Publications

2021 – Current

• Interaction of West Nile virus NS5 with orthoflavivirus SLA RNAs and their effects on viral replication and inhibition. Feinberg M., Le M.T, Carpio, K, Knyazhanskaya K, Barrett A. Choi KH (2025) Journal of Virology. 2025 Aug 18:e0202324.
• Highlighted as an Editor’s Pick
• https://doi.org/10.1128/jvi.02023-24

• The structure of coxsackievirus cloverleaf RNA and 3C^pro dimer establishes the RNA-binding mechanism of enterovirus protease 3C^pro. Dias-SolangeD, Le M.T, GottipatiK, ChoiKH (2025) Science Advances, 11(11), eads6862
• Highlighted in Advanced Light Source (ALS) Science Brief (https://als.lbl.gov/researchers-identify-viral-swiss-army-knife-clarifying-how-replication-occurs/)
• https://www.science.org/doi/10.1126/sciadv.ads6862

• Phi29 Assembly Intermediates Reveal How Scaffold Interactions with Capsid Protein Drive Capsid Construction and Maturation. Woodson M, Prokhorov N, Scott S, Zhao W, Zhang W, Choi KH, Jardine P, Morais MC (2025) Science Advances, 1(12), eadk8779
• https://www.science.org/doi/10.1126/sciadv.adk8779

• Dual conformational states of HIV-1 RRE stem-loop II: Implications for the initial high-affinity Rev interaction. Tipo J, Gottipati K, Slaton M, Gonzalez-Gutierrez G, Choi KH (2024) Nature communications. 15(1):4198
• https://www.nature.com/articles/s41467-024-48162-y

• High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. Tipo J, GottipatiK, and Choi KH (2024) RNA 30 (6):609-623
• https://rnajournal.cshlp.org/content/30/6/609.long

• Binding of MicroRNA-122 to the Hepatitis C Virus 5’ Untranslated Region Modifies Interactions with Poly(C) Binding Protein 2 and NS5B Viral Polymerase. ScottS, You Li Y, BermekO, GriffithJD, LemonSM, and ChoiKH (2023) Nucleic Acid Research. 51(22):12397-12413.
• https://academic.oup.com/nar/article/51/22/12397/7370024?login=true

• Structural basis for cloverleaf RNA-initiated genome replication. Gottipati K, McNeme SC, Tipo J, White MA, and ChoiKH (2023). Nucleic Acid Research. 51(16), 8850-8863.
• https://academic.oup.com/nar/article/51/16/8850/7230094?login=true

• Flavivirus proteases: The viral Achilles heel to prevent future pandemics. Teramoto T, Choi KH*, Padmanabhan R*. (2023) Antiviral Res. 210, 105516
• https://www.sciencedirect.com/science/article/abs/pii/S0166354222002856?via%3Dihub

• The role of the stem-loop A RNA promoter in flavivirus replication. Choi KH (2021) Viruses 13(6), 1107
• https://www.mdpi.com/1999-4915/13/6/1107

• Flaviviral enzymes and their inhibitors. Knyazhanskaya E, MoraisMC, Choi  (2021) Enzymes 49, 265-303. 
• https://pmc.ncbi.nlm.nih.gov/articles/PMC8717743/

• Structure of flavivirus RNA promoters suggest two binding modes with NS5 polymerase. Lee E, Bujalowski PJ, Teramoto T, Gottipati K, Scott SD, Padmanabhan R, Choi KH (2021) Nat Commun 12, 2530
• https://www.nature.com/articles/s41467-021-22846-1

2016 - 2020

• Identification of the viral RNA promoter stem loop A (SLA)-binding site on Zika virus polymerase NS5. Bujalowski PJ, Bujalowski W, and Choi KH (2020) Scientific Reports 10:13306
• https://www.nature.com/articles/s41598-020-70094-y

• Biochemical and biophysical characterization of the dsDNA packaging motor from the Lactococcus lactis bacteriophage Asccphi28. Reyes-Aldretes E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC (2020) Viruses, 13,15 
• https://pubmed.ncbi.nlm.nih.gov/33374840/

• A cocrystal structure of dengue capsid protein in complex of inhibitor. Xia H, Xie X, Zou J, Nobel CG, Russell W, Holthauzen LM, Choi KH, White MA, Shi P-Y (2020) Proc Natl Acad Sci U S A. 117 (30) 17992-18001
• https://www.pnas.org/doi/10.1073/pnas.2003056117

• Membrane Binding of Chikungunya Virus Capping Enzyme nsP1, Gottipati K, Woodson M, and Choi KH (2020) Virology 544:31-41
• https://pubmed.ncbi.nlm.nih.gov/32174512/

• NMR structure of a vestigial nuclease provides insight into functional transitions in viral dsDNA packaging motors. Mahler BP, Bujalowski PJ, Mao H,Dill EA,Choi KH, and Morais MC (2020) Nucleic Acids 48, 11737-11749
• https://pubmed.ncbi.nlm.nih.gov/33089330/

• Ehrlichia chaffeensis TRP120 nucleomodulin binds DNA with disordered tandem repeat domain. Klema VJ, Sepuru KM, Fullbrunn N, Farris TR, Dunphy PS, McBride JW, Rajarathnam K, Choi KH. (2018) PlosOne 13(4): e0194891
• https://pubmed.ncbi.nlm.nih.gov/29641592/

• Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells. Zhou W, Woodson M, Neupane B, Bai F, Sherman MB, Choi KH, Neelakanta G, Sutana H (2018) PLoS Pathogens 14(1): e1006764.
• https://pubmed.ncbi.nlm.nih.gov/29300779/
• Interactions between the dengue virus polymerase NS5 and stem loop A (SLA). Bujalowski PJ, Bujalowski W, Choi KH (2017) Virol. 91 (11): e00047-17.
• https://pmc.ncbi.nlm.nih.gov/articles/PMC5432874/

• Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication. Teramoto T, Balasubramanian A, Choi KH, Padmanabhan R (2017) J Biol Chem. 292 (23):9465-9479.
• https://pmc.ncbi.nlm.nih.gov/articles/PMC5465476/

• Pestivirus Npro directly interacts with interferon regulatory factor 3 (IRF3) monomer and dimer. Gottipati K, Holthauzen LM, Ruggli N, Choi KH (2016) Virol. 90 (17):7740-7.
• https://pmc.ncbi.nlm.nih.gov/articles/PMC4988160/

• Dengue virus nonstructural protein 5 (NS5) assembles into a dimer with a unique methyltransferase and polymerase interface. KlemaV, YeM, HindupurA, Teramoto T, Gottipati K, Padmanabhan R and Choi KH (2016)  PLOS Pathogens 12(2):e1005451.
• https://pubmed.ncbi.nlm.nih.gov/26895240/

• Allosteric inhibitors of Coxsackie virus A24 RNA polymerase. Schein CH, Rowold D, Choi KH (2016) Bioorganic and Medicinal Chemistry, 24 (4), 570-7.
• https://pubmed.ncbi.nlm.nih.gov/26762834/

2010 - 2015

• Flavivirus RNA synthesis in vitro. Padmanabhan R, Takhampunya R, Teramoto T, Choi KH (2015) Methods, S1046-2023(15):30040-2. PMID: 26272247

• Flaviviral Replication Complex: Coordination between RNA Synthesis and 5′-RNA Capping. Klema VJ, Padmanabhan R, Choi KH (2015) Viruses 7 (8):4640-4656. PMID: 26287232

• Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses. Schein CH, Ye M, Paul AV, Oberste MS, Chapman N, van der Heden van Noort GJ, Filippov DV, Choi KH (2015) Virology. 484:80-85. PMID: 26074065

• Substitution of NS5 N-terminal domain of dengue virus type 2 RNA with type 4 domain caused replication and emergence of adaptive mutants with enhanced fitness. Teramoto T, Boonyasuppayakorn S, Handley M,Choi KH, Padmanabhan R. (2014) J Biol Chem. 289(32):22385-400.  PMID: 24904061

• Autocatalytic activity and substrate specificity of the pestivirus N-terminal protease N^pro. Gottipati K, Acholi S, Ruggli N, and Choi KH (2014) Virology 452-453:303-9. PMID: 24606708

• Small angle X-ray scattering and its application to Dengue viral proteins (2014). Choi, KH* and Morais MC.  Dengue (Springer. Padmanabhan RP ed). *Corresponding author

• The structure of classical swine fever virus N^pro: A novel cysteine protease and zinc-binding protein involved in subversion of type I interferon induction. Gottipati K, Ruggli N, Markus Gerber, Jon-Duri Tratschin, Matthew Benning, Henry Bellamy, and Choi KH (2013) PLOS Pathogens Oct;9(10):e1003704. PMID: 24146623

• Dengue virus nonstructural protein 5 adopts multiple conformations in solution. Bussetta C and Choi KH (2012) Biochemistry 51(30):5921-31. PMCID: PMC3448003.

• Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals. Schein, C.H., Bowen, D.M., Lewis, J.A., Choi, KH, Paul, A., van der Heden van Noort, G.J., Lu, W. and Filippov, D.V. (2012) BMC Bioinformatics 13, S9. PMCID:PMC3426803. 

• Viral polymerases (2012). Choi, KH. Viral Molecular Machines (Rossmann MG and V Rao ed), Springer

• Full-length dengue virus RNA-dependent RNA polymerase –RNA/DNA complexes. Stoichiometries, intrinsic affinities, cooperativities, base, and conformational specificities. Szymanski MR, Jezewska MJ, Bujalowski PJ, Bussetta C, Ye M, Choi KH, and Bujalowski W (2011) Biol. Chem. 286(38):33095-108.  PMCID: PMC3190876.                                                      

2007 -2010

• High-throughput crystallography (2010). Choi, KH. International tables for crystallography vol. F: Crystallography of biological macromolecules. (Rossmann MG and Arnold E. ed), published for International Union of Crystallography. Kluwer academic publishers, Dordrecht/Boston/London

• RNA-dependent RNA polymerases from Flaviviridae. Choi KH* and Rossmann MG (2009) Curr. Opin. Struct .Biol. 19(6):746-51. *corresponding author.

• Zinc-binding in pestivirus Npro is required for interferon regulatory factor 3 (IRF3) interaction and degradation. Szymanski MR, Fiebach AR, Tratschin J-D, Gut M, Ramanujam VMS, Patel P, Ye M, Keerthi Gottipati, Ruggli N, Choi KH. (2009) Mol. Biol. 391: 438-49.
• Classical swine fever virus can remain virulent after specific elimination of the interferon regulatory factor 3 degrading function of Npro. Ruggli N, Summerfield A. Fiebach AR, Guzylack L, Bauhofer O, Lamm CG, Waltersperger S, Matsuno K, Liu L, Gerber M, Choi KH, Hofmann MA, Sakoda Y, Tratschin JD.  (2009) Virol.  83(2):817-29.                                              
• Insight into DNA and protein transport in double-stranded DNA viruses: The structure of bacteriophage N4. Choi KH, McPartland J, Kaganman I, Bowman VD, Rothman-Denes LB, Rossmann MG (2008) Mol. Biol. 378(3): 726-36.