Research Papers



Ni P, Cheng Kao C. Non-encapsidation activities of the capsid proteins of positive-strand RNA viruses. Virology.2013.Nov;446(1-2):123-32. doi: 10.1016/j.virol.2013.07.023. Epub 2013 Aug 27. PMID:24074574

Park IW, Ndjomou J, Wen Y, Liu Z, Ridgway ND, Kao CC, He JJ.Inhibition of HCV Replication by Oxysterol-Binding Protein-Related Protein 4 (ORP4) through Interaction with HCV NS5B and Alteration of Lipid Droplet Formation. PLoS One. 2013 Sep 17;8(9):e75648. PMID:24069433

Ni P, Vaughan RC, Tragesser B, Hoover H, Kao CC. The Plant Host Can Affect the Encapsidation of Brome Mosaic Virus (BMV) RNA: BMV Virions Are Surprisingly Heterogeneous. J Mol Biol. 2013 Sep 13. PMID: 2403642

Leen EN, Kwok KY, Birtley JR, Simpson PJ, Subba-Reddy CV, Chaudhry Y, Sosnovtsev SV, Green KY, Prater SN, Tong M, Young JC, Chung LM, Marchant J, Roberts LO, Kao CC, Matthews S, Goodfellow IG, Curry S.Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins. J Virol. 2013 May;87(10):5318-30. Epub 2013 Mar 13. PMID:23487472

Singh D, Qi R, Jordan JL, San Mateo L, Kao CC. The human antimicrobial peptide LL-37, but not the mouse ortholog, mCRAMP, can stimulate signaling by poly(I:C) through a FPRL1-dependent pathway. J Biol Chem. 2013 Mar 22;288(12):8258-68. Epub 2013 Feb 5. PMID:23386607



Vaughan R., W. Running, R. Qi, and C. C. Kao. 2012. Rapid mapping of protein RNA interaction. Virus Adaptations and Treatments. 2012:4 1–13.

Qi R, Singh D, Kao CC. Proteolytic processing regulates Toll-like receptor 3 stability and endosomal localization.J Biol Chem. 2012 Sep 21;287(39):32617-29. Epub 2012 Aug 3.PMID:22865861

Shu C., G. Yi, T. Watts, C. C. Kao, and P. Li. Structure of STING bound to c-di-GMP reveals the mechanism of cyclic dinucleotide recognition by the immune system. Nat. Struct. Mol. Biol. Doi:10.1038/nsmb.2331

Vaughan R, B. Fan, J.-S. You, and C. C. 2012. Identification and functional characterization of the nascent RNA channel of the hepatitis C virus RNA-dependent RNA polymerase. RNA (In press).

Running, W., N. Peng, C. Kao, and J. Reilly. 2012. Mapping the pH-dependent conformational changes in the brome mosaic virus virions. J. Mol. Biol. (In press).

Subba-Reddy Ch. V., Muhammad Amir Yunus, Ian G. Goodfellow, and C. Cheng Kao. 2012. Norovirus RNA synthesis is modulated by an interaction between the Viral RNA-dependent RNA polymerase and the major capsid protein, VP1. J. Virol. (In press).

Vaughan, R., Y, Li, B. Fan, C.T. Ranjith-Kumar and C. C. Kao. 2012. RNAs can modulate the Hepatitis C Virus NS3 protease and ATPase Activities. Virus Res. (in press).

Ni P., Wang Z., Ma X., N. Das, P. J. Sokol, Chiu W., Dragnea B., M. Hagan and C. Cheng Kao. 2012. An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus capsid protein and RNA packaging. J, Mol. Biol. doi:10.1016/j.jmb.2012.03.023

Bhardwaj, K. P. Liu, J. L. Leibowitz, and C. C. Kao. 2012. SARS viral Nsp15 interacts with the retinoblastoma tumor suppressor protein. J. Virol. 86: 4294-4304. doi:10.1128/JVI.07012-11.

Subba-Reddy Ch. V., B. Tragesser, Z. Xu. B. Stein, Ranjith-Kumar CT, and C. C. Kao. 2012. Brome mosaic virus 1a protein modulates 2a polymerase activity in human cells. J. Virol. 86: 4317-4327; doi:10.1128/JVI.00069-12.

Tsevtkova I, C. Chen C., S. Rana, C. Cheng Kao, V. M. Rotello, and B. Dragnea. 2012. Pathway switching in templated virus-like particle assembly. Soft Matter. DOI: 10.1039/c2sm00024e.



Guanghui Yi, Jerome Deval, Baochang Fan, Hui Cai, Charlotte Soulard, C. T. Ranjith-Kumar, David B. Smith, Lawrence Blatt, Leonid Beigelman, and C. Cheng Kao. Comparative Inhibition of the Hepatitis C Virus RNA Polymerase by VX-222 and Filibuvir – a Biochemical Study. AAC 2011

Subba-Reddy CV, Goodfellow I, Kao CC. VPg-Primed RNA Synthesis by Norovirus RNA-Dependent RNA Polymerases Using a Novel Cell-based Assay. J Virol. 2011 Oct 12.

Lai Y, Adhikarakunnathu S, Bhardwaj K, Ranjith-Kumar CT, Wen Y, Jordan JL, Wu LH, Dragnea B, Mateo LS, Kao CC. LL37 and Cationic Peptides Enhance TLR3 Signaling by Viral Double-stranded RNAs. PLoS One 2011;6(10):e26632. Epub 2011 Oct 21.

C. T. Ranjith-Kumar, Yahong Wen, Nielson Baxter, Kanchan Bhardwaj, C. Cheng Kao. A Cell-Based Assay for RNA Synthesis by the HCV Polymerase Reveals New Insights on Mechanism of Polymerase Inhibitors and Modulation by NS5A. PLoS One 2011.

Yvonne Lai, Guanghui Yi, Alice Chen, Kanchan Bhardwaj, Brady J. Tragesser, Rodrigo A. Valverde, Adam Zlotnick, Suchetana Mukhopadhyay, C. T. Ranjith-Kumar, and C. Cheng Kao. Viral Double-strand RNA-binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3. PLoS One 2011.

Goicochea, N. L., S. A. K. Datta, A. Rein, M. Ayaluru, C. C. Kao, Bogdan Dragnea. 2011. Structural properties of template-directed recombinant HIV-1 GAG particles.

Huang, X., Stein, B., Cheng, H., Malyutin, A., Tsvetkova, I., Baxter, D., Remmes, N., Verchot, J., Kao, C., Bronstein, L., and Dragnea, Bogdan. 2011. Magnetic virus-like nanoparticles in N. benthamiana plants – a new paradigm for environmental and agronomic biotechnological research. ACS Nano. In press.

Qi X., T. Droste, and C. C. Kao. 2011. Cell-penetrating peptides derived from viral capsid Proteins. Molec. Plant-Microbe Interact. 24:25-36.



Ranjith-Kumar C. T., Y. Y. Lai, R. T. Sarisky, and C. C. Kao. 2010 Green tea catechin, epigallocatechin gallate, suppresses signaling by the dsRNA innate immune receptor RIG-I. PLoS One 5(9): e12878. doi:10.1371/journal.pone.0012878.

Lu C., C.T. Ranjith-Kumar, L. Hao, C. C. Kao, and P. Li. 2010. Crystal structure of human RIG-I C-terminal domain bound to a blunt-ended double-stranded RNA. NAR 2010, 1-11.

Hwang J., L. Huang, D. G. Cordek, R. Vaughan, S. L. Reynolds, G. Kihara, K. D. Raney, C. Cheng Kao, and C. E. Cameron. 2010. Hepatitis C virus nonstructural protein 5A (NS5A): biochemical characterization of a novel structural class of RNA-binding proteins. J. Virol. 84:12480-12491.

Qi, R. S. Hoose, J. Schreiter, K. V. Sawant, R. Lamb, C.T. Ranjith-Kumar, J. Mills, L. San Mateo, J. L. Jordan, and C. C. Kao. 2010. Secretion of the human Toll-like Receptor 3 ectodomain is affected by single nucleotide polymorphisms and regulated by UNC93B. J. Biol. Chem. 285:36635-36645.

Qi X., T. Droste, and C. C. Kao. 2010. Cell-penetrating peptides derived from viral capsid Proteins. Molec. Plant-Microbe Interact. 24:25-36.

Ortiz-Alcantara, J. K. Bhardwaj, S. Palaninathan, M. Frieman, R. S. Baric, C. C. Kao. 2010. Small molecule inhibitors of the SARS-CoV nsp15 endoribonuclease. Virus Adaptation and Treatment. Virus Adaptation and Treatment 2010:125-133.

Lu C., H. Xu, C.T. Ranjith-Kumar, M. T. Brooks, T. Y. Hu, A. B. Herr, R. K. Strong, C. Cheng Kao, and P. Li. 2010. The structural basis of 5' triphosphate double-stranded RNA recognition by the RIG-I C-terminal domain. Structure 18, 1-12.

Daniel M.-C., I. Tsvetkova, Z. Quinkert, A. Murali, M. De, V. L. Rotello, C. C. Kao, and B. Dragnea. 2010. Critcal surface charge density is required for nanoparticle-templated assembly by bromovirus protein cages. ACS-Nano 4. 3853-3860.

Hema, M., A. Murali, K. Fujisaki, I. Tsvetkova, P. Ni, R. C. Vaughan, B. Dragnea, and C. Cheng Kao. 2010. A single amino acid substitution in the brome mosaic virus capsid protein resulted in biased RNA packaging. Molec. Plant Microb. Interact. 23:1433-1447.

Chinnaswamy, S., H. Cai, and C. C. Kao. 2010. An Update on Small Molecule Inhibitors of the HCV NS5B Polymerase: Effects on RNA Synthesis in vitro and in Cultured Cells, and Potential Resistance in Viral Quasispecies. Virus Treatments and Adaptations 2:73-89.

Chinnaswamy, S., A. Murali, H. Cai, G. Yi, S. Palaninathan, and C. C. Kao. 2010. Conformations of the Monomeric Hepatitis C Virus RNA-dependent RNA Polymerase. Virus Treatments and Adaptation 2010: 21-39.

Chinnaswamy, S., A. Murali, P. Li, and C. C. Kao. 2010. Regulation of de novo initiated RNA synthesis in the Hepatitis C virus RNA-Dependent RNA polymerase by intermolecular interactions. J. Virol. 84: 5923-5935.



Motshwene, P.G., Moncrieffe, M. C., Grossman, J.G., Kao, C. C., Ayaluru, M., Sandercock, A. M., Robinson, C. V., Latz, E., and N. J. Gay. 2009. An oligomeric platform formed by the Toll-like receptor signal transducers MyD88 and IRAK4. J. Biol. Chem. 284: 25404-25411.

Liu, Z., Robida, J. M., Chinnaswamy, S., Yi, G., Robotham, J. M., Nelson, H. B., Irsigler, A., Kao, C.C., and H. Tang. 2009. Mutations in the Hepatitis C virus polymerase that increase RNA binding can confer resistance to Cyclosporine A. Hepatology 50:25-33.

McGivern, D. R., R. A. Villanueva, S. Chinnaswamy, C. Cheng Kao, S. M. Lemon. 2009. Impaired replication of hepatitis C virus containing mutations in a conserved NS5B retinoblastoma protein-binding motif. J. Virol. 83:7422-7433.

Yi, G., R. C. Vaughan, I. Yarbrough, S. Dharmaian, and C. C. Kao. 2009. RNA binding by the brome mosaic virus capsid protein and the regulation of viral RNA accumulation. J. Mol. Biol. 391:314-326.

Li, X., C. T. Ranjith-Kumar, M. T. Brooks, A. B. Herr, S. Dharmaian, C. C. Kao, and Pingwei Li. 2009. The RIG-I-like receptor LGP2 recognizes the termini of double-stranded RNA. J. Biol. Chem. 284:13881-13891.

Yi, G. H., E. Letteney, C.-H. Kim, and C. C. Kao. 2009. Brome Mosaic Virus capsid protein regulates translation of viral replication proteins by binding to the replicase assembly RNA element. RNA 15:6150-626.

Aniagyei, S.E., C. Kennedy, D. Srisathiyanarayanan, A. Murali. B. Stein, D. A. Willits, T. D. Douglas, M. J. Young, D. Mrinmoy, V. B. Rotello, C. C. Kao, and B. Dragnea. 2009. Synergistic effects of mutations and nanoparticle templating in the self-assemby of Cowpea Chlorotic Mottle Virus. Nano Lett. 9:393-398.

Ranjith-Kumar, C.T., A. Murali, W. Dong, D. Srisathiyanarayanan, R. Vaughan, J. Ortiz-Alacantara, K. Bhardwaj, X. Li., P. Li, and C. C. Kao. 2009. Agonists and antagonists recognition by RIG-I, a cytoplasmic innate immunity receptor. J. Biol. Chem. 284:1155-1165.



Aniagyei, S.E., DuFort C., Kao, C., and Dragnea, B. 2008. Self-assembly approaches to nanomaterial encapsulation in viral protein cages. J. Mater. Chem. 18:3763-3744.

Chinnaswamy S., I. Yarbrough, S. Palaninathan, C. T. Ranjith Kumar, V. Vijayaraghavan, B. Demeler, S.M. Lemon, J. C. Sacchettini, and C. C. Kao. 2008. A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase. J. Biol. Chem. 283:20535-20546.

Cited in Chimera for modeling:

Murali, A., X. Li, C.T. Ranjith-Kumar, K. Bhardwaj, A. Holzenburg, P. Li, and C. Kao. 2008. Structure and function of LGP2, a DExD/H helicase that regulates the innate immunity response. J. Biol. Chem. 283:15825-15833.

Ranjith-Kumar, C.T. K.E. Duffy, J.L. Jordan, A. Eaton-Bassiri, R.T. Sarisky, and C. Kao. 2008. Single-stranded deoxyoligonucleotides are potent inhibitors of cytokine production induced by the human Toll-Like Receptor 3. Mol. Cell. Biol 112:9405-9412.

Gangloff, M., A. Murali, J. Xiong, C. J. Arnot, A.N. Weber, A. M. Sandercock, C.V. Robinson, R. T. Sarisky, A. Holzenburg, C. Kao*. N. J. Gay* (Co-corresponding authors). 2008. An indirect alosteric mechanism for activation of the Toll receptor by the dimeric ligand Spatzle. J. Biol. Chem. 283:14629-14635.

Yi, G. and C. Kao. 2008. Cis- and trans-acting functions of brome mosaic virus protein 1a in genomic RNA1 replication. J. Virol. 82:3045-3053.

Bhardwaj, K., S. Palaninathan, L. Yi. J. Ortiz-Alcantara, L. Guarino, J. Sacchettini, and C. Kao. 2008. Structure, function, and substrate specificity for the SARS-CoV Nsp15 endoribonuclease. J. Biol. Chem. 283:3655-3664.



Yi, G., and C. Kao. 2007. Replication and transcription of Brome Mosaic Virus. In "Viral Genome Replication. Eds: M. Götte, K, Raney and C. Cameron. Springer Press.

Huang, X., L.M. Bronstein, J. Retrum, C. Dufort, I. Tsvetkova, S. Aniagyei, B. Stein, G. Stucky, B. McKenna, N. Remmes, D. Baxter, C. C. Kao, B. Dragnea. 2007. Self-assembled virus-like particles with magnetic cores. Nano Lett. 7:2407-2416.

Kang, H. K. Bhardwaj, S. Palaninathan, L. Yi, J. Sacchettini, L. Guarino, J. Leibowitz, and C. Kao. 2007. Biological and biochemical examination of the Mouse Hepatitis Virus Nsp15 endoribonuclease. J. Virol. 81:13587-13597.

Gopinath, K., and C. Kao. 2007. Reconstitution of viral RNA infection through trafficking of viral RNAs in plants. The Plant Cell 19:1-13.

Ranjith-Kumar, C. T. J. Sun,, R. J. Lamb, J. Xiong, J. Santos, K. E. Duffy, W. Miller, A. Holzenburg, R. T. Sarisky, M.L. Mbow and C. Kao. 2007. Effects of single nucleotide polymorphisms in Toll-like Receptor 3 can affect its activity and expression in cultured cells. J. Biol. Chem. 282:17696-17705.

Ranjith-Kumar, C.T., W. Miller, J. Santos, L. Cleveland, M. Park, K. E. Duffy, R. Lamb, R. T. Sarisky, L. Mbow, and C. C. Kao. 2007. Structure-function analyses of the ectodomain of the human TLR3. J. Biol. Chem. 282:7668-7678.

Zhu, J., K. Gopinath, G. Yi, D. Hayward, H, Zhu, and C. Kao. 2007. RNA-binding Proteins that Inhibit RNA Virus Infection. Proc. Natl. Acad. Sci. USA 104:3129-9134.

Sun, J., DuFort, C. A. Murali, M. D. Daniel, C. Chen, K. Gopinath, B. Stein, M. De, Vince Rotello, A. Holzenburg, C. C. Kao, and B. Dragnea. 2007. Core-controlled polymorphism in virus-like particles. Proc. Natl. Acad. Sci. USA 104:1354-1359.

Yi, G. and C. Kao. 2007. Selective repression of translation by the Brome Mosaic Virus 1a RNA replication protein. J. Virol. 81:1601-1609.

Dixit, S., N. L. Goicochea, M. C. Daniel, A. Murali, L. Bronstein, M. De, B. Stein, V. M. Rotello, C. Kao, and B. Dragnea. 2006. Quantum Dot Encapsulation in Viral Capsids. Nano Letters 6:1993-1999. Featured news in Nature Nanotech:

Kim, Y.C., and C. Kao. 2006. Identification and characterization of RNA elements for viral RNA replication. Plant Virology Protocols. P.D. Nagy ed. Humana Press, Totoma, New Jersey.

Bhardwaj, K., J. Sun, R. A. Holzenburg, L. Guarino, and C. Kao. 2006. RNA recognition and cleavage by the SARS coronavirus endoribonuclease. J. Mol. Biol. 353:1106-1117.

Chen, C., M.-C. Daniel, Z. Quinkert, M. De, Barry Stein, V.M. Rotello, C. C. Kao, and B. Dragnea. 2006. High yield synthesis of virus-like particles. Nano Letters 6:611-615.

Sun, J., K. Duffy, C. T. Ranjith-Kumar, H. Masarapu, R. Lamb, A. Holzenburg, M. Cunningham, R. T. Sarisky, M. L. Mbow, and C. Kao. 2006. Functional and structural analyses of the human Toll-like Receptor 3. J. Biol. Chem. 281:11144-11151.

Ranjith-Kumar, C. T., and C. Kao. 2006. RNA-dependent RNA synthesis by the hepatitis C virus polymerase on circular templates: Implications for the initiation of RNA synthesis. RNA 12:303-312.

Kim, Y. C., W. K. Russell, C.T. Ranjith-Kumar, M. Thomson, David H. Russell and C. Cheng Kao. 2005. Functional analysis of RNA binding by the Hepatitis C Virus RNA-dependent RNA polymerase. J. Biol. Chem. 280:38011-38019.