SELECTED PUBLICATIONS

Liu Y, Dai L, Dong J, Chen C, Zhu J, Rao VB, Tao P. (2020) Covalent Modifications of the Bacteriophage Genome Confer a Degree of Resistance to Bacterial CRISPR Systems. J Virology 9;94(23). doi: 10.1128/JVI.01630-20.

Wieczorek L, Peachman K, Steers N, Schoen J, Rao M, Polonis V, Rao V. (2020) Selection and immune recognition of HIV-1 MPER mimotopes. Virology 550:99-108. doi: 10.1016/j.virol.2020.06.016.

Mo Y, Keller N, delToro D, Ananthaswamy N, Harvey SC, Rao VB, Smith DE. (2020) Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence. Nucleic Acids Res 48(20):11602-11614. doi: 10.1093/nar/gkaa875.

Kim J, Rao VB, Rao M. (2020) Primary HIV-1 and Infectious Molecular Clones Are Differentially Susceptible to Broadly Neutralizing Antibodies. Vaccines (Basel) 8(4):782. doi: 10.3390/vaccines8040782.

Zhu, J., Tao, P., Mahalingam, M. and Rao, V. (2020). Preparation of a Bacteriophage T4-based Prokaryotic-eukaryotic Hybrid Viral Vector for Delivery of Large Cargos of Genes and Proteins into Human Cells. Bio-protocol 10(7): e3573. doi: 10.21769/BioProtoc.3573.

Fang Q, Tang WC, Tao P, Mahalingam M, Fokine A, Rossmann MG, Rao VB. (2020). Structural morphing in a symmetry-mismatched viral vertex. Nat Commun. 2020 Apr 6;11(1):1713. doi: 10.1038/s41467-020-15575-4.

Islam MZ, Fokine A, Mahalingam M, Zhang Z, Garcia-Doval C, van Raaij MJ, Rossmann MG, Rao VB. (2019) Molecular anatomy of the receptor binding module of a bacteriophage long tail fiber. PLoS Pathog. 2019 Dec 19;15(12):e1008193. doi: 10.1371/journal.ppat.1008193.

Zhu, J., Tao, P., Mahalingam, M., Sha, J., Kilgore, P., Chopra, A. K. and Rao, V. (2019) A prokaryotic eukaryotic hybrid viral vector for delivery of large cargos of genes and proteins into human cells. Science Advances 5, eaax0064

Chen, Y., Batra, H., Dong, J., Chen, C., Rao, V. B., and Tao, P. (2019) Genetic Engineering of Bacteriophages Against Infectious Diseases. Frontiers of Microbiology 10:954.

Trinh, H. V., Gohain, N., Pham, P. T., Hamlin, C., Song, H., Sanders-Buell, E., Bose, M., Eller, L. A., Jain, S., Uritskiy, G, Rao, V. B., Tovanabutra, S., Michael, N. L., Robb, M. L., Joyce, M. G., Rao, M. (2019) Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort. Cells 8(4). pii: E365.

Ananthaswamy, N., Fang, Q., AlSalmi,W., Jain, S., Chen, Z., Klose, T., Sun, Y., Liu, Y., Mahalingam, M., Chand, S., Tovanabutra, S., Robb, M., Rossmann, M.and Rao, V. B. (2019) A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer. Nature Communications 10(1):873.

Ordyan, M., Alam, I., Mahalingam, M., Rao, V. B. and Smith, D. E. (2018) Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor. Nature Communications 9(1):5434.

Tao P, Mahalingam M, Zhu J, Moayeri M, Sha J, Lawrence WS, Leppla SH, Chopra AK, Rao VB. (2018) A Bacteriophage T4 Nanoparticle-Based Dual Vaccine against Anthrax and Plague. MBio 9(5). pii: e01926-18.

Tao, P., Zhu, J., Mahalingam, M., Batra, H. and Rao, V.B. (2018) Bacteriophage T4 nanoparticles for vaccine delivery against infectious diseases. Advances in Drug Delivery Reviews pii: S0169-409X(18)30164-9. [Epub ahead of print] Review.

Tao, P., Wu, X. and Rao, V.B. (2018) Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9. Science Advances Vol. 4, no. 2, eaar4134

Lin, S., Alam, T.I., Kottadiel, V., VanGessel, C.J., Tang, W-C., Chemla, Y.R. and Rao, V.B. (2017) Altering the speed of a DNA packaging motor from bacteriophage T4. Nucleic Acids Research. 45(19):11437-11448.

Chen Z, Sun L, Zhang Z, Fokine A, Padilla-Sanchez V, Hanein D, Jiang W, Rossmann MG, Rao VB. (2017) Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses. Proc Natl Acad Sci U S A. 2017 Sep 11. pii: 201708483. [Epub ahead of print]

Tao P, Wu X, Tang WC, Zhu J, Rao V. (2017) Engineering of Bacteriophage T4 Genome Using CRISPR-Cas9. ACS Synth Biol. 2017 Jul 13. [Epub ahead of print]

Chand S., Messina E.L., AlSalmi W., Ananthaswamy N., Gao G., Uritskiy G., Padilla-Sanchez V., Mahalingam M., Peachman K.K., Robb M.L., Rao M., Rao V.B. (2017) Glycosylation and oligomeric state of envelope protein might influence HIV-1 virion capture by α4β7 integrin. Virology. pii:S0042-6822(17)30164-2.

Kim J., Jobe O., Peachman K.K., Michael N.L., Robb M.L., Rao M., Rao V.B. (2017) Quantitative analyses reveal distinct sensitivities of the capture of HIV-1 primary viruses and pseudoviruses to broadly neutralizing antibodies. Highlighted in Virology Virology. pii:S0042-6822(17)30165-4.

Tao P., Li Q., Shivachandra S.B., Rao V.B. (2017) Bacteriophage T4 as a Nanoparticle Platform to Display and Deliver Pathogen Antigens: Construction of an Effective Anthrax Vaccine. Methods Mol Biol. 1581:255-267.

Tao, P., Mahalingam, M., Zhu, J., Moayeri, M., Kirtley, M., Fitts, E., Andersson, J., Lawrence, W., Leppla, S., Chopra, A. and Rao, V.B. (2017) A Bivalent Anthrax-Plague Vaccine That Can Protect Against Two Tier-1 Bioterror Pathogens, Bacillus anthracis and Yersinia pestis. Front. Immunol. 8:687

Tao, P., Mahalingam, M., Rao, V.B. (2016) Highly Effective Soluble and Bacteriophage T4 Nanoparticle Plague Vaccines Against Yersinia pestis. Methods Mol. Biol. 1403:499-518.

Gao, S., Zhang, L., Rao, V.B. (2016) Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4. Nucleic Acids Res. pii: gkw184.

Jobe, O., Trinh, H.V., Kim, J., Alsalmi, W., Tovanabutra, S., Ehrenberg, P.K., Peachman, K.K., Gao, G., Thomas, R., Kim, J.H., Michael, N.L., Alving, C.R., Rao, V.B., Rao, M.(2015) Effect of cytokines on Siglec-1 and HIV-1 entry in monocyte-derived macrophages: the importance of HIV-1 envelope V1V2 region. J. Leukoc. Biol. pii: jlb.2A0815-361R.

AlSalmi, W., Mahalingam, M., Ananthaswamy, N., Hamlin, C., Flores, D., Gao, G., Rao, V.B. (2015) A New Approach to Produce HIV-1 Envelope Trimers: BOTH CLEAVAGE AND PROPER GLYCOSYLATION ARE ESSENTIAL TO GENERATE AUTHENTIC TRIMERS. J. Biol. Chem. 290(32):19780-95

Rao, V.B. and Feiss, M. (2015) Mechanisms of DNA Packaging in Large Double Stranded DNA Viruses. Ann. Rev. Virology 2(1):351-78.

Sun, L., Zhang, X., Gao S., Rao, P.A., Padilla-Sanchez V., Chen, Z., Sun, S., Xiang, Y., Subramaniam S., Rao, V.B. & Rossmann, M.G. (2015) Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Nature Communications 6:7548.

Kondabagil, K., Dai, L., Vafabakhsh, R., Ha, T.J., Draper, B. and Rao, V.B. (2014) Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function. Virology 468-470:660-668

Vafabakhsh, R., Kondabagil, K., Earnest, T. M., Lee, K. S., Zhang, Z., Dai, L., Dahmen, K. A., Rao, V. B. and Ha, T. (2014) Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4. Proc. Natl. Acad. Sci. USA 111(42):15096-15101

Migliori, A. D., Kellera, N., Alam, T. I., Mahalingam, M., Rao, V. B., Arya, G., and Smith, D. E. (2014) Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor. Nature Communications 5: 4173

Padilla-Sanchez, V., Gao, S., Kim, H. R., Kihara, D., Sun, L., Rossmann, M. G. and Rao, V. B. (2013) Structure-function analysis of the DNA translocating portal of the bacteriophage T4 packaging machine. J. Mol. Biol. 426:1019-1038.

Rao, M., Peachman, K. K., Kim, J., Gao, G., Alving, C. A., Michael, N. L., Rao, V. B. HIV-1 Variable Loop 2 and its Importance in HIV-1 Infection and Vaccine Development. (2013) Curr. HIV Research 11:427-438.

Tao, P., Mahalingham, M., Kirtley, M., van Lier, C. J., Sha, J., Yeager, L. A., Chopra, A. K. and Rao, V. B. (2013). Mutated and bacteriophage T4 nanoparticle arrayed F1-V immunogens from Yersenia pestis as next generation plague vaccines. PLOS Pathogens 9(7): e1003495.

Tao, P., Mahalingham, M., Marasa, B., Chopra, A. and Rao, V. B. (2013). In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine. Proc. Natl. Acad. Sci. USA 110:5846-5851.

Fokine, A., Zhang, Z., Kanamaru, S., Bowman, V. D., Aksyuk, A. A., Arisaka, F., Rao, V. B. and Rossmann, M. G. (2013). The molecular architecture of the bacteriophage T4 neck. J. Mol. Biol. 425:1731-1744.

Gao G, Wieczorek L, Peachman KK, Polonis VR, Alving CR, Rao M, Rao VB. (2013) Designing a soluble near full-length HIV-1 GP41 trimer. J. Biol. Chem. 288:234-46.

Kottadiel VI, Rao VB, Chemla YR. (2012) The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4. Proc. Natl. Acad. Sci. U S A. 109:20000-20005.

Black, L.W. and Rao, V.B. (2012) Structure, Assembly, and DNA packaging of bacteriophage T4 head Adv. Virus Res: 119-153. COVER PAGE

Hegde, S., Padilla-Sanchez, V., Draper, B., and Rao, V. B. (2012) Portal-Large Terminase Interactions of the Bacteriophage T4 DNA Packaging Machine Implicates a Molecular Lever Mechanism for Coupling ATPase to DNA Translocation. J. Virol. 86:4046-57.     COVER PAGE

Feiss M, Rao VB. (2012) The bacteriophage DNA packaging machine. Adv. Exp. Med. Biol. 726:489-509.

Sun S, Gao S, Kondabagil K, Xiang Y, Rossmann MG, Rao VB. (2012) Structure and function of the small terminase component of the DNA packaging machine in T4-like bacteriophages. Proc Natl Acad Sci U S A. 109(3):817-22.

Peachman KK, Li Q, Matyas GR, Shivachandra SB, Lovchik J, Lyons RC, Alving CR, Rao VB, Rao M. (2012). Anthrax Vaccine Antigen-Adjuvant Formulations Completely Protect New Zealand White Rabbits against Challenge with Bacillus anthracis Ames Strain Spores. Clin Vaccine Immunol. 19(1):11-6.

Kondabagil, K., Draper, B., Rao, V.B. (2012). Adenine recognition is a key checkpoint in the energy release mechanism of phage T4 DNA packaging motor. J. Mol. Biol. 415(2):329-42. COVER PAGE

Ghosh-kumar, M., Alam, T.I., Draper, B., Stack, J. and Rao, V.B. (2011) Regulation by Interdomain Communication of a Headful Packaging Nuclease from Bacteriophage T4. Nucleic Acids Res. 39: 2742-2755.

Zhang, Z., Kottadiel, V., Vafabakhsh, R., Li, Dai, Chemla,Y.R., Ha, T.J. and Rao, V.B. (2011) A promiscuous DNA packaging machine from bacteriophage T4. PLOS Biology 9:e1000592, 1-11. (Featured in "RESEARCH HIGHLIGHTS" Nature Reviews Microbiology, 2011 Vol.9).

Rao, V. B. and Black, L. W. (2010) Structure and Assembly of bacteriophage T4 head. Virol. J. 7:356- COVER PAGE

Gao, S. and Rao, V. B. (2011) Specificity of interactions among the DNA packaging machine components of T4-related bacteriophages. J. Biol. Chem. 286:3944-3956.

Rao, M., Peachman, K., Li, Q., Matyas, G., Shivachandra, S., Borschel, R., Morthole, V.I., Fernandez-Prada, C. R., Alving, C. and Rao, V.B. (2011) Highly effective generic adjuvant systems for orphan or poverty-related vaccines. Vaccine 29:873-877.

Sathaliyawala, T., Islam, Z., Li, Qin., Fokine, A., Rossmann, M.G., Rao, V.B. (2010) Functional analysis of the highly antigenic outer capsid protein, Hoc, a virus decoration protein from T4-related bacteriophages. Molecular Microbiol. 77:444-455. COVER PAGE

Sun, S., Rao, V.B. and Rossmann, M. Genome packaging in viruses. (2010) Curr. Opin. Struct. Biol. 20 (1):114-120.

Li, Q., Peachman, K. K., Sower, L., Leppla, S. H., Shivachandra, S. B., Matyas, G. R., Peterson, J. W., Alving, C. R., Rao, M., Rao, V. B. (2009) Anthrax LFn-PA Hybrid Antigens: Biochemistry, Immunogenicity, and Protection Against Lethal Ames Spore Challenge in Rabbits. Open Vaccine Journal 2:92-99.

Al-Zahrani, A.S., Kondabagil K., Gao, S., Kelly, N., Ghosh-Kumar, M. and Rao, V. B. (2009) The small terminase, gp16, of bacteriophage T4 is a regulator of the DNA packaging motor. J. Biol. Chem. 284:24490-24500.

Rao, V. B. (2009) A virus DNA gate: zipping and unzipping the packed viral genome. Proc. Natl. Acad. Sci. USA 106: 8403-8404.

Kearney, M., Maldarelli, F., Shao, W., Margolick, J.B., Daar, E.S., Mellors, J.W., Rao, V., Coffin, J.M. and Palmer, S. (2009) Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J. Virology 83:2715-27.

Sun, S, Kondabagil, K., Draper, B., Alam, I.T., Baumann, V., Zhang, Z., Hegde., Fokine, A., Rossmann, M.G., and Rao, V.B. (2008) The atomic structure of bacteriophage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251-1262. This paper was featured as a "LEADING EDGE" article; Williams, R.S., Williams, G.J. and Tainer, J.A. Cell 135:1169-71.

Rao, V.B. and Feiss, M. The bacteriophage DNA packaging motor. (2008). Ann. Rev. Genetics 42:642-681.

Alam, T.I., Draper, B., Kondabagil, K., Rentas, F., Ghosh-Kumar, M., Sun, S. Rossmann, M.G., and Rao, V.B. (2008). The headful packaging nuclease of bacteriophage T4. Molecular Microbiology 69:1180-90.

Alam, I. T. and Rao, V. B. (2008) The ATPase domain of the large terminase protein, gp17, from bacteriophage T4 binds DNA: implications to the DNA packaging mechanism. J. Mol. Biol. 376:1272-81.

Fuller, D. N., Raymer, D. M., Kottadiel, V. I., Rao, V. B. and Smith, D. E. (2007). Single Phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc. Natl. Acad. Sci. U.S.A. 104:16868-16873.

Fokine, A., Bowman, V. D., Battisti, A. J., Li, Q., Chipman, P. R., Rao, V. B. and Rossmann, M. G. (2007) Cryo-electron microscopy study of bacteriophage T4 displaying anthrax toxin proteins. Virology 367:422-427. COVER PAGE

Sun S, Kondabagil K, Gentz PM, Rossmann MG, and Rao V. B. (2007). The Structure of the ATPase that Powers DNA Packaging into Bacteriophage T4 Procapsids. Mol. Cell. 25(6):943-949.

Li, Q., Shivachandra, S.B., Zhang, Z. and Rao, V. B. (2007). Assembly of the Small Outer Capsid protein, Soc, on bacteriophage T4: a novel system for high density display of multiple large anthrax toxins and foreign proteins on phage capsid. J. Mol. Biol, 370:1006-1019. COVER PAGE

Draper, B and Rao, V. B. (2007) An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests inchworm type translocation mechanism. J. Mol. Biol. 367:79-94.

Shivachandra, S. B., Li, Q., Peachman, K. K., Matyas G. R., Leppla S. H., Alving C. R., Rao, M., Rao V. B. (2007) Multicomponent anthrax toxin display and delivery using bacteiophage T4. Vaccine, 25(7):1225-35.

Kondabagil,K. R., Zhang, Z. B. and Rao, V. B. (2006) The DNA translocating ATPase of bacteriophage T4 packaging motor. J. Mol. Biol. 363: 786-799.

Li, Q., Shivachandra, S., Leppla, S. H. and Rao, V. B. (2006) Bacteriophage T4 Capsid: Unique Platform for Efficient Surface Assembly of Macromolecular Complexes J. Mol. Biol. 363: 577-578. COVER PAGE

Sathaliyawala, T., Rao, M., Maclean, D. M., Birx, D. L., Alving, C. R. and Rao, V. B. (2006) Assembly og Human Immunodeficiency Virus (HIV) antigens on Bacteriophage T4: a Novel In Vitro Approach To Construct Multicomponent HIV Vaccines. J. Virol. 80: 7688-7698.

Kondabagil, K. R. and Rao, V. B. (2006) A critical coiled coil motif in the small terminase, gp16, from bacteriophage T4: insights into DNA packaging initiation and assembly of packaging motor J. Mol. Biol. 358: 67-82.

Peachman, K. K., Rao, M., Alving, C. R., Burge, R., Leppla, S. H., Rao, V. B., and Matyas, G. R. (2006) Correlation between lethal toxin neutralizing antibody titers and protection from intranasal challenge with Bacillus Anthracis Ames strain spores in mice after transcutaneous immunization with recombinant anthrax protective antigen. Infection and Immunity 74: 794-797.

Shivachandra S. B., RaoM., Janosi L., Sathaliyawala T., Matyas G. R., Alving C. R., Leppla S. H., Rao V. B. (2006) In vitro binding of anthrax protective antigen on bacteriophage T4 capsid surface through Hoc-capsid interactions: astrategy for efficient display of large full-length proteins. Virology 345: 190-198.

Mitchell, M. and Rao, V. B. (2006) Functional analysis of the bacteriophage T4 DNA packaging ATPase motor. J. Biol. Chem. 281: 518-527.

Kanamaru, S., Kondabagil, K., Rossmann, M. and Rao, V. B. (2004) The functional domains of bacteriophage T4 terminase. J. Biol. Chem. 279: 40795-40801.

Fokine, A., Chipman, P., Leiman, P., Mesyanzhimov, V., Rao, V. and Rossmann, M., (2004) Molecular architecture of the prolate head of bacteriophage T4, Proc. Natl. Acad. Sci. USA 101: 6003-6008.

Goetzinger, K. and Rao, V. B. (2003) Defining the ATPase center of bacteriophage T4 DNA packaging machine: requirement for a catalytic glutamate in the large terminase subunit gp17. J. Mol. Biol. 331: 139-154.

Mitchell, M., Matsuzaki, S., Imai, S. and Rao, V. B. (2002) Sequence analysis of bacteriophage T4 DNA-packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Res. 30: 4009-4021.

Rao, V. B. and Mitchell, M. (2001) The N-terminal ATPase Site in the Large Terminase Protein Gp17 is Critically Required for DNA Packaging in Bacteriophage T4. J. Mol. Biol. 314: 411-421.

Leffers, G. and Rao, V. B. (2000) Biochemical Characterization of an ATPase Activity Associated with the Large Packaging Subunit Gp17 from Bacteriophage T4. J. Biol. Chem. 275: 37127-37136.

Iwasaki, K., Trus, B. L., Wingfield, P. T., Cheng, N., Campusano, G., Rao, V. B. and Steven, A. C. (2000) Molecular Architecture of Bacteriophage T4 Capsid: Vertex Structure and Bimodal Binding of the Stabilizing Accessory Protein, Soc. Virology 271: 321-333. COVER PAGE

Kuebler, D. and Rao, V. B. (1998) Functional Analysis of the DNA Packaging/Terminase Protein Gp17 from Bacteriophage T4. J. Mol. Biol. 281:803-814.

Jiang, J., Abu-Shilbayeh, L. and Rao, V. B. (1997) Display of a PorA Peptide form Neisseria meningitidis on the Bacteriophage T4 Capsid surface. Infection and Immunity 65:4770-4777.

Leffers, G. and Rao, V.B. (1996) A discontinuous headful packaging model for packaging less than headful length DNA molecules by bacteriophage T4. J. Mol. Biol. 258:839-850.

Bhattacharyya, S. and Rao, V.B. (1993) A novel endonuclease activity associated with the DNA packaging protein gp 17 of bacteriophage T4. Virology 196: 34-44.

Rao, V.B. and Leffers, G. (1993) Purification and characterization of giant empty proheads from packaging-defective 23ptg mutants of bacteriophage T4. Virology 196: 896-899.

Rao, V.B., Thaker, V. and Black, L.W. (1992) A phage T4 in vitro packaging system for cloning long DNA molecules. Gene 113: 25-33.

Rao, V.B. and Black, L.W. (1988) Cloning, overexpression and purification of the terminase proteins gp16 and gp17 of bacteriophage T4; Construction of a defined in vitro DNA packaging system using purified terminase proteins. J. Mol. Biol. 200: 475-485.

Rao, V.B. and Black, L.W. (1985) Evidence that a phage T4 DNA packaging enzyme is a processed form of the major capsid gene product. Cell 42: 967-977.

Rao, V.B. and Black, L.W. (1985) DNA packaging of bacteriophage T4 proheads in vitro: Evidence that prohead expansion is not coupled to DNA packaging. J. Mol. Biol. 185: 565-578.