Publications

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  1. Zerio, C.J., Sivinski, J., Wijeratne, E.M.K., Xu, Y.M., Ngo, D.T., Ambrose, A.J., Villa-Celis, L., Ghadirian, N., Clarkson, M.W., Zhang, D.D., Horton, N.C, Gunatilaka, A.A.L., Fromme, R., Chapman. E.J. (2023) “Physachenolide C is a Potent, Selective BET Inhibitor” J. Med. Chem. 2023, 66, 1, 913–933. https://doi.org/10.1021/acs.jmedchem.2c01770. doi: 10.1021/acs.jmedchem.2c01770. PMID: 36577036.

  2. Lyumkis, D & Horton, N.C. (2022) "The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI", (2022)Biochem Soc Trans 50 (6): 1703–1714. https://doi.org/10.1042/BST20220547.

  3. Sanchez, J.L., Ghadirian, N., & Horton, N.C. (2022) “Structure of the N-terminal Nuclease and Origin Binding Domain of Human Parvovirus B19 Main Replicative Protein NS1”, J. Virology, PMID: 35435730, DOI: 10.1128/jvi.02164-21.

  4. Shan, Z., Ghadirian, N., Lyumkis, D. and Horton, N. C. (2022) "Pre-Transition State and Apo Structures of the Filament-Forming Enzyme SgrAI Elucidate Mechanisms of Activation and Substrate Specificity", J. Biol. Chem., 298, 10176. (PMID: 35202658. DOI: 10.1016/j.jbc.2022.101760).

  5. Townsend, J., Sanders, H., Rolland, A., Park, C., Horton, N., Prell, J., Wang, J., Marty, M. (2021) "Influenza A M2 Channel Oligomerization is Sensitive to its Chemical Environment", Analytical Chem. 93, 16273-16281, doi: 10.1021/acs.analchem.1c04660, PMID: 34813702.

  6. Park, C. K. & Horton, N.C. (2020) “Novel insights into filament forming enzymes”, Nature Reviews Molecular Cell Biology, 21(1):1-2. doi: 10.1038/s41580-019-0188-1.

  7. Horton, N.C. (2020) “The Filament Forming Mechanism of SgrAI Endonuclease‐Structural and Kinetic Analysis”, The FASEB Journal 34 (S1), 1-1. https://doi.org/10.1096/fasebj.2020.34.s1.04300

  8. Horton, N.C. (2020) “Filament Formation Induces a Shape Change and Activation of the Nuclease SgrAI”, The FASEB Journal 34 (S1), 1-1. https://doi.org/10.1096/fasebj.2020.34.s1.00728

  9. Ghadirian, N., Horton, N. (2020) “Structure‐Function Studies of the Helicase Domain of NS1 Protein of Human Parvovirus B19”, The FASEB Journal 34 (S1), 1-1. https://doi.org/10.1096/fasebj.2020.34.s1.00730

  10. Park, C. K. & Horton, N.C. (2019) “Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation”, Biophysical Reviews, 11(6):927-994. doi: 10.1007/s12551-019-00602-6.

  11. Polley, S., Lyumkis, D., and Horton, N. C. (2019) “Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease”, Structure 27, 1-11.

  12. Barahona, C., Basantes, L. E., Tomkins, K. J., Heitman, D. M., Chukwu, B. I., Sanchez, J., Sanchez, J. L., Ghadirian, N., Park, C. K., and Horton, N. C. (2019) “The Need for Speed: Run-On Oligomer Filament formation provides Maximum Speed with Maximum Sequestration of Activity”, J. Virol, 93 (5), e01647-18. doi: 10.1128/JVI.01647-18. PMID: 30518649.

*Featured on the cover

  1. Xu, P., Ganaie, S., Wang, X., Wang, Z., Kleiboeker, S., Horton, N.C., Heier, R., Meyers, M., Tavis, J., and Qiu, J. (2019) "Endonuclease Activity Inhibition of the NS1 Protein of Parvovirus B19 as a Novel Target for Antiviral Drug Development", Antimicrob Agents Chemother, 63 (3), e01879-18. doi: 10.1128/AAC.01879-18. PMID: 30530599.

  2. Park, C. K. & Horton, N.C. (2019) “Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation”, arXiv: arXiv:1909.13141 [q-bio.BM].

  3. Polley, S., Lyumkis, D., and Horton, N. C. (2019) “Indirect Readout of DNA Controls Filamentation and Activation of a Sequence-Specific Endonuclease”, bioRxiv, DOI: https://doi.org/10.1101/585943.

  4. Horton, N.C., Park, C.K., Barahona, C., Basantes, L.E., & Ghadirian, N. (2019) “Kinetic Advantages of the Run-On Oligomer or Filamentation Mechanism of a DNA Cleaving Enzyme”, FASEB J., 33 (1_supplement), 633.12-633.12.

  5. Park, C. K., Sanchez, J. L., Barahona, C. J., Basantes, L. E., Sanchez, J., Hernandez, C., and Horton, N. C. (2018) “The Run-on Oligomer Filament Enzyme Mechanism of SgrAI. Part 1: Assembly Kinetics of the Run-on Oligomer Filament”, J. Biol. Chem., 293(38):14585-14598.

  6. Park, C. K., Sanchez, J. L., Barahona, C. J., Basantes, L. E., Sanchez, J., Hernandez, C., and Horton, N. C. (2018) “The Run-on Oligomer Filament Enzyme Mechanism of SgrAI. Part 2: Kinetic Modeling of the Full DNA Cleavage Pathway”, J. Biol. Chem., 293(38):14599-14615.

  7. Horton, N., Park, C., Sanchez, J., Barahona, C., & Basantes, L.E. (2018) “Enzyme activity and specificity modulated by protein filamentation”, Prot. Sci., 27, 117-11.

  8. Hernandez, C.J., Sanchez, J.L. & Horton, N.C. (2017) “Investigating the role of the human parvovirus B19’s main viral protein, NS1, in viral replication and interactions with host DNA,” (2017) FASEB J. 31, 912.16-912.16

  9. Sanchez , J.L., Romero, Z., Quinones, A., Torgeson, K.R. & Horton, N.C. (2016) “DNA Binding and Cleavage by Human Parvovirus B19 NS1 Nuclease Domain”, Biochemistry, 55, 6577-6593. PMID: 27809499.

  10. Shah, S., Sanchez, J., Stewart, A., Piperakis, M.A., Cosstick, R., Nichols, C., Park, C.P., Ma, X., Wysocki, V., Bitinaite, J. & Horton, N.C. (2015) “Probing the Run-on Oligomer of Activated SgrAI bound to DNA”, PLoS One, Apr 16;10(4):e0124783.

  11. Shah, S, Dunten, P., Stiteler, A., Park, C.K. & Horton, N.C. (2015) “Structure and Specificity of FEN-1 from Methanopyrus kandleri”, Proteins, 83, 188-194.

  12. Lyumkis, D., Talley, H., Stewart, A., Shah, S., Park, C.K., Tama, F., Potter, C.S., Carragher, B., Horton, N.C. (2013) “Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization”, Structure, 21, 1848-1858.

  13. Ma, X., Shah, S., Zhou, M., Park, C.K., Wysocki, V.H., Horton, N.C. (2013) “Structural Analysis of Activated SgrAI-DNA Oligomers Using Ion Mobility Mass Spectrometry”, Biochemistry, 52, 4373-81.

  14. Horton, N.C., Park, C.K., Stewart, A.M., Shah, S., Talley, H., Ma, X., Wysocki, V., Piperakis, M., Cosstick, R. & Jacovetty, E. (2012) “Activation by oligomerization of an allosteric sequence specific endonuclease,” FASEB J. 26, ib91-ib91.

  15. Little, E.J., Dunten, P.W., Bitinaite, J. & Horton, N.C. (2011) “New Clues in the Allosteric Activation of DNA Cleavage by SgrAI; Structures of SgrAI Bound to Cleaved Primary Site DNA and Uncleaved Secondary Site DNA”, Acta Cryst., 67, 67-74.

  16. Techner, J.-M. & Horton, N.C. (2011) “Small molecule modulation of zinc-finger sequence specificity,” FASEB J. 25, 688.6-688.6.

  17. Park, C.K., Stiteler, A.P., Shah, S., Ghare, M.I., Bitinaite, J. & Horton, N.C. (2010) “Activation of DNA Cleavage by Oligomerization of DNA bound SgrAI”, Biochemistry, 49, 8818-8830.

  18. Park, C.K., Joshi, H.K., Agrawal, A., Ghare, M.I., Little, E.J., Dunten, P.W., Bitinaite, J. & Horton, N.C. (2010) “Domain Swapping in Allosteric Modulation of DNA Specificity”, PLoS Biology, 8(12):e1000554.

  19. Horton, N.C. & Park, C.K., (2010) “Crystallization of Zinc Finger Proteins bound to DNA”, Methods Mol Biol. 649:457-77.

  20. Dunten, P.W., Little, E.J. & Horton, N.C. (2009), “The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.”, Acta Cryst. D65, 393-8.

  21. Little, E.J., Babic, A.C., & Horton, N.C. (2008) “Early interrogation and recognition of DNA sequence by indirect readout”, Structure 16, 1828-37. (Given F1000 “must read”)

  22. Babic, A.C., Little, E.J., Manohar, V.M., Bitinaite, J., & Horton, N.C. (2008) “DNA distortion and specificity in a sequence-specific endonuclease” J. Mol. Biol. 383, 186-204.

  23. Dunten, P.W., Little, E.J., Gregory, M.T., Manohar, V.M., Dalton, M., Hough, D., Bitinaite, J., Horton, N.C. (2008) “The structure of SgrAI bound to DNA; recognition of an 8 base pair target”, Nucleic Acids Res. 36, 5405-16.

  24. Horton, N.C. (2008) “Deoxyribonucleases”. In Protein-Nucleic Acid Interactions: Structural Biology; Carl C. Correll, Pheobe Rice, Eds.; RSC Publishing: Cambridge, United Kingdom, 2008.

  25. Segal, D.J., Crotty, J., Bhakta, M., Barbas III, C.F. & Horton, N.C. (2006) "Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA", J. Mol. Biol. 363, 405-421.

  26. Joshi, H.K., Etzkorn, C., Chatwell, L., Bitinaite, J., & Horton, N.C. (2006) "Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism." J. Biol. Chem. 281, 23852-69.

  27. Little, E.J. & Horton, N.C. (2005) "DNA induced conformational changes in type II endonucleases; the structure of unliganded HincII" J. Mol. Biol. 351, 76-88.

*Featured on the cover.

  1. Crotty, J.W., Etzkorn, C., Barbas, III, C.F., Segal, D.J. & Horton, N.C. (2005) "Crystallization and preliminary X-ray crystallographic analysis of Aart, a designed six-finger zinc-finger peptide, bound to DNA" Acta. Cryst. F61, 573-576.

  2. Etzkorn, C. & Horton, N.C. (2004) "Ca2+ Binding in the active site of HincII: Implications for the catalytic mechanism", Biochemistry 43, 13256-70.

  3. Etzkorn, C. & Horton, N.C. (2004) Mechanistic insights from the structure of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+. J. Mol. Biol. 343, 833-49.

  4. Horton, N.C., & Perona, J.J. (2004) "DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites", Biochemistry 43, 6841-57.

  5. Horton, N.C., Otey, C., Lusetti, S., Sam, M. D., Kohn, J., Martin, A. M., Ananthnarayan, V., & Perona, J.J. (2002) "Electrostatic Contributions to Site Specific DNA Cleavage by EcoRV Endonuclease", Biochemistry 41, 10754-10763.

  6. Horton, N.C., Dorner, L.F., & Perona, J.J. (2002) "Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation", Nature Struct. Biology 9, 42-47.

  7. Horton, N.C., & Perona, J.J. (2001) "Making the most of metal ions", Nature Struct. Biology, 8, 290-293.

  8. Sam, M.D., Horton, N.C., Nissan, T.A. & Perona, J.J. (2001) "Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site", J. Mol. Biol. 306, 851-861.

  9. Horton, N.C., Connolly, B.A. & Perona, J.J. (2000) "Mechanism of inhibition of phosphoryl transfer in EcoRV by 3’S phosphorothiolates", JACS 122, 3314-3324.

  10. Horton, N.C. & Perona, J.J. (2000) "Crystallographic snapshots along a protein-induced DNA bending pathway", Proc. Natl. Acad. Sci, USA 97, 5729-5734.

  11. Perona, J.J., Horton, N.C., Connolly, B.A. & Sam, M.D. (2000) “Catalytic mechanism of EcoRV endonuclease derived from crystal structures and transient kinetics,” Trans. Amer. Cryst. Assoc. 35, 9-

  12. Horton, N.C., Dorner, L.F., Schildkraut, I. & Perona, J.J. (1999) “Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease –DNA complex”, Acta Cryst. D. 55, 1-3.

  13. Martin, A.M., Horton, N.C., Lusetti, S., Reich, N.O., & Perona, J.J. (1999) “Divalent metal dependence of site-specific DNA binding in EcoRV endonuclease”, Biochemistry 38, 8430-8439.

  14. Horton, N.C., Newberry, K.J. & Perona, J.J. (1998) “Metal ion mediated substrate-assisted catalysis in type II restriction endonucleases”, Proc. Natl. Acad. Sci., USA 95, 13489-13494.

  15. Horton, N.C. & Perona, J.J. (1998) “Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts”, J. Biol. Chem. 273, 21721-21729.

  16. Horton, N.C. & Perona, J.J. (1998) “Role of protein-induced bending in the specificity of DNA recognition: Crystal structure of EcoRV endonuclease complexed with d(AAAGAT)+d(ATCTT)”, J. Mol. Biol. 277, 779-787.

  17. Baldwin, E.T., Sarver, R.W., Bryant, G.L.,Jr., Curry, K.A., Fairbanks, M.B., Finzel, B.C., Garlick, R.L., Heinrikson, R.L., Horton, N.C., Kelley, L.C., Mildner, A.M., Moon, J.B., Mott, J.E., Mutchler, V.T., Tomich, C.C., Watenpaugh, K.D., & Wiley, V.H. (1998) “Cation binding to the integrin CD11b I domain and activation model assessment”, Structure 6, 923-935.

  18. Horton, N.C., Lewis, M. & Lu, P. (1997) “Escherichia coli lac repressor-lac operator interaction and the influence of allosteric effectors”, J Mol. Biol. 265, 1-7.

  19. Horton, N.C. & Finzel, B.C. (1996) “The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase”, J. Mol. Biol. 264, 521-533.

  20. Kercher, M.A., Chang, G., Horton, N.C., Lu, P., Miller, J.H., Pace, H.C. & Lewis, M. (1996) “Structure of the E. coli lactose operon repressor and its complexes with DNA and inducer,” Biophys. J. 70, TUAM5-TUAM5.

  21. Kercher, M.A., Chang, G., Horton, N.C., Lu, P., Miller, J.H., Pace, H.C. & Lewis, M. (1996) “Structure and genetics of the lactose operon repressor,” FASEB J. 10, 6-6.

  22. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.G., & Lu, P. (1996) “Crystal structure of the lactose operon repressor and its complexes with DNA and inducer”, Science 271, 1201-1332.

          1. *Featured on the cover.

  23. Horton, N. & Lewis, M. (1992) “Calculation of the free energy of association for protein complexes”, Protein Science 1, 169-181.


Structural Coordinates Contributed:


RCSB PDB submissions (52 total): 7S3P, 7SS5, 7S8D, 6OBJ, 4WA8, 4C3G, 3MQY, 3N78, 3NY8, 3MQ6, 3DPG, 3DVO, 3DW9, 3E3Y, 3E40, 3E41, 3E42, 3E43, 3E44, 3E45, 3EBC, 2AUD, 2GIG, 2GIH, 2GII, 2GIJ, 1XHU, 1TX3, 2I13, 1KC6, 1TW8, 1XHV, 2GIE, 1STX, 1SUZ, 1SX5, 1SX8, 1EO3, 1EO4, 1EON, 1EOO, 1EOP, 1RV5, 1BHO, 1BHQ, 1IDN, 1BGB, 1BSS, 1FIX, 1LBH, 1LBI, 1LBG


EMDB: EMD-20015, EMD-2441, EMD-25404


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