | |
| Kovvali S, Gao Y, Cool A, Lindert S, Wysocki VH*, Bell CE*, Gopalan V*. (2023) Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose-lysine. Protein Sci.: e4695. | |
| Elkholi IE, Boulais J, Thibault M-P, Phan H-D, Robert A, Lai LB, Faubert D, Smith MJ, Gopalan V, Côté J-F (2023) Mapping the MOB proteins’ proximity network reveals a unique interaction between human MOB3C and the RNase P complex J. Biol. Chem., 299: 105123 | |
| Roth K, Bannerman T, and Gopalan V. (2023) An outreach activity to enhance pedagogy. Trends Biochem. Sci., 48(5):410-413 | |
| Sabag-Daigle A°, Boulanger EF, Thirugnanasambantham P, Law JD, Bogard AJ, Behrman EJ*, Gopalan V*, and Ahmer BMM*. (2023) Identification of small molecule inhibitors of the Salmonella FraB deglycase using a live-cell assay. Microbiology Spectrum,11: e04606-22. | |
| Thirugnanasambantham P°, Bashian E°, Zaleski R, and Gopalan V*. (2022) GlycoForum-Technical Note Demonstrating the utility of sugar-phosphate phosphatases in coupled enzyme assays: galactose-1-phosphate uridylyltransferase as proof-of-concept. Glycobiology, 33: 95-98. °joint first authors | |
2022 |
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| Lucks JB, and Gopalan V. (2022) Sidney Altman: In his own words. RNA, 28: 1428-1429. | |
| Gopalan V. (2022) Sidney Altman: An exemplary scientist, teacher, and friend (1939-2022).RNA, 28: 1393-1397. | |
| Thirugnanasambantham P, Kovvali S, Cool A, Gao Y, Sabag-Daigle A, Boulanger EF, Mitton-Fry M, Di Capua A, Behrman EJ, Wysocki VH, Lindert S, Ahmer BMM, and Gopalan V*. (2022) Serendipitous Discovery of a Competitive Inhibitor of FraB, a Salmonella Deglycase and Drug Target. Pathogens, 11: 1102. | |
| Phan H-D°, Norris A°, Du C, Stachowski K, Khairunisa B, Sidharthan V, Mukhopadhyay B, Foster MP, Wysocki VH*, and Gopalan V*. (2022) Elucidation of structure-function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein. Nucleic Acids Res.., 50: 8154-8167 °joint first authors | |
| Szkoda BE°, Di Capua A°, Shaffer J, Behrman EJ, Wysocki VH*, and Gopalan V*. (2022) Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer metabolite by native mass spectrometry. J. Mol. Biol., 7: 167480. °joint first authors | |
| Lai LB, Lai SM, Szymanski ES, Kapur M, Choi EK, Al-Hashimi HM, Ackerman SL*, and Gopalan V*. (2022) Structural basis for impaired 5′ processing of a mutant tRNA associated with defects in neuronal homeostasis. Proc Natl Acad Sci USA, 119: e2119529119. | |
2021 |
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| Phan H-D, Lai LB*, Zahurancik WJ, and Gopalan V*. (2021) The many faces of RNA-based RNase P: An RNA-world relic. Trends Biochem. Sci., 46: 976-991. | ||
| Marathe IA, Lai SM°, Zahurancik WJ°, Poirier MG, Wysocki VH, and Gopalan V*. (2021) Protein cofactors and substrate dictate Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P. Nucleic Acids Res., 49: 9444-9458. °joint second authors | ||
| Boulanger EF, Sabag-Daigle A°, Thirugnanasambantham P°, Gopalan V*, and Ahmer BMM*. (2021) Sugar phosphate toxicities. Microbiol. Mol. Biol. Rev., 85: e0012321. °joint second authors | ||
| Lai SM, Thirugnanasambantham P°, Sidharthan V°, Norris AS, Law JD, Gopalan V*, and Wysocki VH*. (2021) Advancing overexpression and purification of recombinant proteins by pilot optimization through tandem affinity-buffer exchange chromatography online with native mass spectrometry. Methods Enzymol., 659: 37-70. °joint second authors | ||
| Zahurancik WJ, Norris AS, Lai SB, Snyder DT, Wysocki VH*, and Gopalan V*. (2021) Purification, reconstitution, and mass analysis of archaeal RNase P, a multi-subunit ribonucleoprotein enzyme. Methods Enzymol., 659: 71-103. | ||
| Ujor VC, Lai LB, Okonkwo CC, Gopalan V*, and Ezeji T*. (2021) Ribozyme-mediated downregulation uncovers DNA integrity scanning protein A (DisA) as a solventogenesis determinant in Clostridium beijerinckii. Front. Bioeng. Biotechnol., 9: 669462. | ||
| Busch F, VanAernum ZL, Lai SM, Gopalan V, and Wysocki VH* (2021) Analysis of Tagged Proteins Using Tandem Affinity-Buffer Exchange Chromatography Online with Native Mass Spectrometry. Biochemistry, 45: 1876-84. | ||
| Lai SM and Gopalan V*. (2021) Using an L7Ae-tethered, hydroxyl radical-mediated footprinting strategy to identify and validate kink-turns in RNAs. Methods Mol. Biol., 2167: 147-69. | ||
| Li W, Xiong Y, Lai LB, Zhang K, Li Z, Kang H, Dai L, Gopalan V*, Wang G-L*, and Liu W* (2021) The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens. Plant Biotechnol. J., 19: 1988-1999 | ||
| Kadowaki J, Jones T, Sengupta A, Gopalan V*, and Subramaniam V* (2021) Copper oxide-based cathode for direct NADPH regeneration. Sci. Rep., 11: 1-12. | ||
| Yu AM, Gaspar P, Cheng L, Lai LB, Kaur S, Gopalan V, Chen AA*, and Lucks JB* (2021) Computationally reconstructing co-transcriptional RNA folding pathways from experimental data reveals rearrangement of non-native folding intermediates. Mol. Cell, 81: 870-883. | ||
2020 |
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| Lai LB, Phan H-D, Zahurancik WJ, and Gopalan V* (2020) Alternative protein topology-mediated evolution of a catalytic ribonucleoprotein. Trends Biochem. Sci., 45: 825-828. | |
| Zahurancik WJ, Szkoda BE, Lai LB*, and Gopalan V* (2020) Ramping recombinant protein expression in bacteria. Biochemistry, 59: 2122-2124. | |
| Gray MW* and Gopalan V*. (2020) Piece by piece: Building a ribozyme. J. Biol. Chem., 295: 2313-2323. | |
2018 |
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| Lyon SE, Chen T-H, Wallace AJ, Adib KL, and Gopalan V*. (2018) An RNase P-based assay for accurate determination of the 5′-deoxy-5′-azidoguanosine-modified fraction of in vitro transcribed RNAs. ChemBioChem, 19: 2353-2359. | |
| Agu CV, Lai SM, Ujor V, Biswas PK, Jones A, Gopalan V, and Ezeji TC*. (2018) Development of a high-throughput assay for rapid screening of butanologenic strains. Sci. Rep., 8: 3379. [SI] | |
| Wu J°, Sabag-Daigle A°, Borton MA^, Kop LFM^, Szkoda BE^, Deatherage Kaiser BL, Lindemann SR, Renslow RS, Wei S, Nicora CD, Weitz KK, Kim Y-M, Adkins JN, Metz TO, Boyaka P, Gopalan V, Wrighton KC, Wysocki VH*, and Ahmer BMM*. (2018) Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut. Infect. Immun., 86: e00945-17. °joint first authors; ^joint second authors | |
| Wu J, Sabag-Daigle A, Metz TO, Deatherage Kaiser BL, Gopalan V, Behrman EJ, Wysocki VH*, and Ahmer BMM*. (2018) Measurement of fructose–asparagine concentrations in human and animal foods. J. Agric. Food Chem., 66: 212-217. | |
| Sabag-Daigle A, Wu J, Borton MA, Sengupta A, Gopalan V, Wrighton KC, Wysocki VH, and Ahmer BMM*. (2018) Identification of bacterial species that can utilize fructose-asparagine. Appl. Environ. Microbiol., 84: e01957-17. | |
| Lyon S and Gopalan V*. (2018) A T7 RNA polymerase mutant enhances the yield of 5′-thienoguanosine-initiated RNAs. ChemBioChem, 19: 142-146. (Highlighted on the cover) | |
| Gopalan V*, Jarrous N*, and Krasilnikov AS*. (2018) Chance and necessity in the evolution of RNase P. RNA, 24: 1-5. | |
2017 |
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| Sabag-Daigle A, Sengupta A, Blunk HM, Biswas PK, Cron MC, Bogard AJ, Behrman EJ, Gopalan V, and Ahmer BMM*. (2017) Salmonella FraE, an asparaginase homolog, contributes to fructose-asparagine but not asparagine utilization. J. Bacteriol., 199: e00330-17. | |
| Sengupta A, Zabala A^, Tan SY^, Broadstock A^, Suryanarayanan TS, and Gopalan V*. (2017) Characterization of an ionic liquid-tolerant ß-xylosidase from a marine-derived fungal endophyte. Biochem. Cell Biol., 95: 585-591. ^joint second authors | |
| Lai LB*, Tanimoto A^, Lai SM^, Chen W-Y, Marathe IA, Westhof E, Wysocki VH, and Gopalan V*. (2017) A novel double kink-turn module in euryarchaeal RNase P RNAs. Nucleic Acids Res., 45: 7432-7440. [SI] ^joint second authors | |
| Suryanarayanan TS, Gopalan V, Uma Shaanker R, Sengupta A, and Ravikanth G. (2017) Translating endophyte research to applications: prospects and challenges. In JL de Azevedo and MC Quecine (Eds.), Diversity and Benefits of Microorganisms from the Tropics (pp. 343-365). Cham, Switzerland: Springer International Publishing AG. | |
| Biswas PK, Behrman EJ*, and Gopalan V*. (2017) Characterization of a Salmonella sugar kinase essential for utilization of fructose-asparagine. Biochem. Cell Biol., 95: 304-309. | |
2007 |
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| Behrman EJ* and Gopalan V. (2007) The anomeric specificity of enzymes which act on sugars. J. Chem. Educ., 84: 1608. | |
| Gopalan V*. (2007) Uniformity amid diversity in RNase P. Proc. Natl. Acad. Sci. USA, 104: 2031-2032. | |
| Gopalan V and Altman S*. (2007) Ribonuclease P: structure and catalysis. In RF Gesteland, TR Cech, and JF Atkins (Eds.), The RNA World (3rd edition; online version only). New York, NY: Cold Spring Harbor Laboratory Press. | |
2006 |
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| Gopichandran V, Lai LB, and Gopalan V*. (2006) Protein-energy malnutrition. In RH Glew and MD Rosenthal (Eds.), Clinical Studies in Medical Biochemistry, (3rd edition; pp. 255-265). New York, NY: Oxford University Press. | |
| Lai LB, Gopichandran V, and Gopalan V*. (2006) Tangier disease: a disorder in the reverse cholesterol transport pathway. In RH Glew and MD Rosenthal (Eds.), Clinical Studies in Medical Biochemistry, (3rd edition; pp. 159-166). New York, NY: Oxford University Press. | |
| Tsai H-Y, Pulukkunat DK, Woznick WK, and Gopalan V*. (2006) Functional reconstitution and characterization of Pyrococcus furiosus RNase P. Proc. Natl. Acad. Sci. USA, 103: 16147-16152. [SI] | |
2005 |
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| Behrman EJ* and Gopalan V. (2005) Cholesterol and plants. J. Chem. Educ., 82: 1791-1793. | |
2004 |
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| Rangarajan S, Stephen Raj ML, Hernandez JM, Grotewold E, and Gopalan V*. (2004) RNase P as a tool for disruption of gene expression in maize cells. Biochem. J., 380: 611-616. | |
| Gopalan V, Vioque A, and Altman S*. (2004) RNase P: variations and uses. In E Keinan, I Schechter, and M Sela (Eds.), Life Sciences for the 21st Century, (pp. 49-59). Weinheim, Germany: Wiley-VCH. | |
2003 |
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| Boomershine WP, McElroy CA, Tsai H-Y, Wilson RC, Gopalan V, and Foster MP*. (2003) Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P. Proc. Natl. Acad. Sci. USA, 100: 15398-15403. | |
| Eder PS, Hatfield C, Vioque A, and Gopalan V*. (2003) Bacterial RNase P as a potential target for novel anti-infectives. Curr. Opin. Investig. Drugs, 4: 937-943. | |
| Boomershine WP, Stephen Raj ML, Gopalan V, and Foster MP*. (2003) Preparation of uniformly labeled NMR samples in Escherichia coli under the tight control of the araBAD promoter: expression of an archaeal homolog of the RNase P Rpp29 protein. Protein Expr. Purif., 28: 246-251. | |
| Pulukkunat DK, Stephen Raj ML, Pattanayak D, Lai LB, and Gopalan V*. (2003) Exploring the potential of plant RNase P as a functional genomics tool. In E. Grotewold (Ed.), Plant Functional Genomics (Methods in Molecular Biology, vol. 236; pp. 295-309). Totowa, NJ: Humana Press, Inc. | |
| Tsai H-Y, Masquida B, Biswas R, Westhof E, and Gopalan V*. (2003) Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J. Mol. Biol., 325: 661-675. | |
2002 |
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| Jovanovic M, Sanchez R, Altman S, and Gopalan V*. (2002) Elucidation of structure–function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach. Nucleic Acids Res., 30: 5065-5073. [SI] | |
| Tsai H-Y°, Lai LB°, and Gopalan V*. (2002) A modified pBluescript-based vector for facile cloning and transcription of RNAs. Anal. Biochem., 303: 214-217. °joint first authors | |
| Eubank TD, Biswas R, Jovanovic M, Litovchick A, Lapidot A, and Gopalan V*. (2002) Inhibition of bacterial RNase P by aminoglycoside–arginine conjugates. FEBS Lett., 511: 107-112. | |
| Guerrier-Takada C, Eder PS, Gopalan V, and Altman S*. (2002) Purification and characterization of Rpp25, an RNA-binding protein subunit of human ribonuclease P. RNA, 8: 290-295. | |
| Gopalan V, Vioque A, and Altman S*. (2002) RNase P: variations and uses. J. Biol. Chem., 277: 6759-6762. | |
2001 |
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| Wu C-W, Eder PS, Gopalan V*, and Behrman EJ*. (2001) Kinetics of coupling reactions that generate monothiophosphate disulfides: implications for modification of RNAs. Bioconjug. Chem., 12: 842-844. | |
| Biswas R, Kühne H, Brudvig GW, and Gopalan V*. (2001) Use of EPR spectroscopy to study macromolecular structure and function. Sci. Prog., 84: 45-68. | |
| Stephen Raj ML, Pulukkunat DK, Reckard JF III, Thomas G, and Gopalan V*. (2001) Cleavage of bipartite substrates by rice and maize ribonuclease P. Application to degradation of target mRNAs in plants. Plant Physiol., 125: 1187-1190. | |
2000 |
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| Altman S*, Gopalan V, and Vioque A. (2000) Varieties of RNase P: a nomenclature problem? RNA, 6: 1689-1694. | |
| Biswas R, Ledman DW, Fox RO, Altman S, and Gopalan V*. (2000) Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe. J. Mol. Biol., 296: 19-31. | |
1999 |
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| Gopalan V*, Kühne H, Biswas R, Li H, Brudvig GW, and Altman S. (1999) Mapping RNA–protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy. Biochemistry, 38: 1705-1714. | |