56. Delineation of a novel assembly intermediate in retroviral integration pathway
Rahul Chadda, Sibes Bera, Mohamed Ghoneim, Tamara De Melo, Duane P Grandgenett, Edwin Antony, Krishan K Pandey
bioRxiv. 2025, 10.1101/2025.09.09.675266;
doi: https://doi.org/10.1101/2025.09.09.675266
In Press: Nucleic Acids Research.
Rahul Chadda, Sibes Bera, Mohamed Ghoneim, Tamara De Melo, Duane P Grandgenett, Edwin Antony, Krishan K Pandey
bioRxiv. 2025, 10.1101/2025.09.09.675266;
doi: https://doi.org/10.1101/2025.09.09.675266
In Press: Nucleic Acids Research.
55. Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex
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Rajnandani Kashyap, Thomas M Deere, Ahmad Dhamad, Melissa Chanderban, Monika Tokmina-Lukaszewska, Brian Bothner, Daniel J Lessner, Edwin Antony
bioRxiv 2025.09.09.675011; doi: https://doi.org/10.1101/2025.09.09.675011 Manuscript under revision: Nature |
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54. PCNA encircling primer/template junctions is eliminated by exchange of RPA for Rad51: Implications for the interplay between human DNA damage tolerance pathways.
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Jessica L. Norris, Lindsey O. Rogers, Grace Young, Kara G. Pytko, Rachel L. Dannenberg, Samuel Perreault, Vikas Kaushik,
Edwin Antony, and Mark Hedglin. Nucleic Acids Research. 2026 54:1. doi.org/10.1093/nar/gkaf1478 |
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53. Mechanism of RPA phosphocode priming and tuning by Cdk1/Wee1 signaling circuit.
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Roshan P., Kaushik V., Mistry A., Vayyeti A., Antony A., Lubbers R., Deveryshetty J., Antony E., and Origanti S. Nature Communications. 2026 17:92. doi: 10.1038/s41467-025-66794-6 |
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52. Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA.
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Paul T, Lee IR, Pangeni S, Rashid F, Yang O, Antony E, Berger JM, Myong S, Ha T. Nucleic Acids Res. 2025 Jun 20;53(12):gkaf642. doi: 10.1093/nar/gkaf642. |
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51. Rad52 sorts and stacks Rad51 at the DNA junction to promote homologous recombination.
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Deveryshetty J., Mistry, A., Pangeni S., Ghoneim M., Tokmina-Lukaszewska M., Kaushik V., Taddei A., Ha T., Bothner B., and Antony E. Nature Communications. 2025. 16:6685. https://doi.org/10.1038/s41467-025-61811-0 |
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50. Cryo-EM captures the coordination of asymmetric electron transfer through a bi-copper cluster in DPOR.
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Kashyap R., Walsh N., Deveryshetty J., Tokmina-Lukaszewska M., Zhao K., Gan Y.J., Hoffman B.M., Sarangi R., Bothner B., Bennett B., and Antony E. Nature Communications. 2025. 16:3866. https://doi.org/10.1038/s41467-025-59158-7ht |
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49. Partial wrapping of single-stranded DNA by Replication Protein A and modulation through phosphorylation.
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Chadda R., Kaushik V., Ahmad I.M., Deveryshetty J., Holehouse A., Sigurdsson S.T., Biswas G., Levy Y., Bothner B., Cooley R.B., Mehl R.A., Dastvan R., Origanti S., and Antony E. Nucleic Acids Research. 2024. doi: 10.1093/nar/gkae584 |
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48. Human hnRNPA1 reorganizes telomere-bound Replication Protein A.
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Granger SL, Sharma R, Kaushik V, Razzaghi M, Honda M, Gaur P, Bhat DS, Labenz SM, Heinen JE, Williams BA, Tabei SMA, Wlodarski MW, Antony E, Spies M. Nucleic Acids Research. 2024. 52(20):12422-12437. doi: 10.1093/nar/gkae834. |
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47. Replication protein A dynamically re-organizes on primer/template junctions to permit DNA polymerase δ holoenzyme assembly and initiation of DNA synthesis
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Norris J.L., Rogers L.O., Pytko K.G., Dannenberg R.L., Perreault S., Kaushik V., Kuppa S., Antony E., and Hedglin M. Nucleic Acids Research. 2024. 52(13):7650-7664. doi: 10.1093/nar/gkae475. |
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46. Rapid long-distance migration of RPA on single stranded DNA occurs through intersegmental transfer utilizing multivalent interactions.
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Pangeni S., Biswas G., Kaushik V., Kuppa S., Yang O., Chang-Tin L., Mishra G., Levy Y., Antony E., and Ha T.J. J. Mol. Biol. 2024. doi: 10.1016/j.jmb.2024.168491 |
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45. Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair.
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44. Fluorescent human RPA to track assembly dynamics on DNA.
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Kaushik V., Chadda R., Kuppa S., Pokhrel N., Vayyeti A., Grady S., Arnatt C., and Antony E. Methods. 2024. S1046-2023(24)00043-4. doi: 10.1016/j.ymeth.2024.01.019. |
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43. C-terminus induced asymmetry within a Rad52 homodecamer dictates single-position Rad51 nucleation in homologous recombination.
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Deveryshetty J., Chadda R., Mattice J., Karunakaran S., Rau M.J., Basore K., Pokhrel N., Englander N., Fitzpatrick J, A., Bothner B., and Antony E. Nature Communications. 2023. 14(1):6215. doi: 10.1038/s41467-023-41993-1. |
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42. An Aurora B-RPA signaling axis secures chromosome segregation fidelity.
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Roshan P., Kuppa S., Mattice J., Kaushik V., Chadda R., Pokhrel N., Tumala B., Biswas A., Bothner B., Antony E., and Origanti S. Nature Communications. 2023. 14(1):3008. doi: 10.1038/s41467-023-38711-2. |
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41. Mechanistic insight into AP-Endonuclease I cleavage of abasic sites at stalled replication forks.
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Hoitsma N.M., Norris J., Khoang T.H., Kaushik V., Antony E., Hedglin M., and Freudenthal B.D. Nucleic Acids Research. 2023. 51(13):6738. DOI: 10.1093/nar/gkad481 |
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40. Dynamic states of eIF6 and SDS variants modulate interaction with uL14 of the 60S ribosomal subunit.
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Eliff J., Biswas A., Kuppa S., Roshan P., Patterson A., Mattice J., Chinnaraj M., Burd R., Walker S.E., Pozzi N., Antony E., Bothner B., and Origanti S. Nucleic Acids Res. 2023. 51(4):1803-1822.doi: 10.1093/nar/gkac1266. |
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39. Rtt105 configurationally staples RPA and blocks facilitated exchange and interactions with RPA-interacting proteins.
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Kuppa S., Deveryshetty J., Chadda R., Mattice J., Pokhrel H., Kaushik V., Patterson A., Dhingra N., Pangeni S., Sadauskas M.K., Shiekh S., Balci H., Ha T., Zhao X., Bothner B., and Antony E. Nature Communications. 2022. 13(1):5152. doi: 10.1038/s41467-022-32860-6. |
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37. Human HELB is a processive motor protein which catalyses RPA clearance from single-stranded DNA.
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Hormeno S, Wilkinson O.J., Aicart-Ramos C., Kuppa S., Antony E. , Dillingham M.S., and Moreno-Herrero F. Proc Natl Acad Sci U S A. 2022 12;119(15):e2112376119. doi: 10.1073/pnas.2112376119 |
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38. Graziano S., Coll-Bonfill N., Teodoro-Castro B., Kuppa S., Jackson J., Shaskova E., Mahajan U., Vindigni A., Antony E., and Gonzalo S. A-type lamins are critical for the recruitment of RPA and RAD51 to stalled replication forks to maintain fork stability.
J. Biological Chemistry. 2021. 297(5):101301.www.sciencedirect.com/science/article/pii/S0021925821011078 |
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36. Bednar R.M., Jana S., Kuppa S., Franklin R., Beckman J., Antony E., Cooley R.B., Mehl R.A.. Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells.
ACS Chemical Biology. 2021 https://pubs.acs.org/doi/10.1021/acschembio.1c00649. |
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35. Corless E.I., and Antony E. Methods for heterologous overproduction of Fe-S proteins.
Methods Mol. Biol. 2021.2353:69-78. doi: 10.1007/978-1-0716-1605-5_4. |
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34. Kuppa S., Pokhrel N., Corless E., Origanti S., and Antony E. Generation of fluorescent versions of Saccharomyces cerevisiae RPA to study the conformational dynamics of its ssDNA-binding domains.
Methods Mol. Biol. 2021. doi: 10.1007/978-1-0716-1290-3_9. https://link.springer.com/protocol/10.1007%2F978-1-0716-1290-3_9 |
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33. Dhingra, N., Kuppa, S., Wei, L., Pokhrel, N., Baburyan, S., Meng, X., Antony, E., and Zhao, X. The Srs2 helicase dampens DNA damage checkpoint by recycling RPA from chromatin. Proc Natl Acad Sci U S A. 2021. 119(15):e2112376119. doi: 10.1073/pnas.2020185118
https://www.pnas.org/content/118/8/e2020185118 |
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32. Ahmad, F., Patterson, A., Deveryshetty, J., Mattice, J., Pokhrel, N., Bothner, B., and Antony, E. Hydrogen-deuterium exchange reveals a dynamic DNA binding map of Replication Protein A.
Nucleic Acids Research. 2021. 49(3):1455-1469. doi: 10.1093/nar/gkaa1288. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa1288/6097544 |
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31. Corless, E.I., Imran S.M.S., Watkins, M.B., Bacik, J.P., Mattice J., Patterson A., Danyal, L.C., Soffe, M., Kitelinger, R., Seefeldt L.C., Origanti, S., Bennett, B., Ando, A., and Antony, E. The flexible N-terminus of BchL autoinhibits activity through interaction with its [4Fe-4S] and relieved upon ATP binding.
J. Biol. Chem. 2020. doi: 10.1074/jbc.RA120.016278. LINK. |
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30. Quinn, S.M., Vargason, T., Pokhrel, N., Antony, E., Hahn, J., and Gilbert S.P. KIF3A accelerates KIF3C within the kinesin-2 heterodimer to generate symmetrical phosphate release rates for each processive step.
J. Biol. Chem. 2020. doi: 10.1074/jbc.RA120.015272. LINK.
J. Biol. Chem. 2020. doi: 10.1074/jbc.RA120.015272. LINK.
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29. Corless, E.I., Bennet, B.B., and Antony, E. Substrate recognition induces sequential electron transfer across subunits in the nitrogenase-like DPOR complex. Journal of Biological Chemistry.
J Biol Chem. 2020. 295(39):13630-13639. doi: 10.1074/jbc.RA120.015151. LINK. |
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28. Corless, E. I., Mettert, E. L., Kiley, P. J. and Antony, E. Elevated Expression of a Functional Suf Pathway in the E.coli BL21(DE3) Cell Line Enhances Recombinant Production of an Iron-Sulfur Cluster Containing Protein.
J Bacteriol. 2020. 202(3):e00496-19. doi: 10.1128/JB.00496-19. LINK.
J Bacteriol. 2020. 202(3):e00496-19. doi: 10.1128/JB.00496-19. LINK.
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27. Pokhrel N., Caldwell, C.C., Corless, E.I., Tillison, E.A., Tibbs, J., Jocic, N., Ali Tabei, S.M., Wold, M.S., Spies, M. and Antony E. Dynamics and Selective Remodeling of the DNA Binding Domains of RPA.
Nature Structural & Molecular Biology. 2019. 26, p129–136 (2019). https://www.nature.com/articles/s41594-018-0181-y Featured as cover |
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26. Yates LA, Aramayo RJ, Pokhrel N, Caldwell CC, Kaplan JA, Perera RL, Spies M, Antony E, and Zhang X. A structural and dynamic model for the assembly of Replication Protein A on single stranded DNA.
Nature Communications. 2018. doi: 10.1038/s41467-018-07883-7 |
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25. Venkiteshwaran K., Pokhrel N., Hussein F., Antony E., and Mayer B.K. Phosphate removal and recovery using phosphate binding proteins.
Water Research X. 2018. https://doi.org/10.1016/j.wroa.2018.09.003 |
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24. Mustafa G., Chuang C. , Roy W.A., Farhath M.A., Pokhrel N., Ma Y., Nagasawa K., Antony E., Comstock M.J., Basu S., and Balci H. A Force Sensor that Converts Fluorescence Signal into Force Measurement Utilizing Short Looped DNA.
Biosensors and Bioelectronics. 2018. doi: 10.1016/j.bios.2018.08.073
Biosensors and Bioelectronics. 2018. doi: 10.1016/j.bios.2018.08.073
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23. Seefeldt L., Hoffman B., Peters J., Raugei S., Antony E., and Dean D. Energy Transduction in Nitrogenase.
Accounts of Chemical Research. 2018. doi: 10.1021/acs.accounts.8b00112 |
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22. Singh S.P., Kukshal V., De Bona P., Antony E., and Galletto R. The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers. Nucleic Acids Research. 2018. doi: 10.1093/nar/gky530
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21. Antony E., and Lohman T.M. Dynamics of E. coli single stranded DNA binding (SSB) protein-DNA complexes.
Seminars in Cell and Developmental Biology. 2018. S1084-9521(17)30432-9. DOI: 10.1016/j.semcdb.2018.03.017 |
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20. Pokhrel N., Origanti S., Davenport E.P., Gandhi D., Kaniecki K., Mehl R., Greene E., Dockdendorff C., and Antony E. Monitoring Replication Protein A (RPA) dynamics through site-specific incorporation of non-canonical amino acids.
Nucleic Acids Research. 2017. 45(16):9413-9426. DOI: https://doi.org/10.1093/nar/gkx598 |
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18. Davenport E.P., Harris D.F., Origanti S., and Antony E. Rad51 nucleoprotein filament disassembly captured using fluorescent Plasmodium falciparum SSB as a reporter for single-stranded DNA. PLos One. 2016.
http://dx.doi.org/10.1371/journal.pone.0159242 |
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17. Yang Z.Y., Lebbetter R., Shaw S., Pence N., Tokmina-Lukaszewska M., Eilers B., Guo Q., Pokhrel N., Cash V.L., Dean D.R., Antony E., Bothner B., Peters J.W., and Seefeldt L.C. Evidence that the Pi release event is the rate limiting step in the nitrogenase catalytic cycle. Biochemistry. 2016. 5:55(26):3625-3635.
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16. Burgess J., Jones H.B., Kumar P., Toth R., Middaugh C.R., Antony E.* and Dickenson N.E.*. Spa47 is an oligomerization-activated type three secretion system (T3SS) ATPase from Shigella flexneri. Protein Science. 2016. 25(5):1037-48. (*Co-Corresponding Authors)
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15. Duval S., Danyal K., Shaw S., Dean D.R., Hoffman B.M., Antony E*. and Seefeldt L.C.* Establishing the order of electron transfer and ATP hydrolysis in Nitrogenase . PNAS. 2013. 110:16414-16419 (*Co-Corresponding Authors).
Highlighted in Science USU Press Release |
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14. Lytle, A.K., Origanti, S., Vongermeten, G., and Antony E. Context dependent remodeling of Rad51-DNA complexes by Srs2 is mediated by a specific protein-protein interaction. J. Mol. Biol. 2014. 426:1888-1897.
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Postdoctoral and Graduate Publications
13. Kozlov A.G., Weiland E., Mittal A., Waldman V., Antony E., Fazio N., Pappu R.V. and Lohman T.M. Intrinsically disordered C-terminal tails of E. coli single stranded DNA binding protein regulate cooperative binding to single stranded DNA. J. Mol. Biol. 2015. 427:763-774
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12. Antony E., Weiland, E, Yuan Q., Manhart, C.M., Nguyen B., Kozlov A.K., McHenry S.S., and Lohman T.M. Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair. J. Mol. Biol. 2013.
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11. Yupeng Q., Antony E., Doganay S., Koh H.R., Lohman T.M., and Myong S. Srs2 prevents Rad51 filament formation by repetitive motion on DNA. Nature Communications. 2013. 4:2281
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10. Antony E., Kozlov A.J., Nguyen B., and Lohman T.M. Plasmodium falciparum SSB tetramer binds single-stranded DNA only in a fully wrapped mode. J. Mol. Biol. 2012. 420: 284-295. Featured as cover 9. Antony E., Weiland E.A., Korolev S., and Lohman T.M. Plasmodium falciparum SSB tetramer wraps single-stranded DNA with similar topology but opposite polarity to E. coli SSB. J. Mol. Biol. 2012. 420: 269-283. |
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8. Majka A.M., Maluf K.M., Antony E., and Lohman T.M. Self-assembly of E. coli MutL and its complexes with DNA. Biochemistry. 2011.37:7868-80
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7. Antony E., and Lohman T.M. "Non-hexameric SF1 DNA helicases and translocases". Encyclopedia of Biological Chemistry, (2nd edition) W.J. Lennarz and M.D. Lane, eds. Elsevier Science (2010).
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6. Antony E., Tomko E.J., Xiao Q.*, Krejci L., Lohman T.M., and Ellenberger T.E. Srs2 dismantles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA. Molecular Cell. 2009. 35:105-115. Featured as cover |
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5. Antony E., Khubchandani S., Chen S., and Hingorani M.M. Contribution of Msh2 and Msh6 subunits to the asymmetric ATPase and DNA mismatch binding activities of Saccharomyces cerevisiae Msh2-Msh6 mismatch repair protein. DNA Repair. 2006. 5(2):153-62.
4. Zito C.R. *, Antony E.*, Hunt J.F., Oliver D.B., and Hingorani M.M. Role of a conserved glutamate residue in the Escherichia coli SecA ATPase mechanism. J. Biol. Chem. 2005. 280:14611-14619 (* Co-first authors).
3. Antony E. and Hingorani M.M. Asymmetric ATP binding and hydrolysis activity of the Thermus aquaticus MutS dimer is key to modulation of its interactions with mismatched DNA. Biochemistry. 2004. 43:13115-13128.
2. Antony E. and Hingorani M.M. Mismatch recognition-coupled stabilization of Msh2-Msh6 in an ATP-bound state at the initiation of DNA repair. Biochemistry. 2003. 42:7682-93.
1. Finkelstein J., Antony E., Hingorani M.M., and O'Donnell M. Overproduction and analysis of eukaryotic multiprotein complexes in Escherichia coli using a dual-vector strategy. Anal. Biochem. 2003. 319:78-87.
4. Zito C.R. *, Antony E.*, Hunt J.F., Oliver D.B., and Hingorani M.M. Role of a conserved glutamate residue in the Escherichia coli SecA ATPase mechanism. J. Biol. Chem. 2005. 280:14611-14619 (* Co-first authors).
3. Antony E. and Hingorani M.M. Asymmetric ATP binding and hydrolysis activity of the Thermus aquaticus MutS dimer is key to modulation of its interactions with mismatched DNA. Biochemistry. 2004. 43:13115-13128.
2. Antony E. and Hingorani M.M. Mismatch recognition-coupled stabilization of Msh2-Msh6 in an ATP-bound state at the initiation of DNA repair. Biochemistry. 2003. 42:7682-93.
1. Finkelstein J., Antony E., Hingorani M.M., and O'Donnell M. Overproduction and analysis of eukaryotic multiprotein complexes in Escherichia coli using a dual-vector strategy. Anal. Biochem. 2003. 319:78-87.