Bob Duda's Publications

Publications and references to relevant phage and virus literature

(R. Duda) Assembly, structure and genetics of the bacteriophage HK97 capsid:

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A thermally induced phase transition in a viral capsid transforms the hexamers, leaving the pentamers unchanged.: Conway, J. F., N. Cheng, P. D. Ross, R. W. Hendrix, R. L. Duda, and A. C. Steven.; 2007. J Struct Biol 158:224-32.

Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM.: Gan, L., J. A. Speir, J. F. Conway, G. Lander, N. Cheng, B. A. Firek, R. W. Hendrix, R. L. Duda, L. Liljas, and J. E. Johnson.; 2006. Structure 14:1655-65.

A free energy cascade with locks drives assembly and maturation of bacteriophage HK97 capsid.: Ross, P. D., J. F. Conway, N. Cheng, L. Dierkes, B. A. Firek, R. W. Hendrix, A. C. Steven, and R. L. Duda.; 2006. J Mol Biol 364:512-25.

Shared architecture of bacteriophage SPO1 and herpesvirus capsids.: Duda, R. L., R. W. Hendrix, W. M. Huang, and J. F. Conway.; 2006. Curr Biol 16:R11-3.

A thermally induced phase transition in a viral capsid transforms the hexamers, leaving the pentamers unchanged.: Conway, J. F., N. Cheng, P. D. Ross, R. W. Hendrix, R. L. Duda, and A. C. Steven.; 2006. J Struct Biol.

Time-resolved molecular dynamics of bacteriophage HK97 capsid maturation interpreted by electron cryo-microscopy and X-ray crystallography.: Wikoff, W. R., J. F. Conway, J. Tang, K. K. Lee, L. Gan, N. Cheng, R. L. Duda, R. W. Hendrix, A. C. Steven, and J. E. Johnson.; 2006. J Struct Biol 153:300-6.

Control of Virus Assembly: HK97 "Whiffleball" Mutant Capsids Without Pentons.: Li, Y., J. F. Conway, N. Cheng, A. C. Steven, R. W. Hendrix, and R. L. Duda.; 2005. J Mol Biol 348:167-82.

Crosslinking renders bacteriophage HK97 capsid maturation irreversible and effects an essential stabilization.: Ross, P. D., N. Cheng, J. F. Conway, B. A. Firek, R. W. Hendrix, R. L. Duda, and A. C. Steven.; 2005. Embo J.

Control of crosslinking by quaternary structure changes during bacteriophage HK97 maturation.: Gan, L., J. F. Conway, B. A. Firek, N. Cheng, R. W. Hendrix, A. C. Steven, J. E. Johnson, and R. L. Duda.; 2004. Mol Cell 14:559-69.

Domain structures and roles in bacteriophage HK97 capsid assembly and maturation.: Benevides, J. M., P. Bondre, R. L. Duda, R. W. Hendrix, and G. J. Thomas, Jr.; 2004. Biochemistry 43:5428-36.

Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid.: Lee, K. K., L. Gan, H. Tsuruta, R. W. Hendrix, R. L. Duda, and J. E. Johnson.; 2004. J Mol Biol 340:419-33.

Crystallization and preliminary analysis of a dsDNA bacteriophage capsid intermediate: Prohead II of HK97.: Wikoff, W. R., Z. Che, R. L. Duda, R. W. Hendrix, and J. E. Johnson.; 2003. Acta Crystallogr D Biol Crystallogr 59:2060-4.

The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution.: Helgstrand, C., W. R. Wikoff, R. L. Duda, R. W. Hendrix, J. E. Johnson, and L. Liljas.; 2003. J Mol Biol 334:885-99.

Virus maturation involving large subunit rotations and local refolding.: Conway, J. F., W. R. Wikoff, N. Cheng, R. L. Duda, R. W. Hendrix, J. E. Johnson, and A. C. Steven.; 2001. Science 292:744-8.

Bacteriophage T4 self-assembly: localization of gp3 and its role in determining tail length.: Vianelli, A., G. R. Wang, M. Gingery, R. L. Duda, F. A. Eiserling, and E. B. Goldberg.; 2000. J Bacteriol 182:680-8.

Genome organization and characterization of mycobacteriophage Bxb1.: Mediavilla, J., S. Jain, J. Kriakov, M. E. Ford, R. L. Duda, W. R. Jacobs, Jr., R. W. Hendrix, and G. F. Hatfull.; 2000. Mol Microbiol 38:955-70.

Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.: Juhala, R. J., M. E. Ford, R. L. Duda, A. Youlton, G. F. Hatfull, and R. W. Hendrix.; 2000. J Mol Biol 299:27-51.

Maturation dynamics of a viral capsid: visualization of transitional intermediate states.: Lata, R., J. F. Conway, N. Cheng, R. L. Duda, R. W. Hendrix, W. R. Wikoff, J. E. Johnson, H. Tsuruta, and A. C. Steven.; 2000. Cell 100:253-63.

Topologically linked protein rings in the bacteriophage HK97 capsid.: Wikoff, W. R., L. Liljas, R. L. Duda, H. Tsuruta, R. W. Hendrix, and J. E. Johnson.; 2000. Science 289:2129-33.

Crystallographic analysis of the dsDNA bacteriophage HK97 mature empty capsid.: Wikoff, W. R., R. L. Duda, R. W. Hendrix, and J. E. Johnson.; 1999. Acta Crystallogr D Biol Crystallogr 55 (Pt 4):763-71.

Bacteriophage HK97 head assembly: a protein ballet.: Hendrix, R. W., and R. L. Duda.; 1998. Adv Virus Res 50:235-88.

Crystallization and preliminary X-ray analysis of the dsDNA bacteriophage HK97 mature empty capsid.: Wikoff, W. R., R. L. Duda, R. W. Hendrix, and J. E. Johnson.; 1998. Virology 243:113-8.

Protein chainmail: catenated protein in viral capsids.: Duda, R. L.; 1998. Cell 94:55-60.

Bacteriophage HK97 head assembly.: Duda, R. L., K. Martincic, Z. Xie, and R. W. Hendrix.; 1995. FEMS Microbiol Rev 17:41-6.

Complexes between chaperonin GroEL and the capsid protein of bacteriophage HK97.: Ding, Y., R. L. Duda, R. W. Hendrix, and J. M. Rosenberg.; 1995. Biochemistry 34:14918-31.

Genetic basis of bacteriophage HK97 prohead assembly.: Duda, R. L., K. Martincic, and R. W. Hendrix.; 1995. J Mol Biol 247:636-47.

Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system.: Conway, J. F., R. L. Duda, N. Cheng, R. W. Hendrix, and A. C. Steven.; 1995. J Mol Biol 253:86-99.

Structural transitions during bacteriophage HK97 head assembly.: Duda, R. L., J. Hempel, H. Michel, J. Shabanowitz, D. Hunt, and R. W. Hendrix.
(1995) J Mol Biol 253, 86-99

(R. Duda) Genetics, structure, and assembly of bacteriophage tails and tail fibers:

Bacteriophage lambda PaPa: not the mother of all lambda phages.: Hendrix, R. W., and R. L. Duda.; 1992. Science 258:1145-8.

Conserved translational frameshift in dsDNA bacteriophage tail assembly genes.: Xu, J., R. W. Hendrix, and R. L. Duda.; 2004. Mol Cell 16:11-21.

Expression of plasmid-encoded structural proteins permits engineering of bacteriophage T4 assembly.: Duda, R. L., M. Gingery, L. K. Ishimoto, and F. A. Eiserling.; 1990. Virology 179:728-37.

Potential length determiner and DNA injection protein is extruded from bacteriophage T4 tail tubes in vitro.: Duda, R. L., M. Gingery, and F. A. Eiserling.; 1986. Virology 151:296-314.

Mass distribution of a probable tail-length-determining protein in bacteriophage T4.: Duda, R. L., J. S. Wall, J. F. Hainfeld, R. M. Sweet, and F. A. Eiserling.; 1985. Proc Natl Acad Sci U S A 82:5550-4.

Evidence for an internal component of the bacteriophage T4D tail core: a possible length-determining template.: Duda, R. L., and F. A. Eiserling.; 1982. J Virol 43:714-20.

Reports about Bob Duda's research

Johnson JE and Wikoff WR.: Chainmail stabilization of a viral capsid.
Curr Biol. 1998 Dec 17-31

Pittsburgh Post Gazette article: Viruses protect selves with protein armor

Science News article

More complete list of Bacteriophage HK97 related publications

Solution NMR studies of the maturation intermediates of a 13 MDa viral capsid.: Szymczyna, B. R., L. Gan, J. E. Johnson, and J. R. Williamson.; 2007. J Am Chem Soc 129:7867-76.

A thermally induced phase transition in a viral capsid transforms the hexamers, leaving the pentamers unchanged.: Conway, J. F., N. Cheng, P. D. Ross, R. W. Hendrix, R. L. Duda, and A. C. Steven.; 2007. J Struct Biol 158:224-32.

Time-resolved molecular dynamics of bacteriophage HK97 capsid maturation interpreted by electron cryo-microscopy and X-ray crystallography.: Wikoff, W. R., J. F. Conway, J. Tang, K. K. Lee, L. Gan, N. Cheng, R. L. Duda, R. W. Hendrix, A. C. Steven, and J. E. Johnson.; 2006. J Struct Biol 153:300-6.

Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM.: Gan, L., J. A. Speir, J. F. Conway, G. Lander, N. Cheng, B. A. Firek, R. W. Hendrix, R. L. Duda, L. Liljas, and J. E. Johnson.; 2006. Structure 14:1655-65.

Crosslinking in viral capsids via tiling theory.: Twarock, R., and R. W. Hendrix.; 2005. J Theor Biol.

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis.: Tama, F., and C. L. Brooks, 3rd.; 2005. J Mol Biol 345:299-314.

Crosslinking renders bacteriophage HK97 capsid maturation irreversible and effects an essential stabilization.: Ross, P. D., N. Cheng, J. F. Conway, B. A. Firek, R. W. Hendrix, R. L. Duda, and A. C. Steven.; 2005. Embo J 24:1352-63.

Maturation dynamics of bacteriophage HK97 capsid.: Rader, A. J., D. H. Vlad, and I. Bahar.; 2005. Structure (Camb) 13:413-21.

Control of virus assembly: HK97 "Whiffleball" mutant capsids without pentons.: Li, Y., J. F. Conway, N. Cheng, A. C. Steven, R. W. Hendrix, and R. L. Duda.; 2005. J Mol Biol 348:167-82.

Cooperative reorganization of a 420 subunit virus capsid.: Lee, K. K., H. Tsuruta, R. W. Hendrix, R. L. Duda, and J. E. Johnson.; 2005. J Mol Biol 352:723-35.

Rigid-cluster models of conformational transitions in macromolecular machines and assemblies.: Kim, M. K., R. L. Jernigan, and G. S. Chirikjian.; 2005. Biophys J 89:43-55.

Bacteriophage HK97: assembly of the capsid and evolutionary connections.: Hendrix, R. W.; 2005. Adv Virus Res 64:1-14.

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.: Chennubhotla, C., A. J. Rader, L. W. Yang, and I. Bahar.; 2005. Phys Biol 2:S173-80.

Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid.: Lee, K. K., L. Gan, H. Tsuruta, R. W. Hendrix, R. L. Duda, and J. E. Johnson.; 2004. J Mol Biol 340:419-33.

Control of crosslinking by quaternary structure changes during bacteriophage HK97 maturation.: Gan, L., J. F. Conway, B. A. Firek, N. Cheng, R. W. Hendrix, A. C. Steven, J. E. Johnson, and R. L. Duda.; 2004. Mol Cell 14:559-69.

Domain structures and roles in bacteriophage HK97 capsid assembly and maturation.: Benevides, J. M., P. Bondre, R. L. Duda, R. W. Hendrix, and G. J. Thomas, Jr.; 2004. Biochemistry 43:5428-36.

Crystallization and preliminary analysis of a dsDNA bacteriophage capsid intermediate: Prohead II of HK97.: Wikoff, W. R., Z. Che, R. L. Duda, R. W. Hendrix, and J. E. Johnson.; 2003. Acta Crystallogr D Biol Crystallogr 59:2060-4.

An elastic network model of HK97 capsid maturation.: Kim, M. K., R. L. Jernigan, and G. S. Chirikjian.; 2003. J Struct Biol 143:107-17.

The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution.: Helgstrand, C., W. R. Wikoff, R. L. Duda, R. W. Hendrix, J. E. Johnson, and L. Liljas.; 2003. J Mol Biol 334:885-99.

Virus maturation involving large subunit rotations and local refolding.: Conway, J. F., W. R. Wikoff, N. Cheng, R. L. Duda, R. W. Hendrix, J. E. Johnson, and A. C. Steven.; 2001. Science 292:744-8.

High-temperature protein mass mapping using a thermophilic protease.: Bark, S. J., N. Muster, J. R. Yates, 3rd, and G. Siuzdak.; 2001. J Am Chem Soc 123:1774-5.

Topologically linked protein rings in the bacteriophage HK97 capsid.: Wikoff, W. R., L. Liljas, R. L. Duda, H. Tsuruta, R. W. Hendrix, and J. E. Johnson.; 2000. Science 289:2129-33.

Maturation dynamics of a viral capsid: visualization of transitional intermediate states.: Lata, R., J. F. Conway, N. Cheng, R. L. Duda, R. W. Hendrix, W. R. Wikoff, J. E. Johnson, H. Tsuruta, and A. C. Steven.; 2000. Cell 100:253-63.

Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.: Juhala, R. J., M. E. Ford, R. L. Duda, A. Youlton, G. F. Hatfull, and R. W. Hendrix.; 2000. J Mol Biol 299:27-51.

Virus assembly: Imaging a molecular machine.: Wikoff, W. R., and J. E. Johnson.; 1999. Curr Biol 9:R296-300.

Crystallographic analysis of the dsDNA bacteriophage HK97 mature empty capsid.: Wikoff, W. R., R. L. Duda, R. W. Hendrix, and J. E. Johnson.; 1999. Acta Crystallogr D Biol Crystallogr 55 (Pt 4):763-71.

Family values in the age of genomics: comparative analyses of temperate bacteriophage HK022.: Weisberg, R. A., M. E. Gottesmann, R. W. Hendrix, and J. W. Little.; 1999. Annu Rev Genet 33:565-602.

Crystallization and preliminary X-ray analysis of the dsDNA bacteriophage HK97 mature empty capsid.: Wikoff, W. R., R. L. Duda, R. W. Hendrix, and J. E. Johnson.; 1998. Virology 243:113-8.

Macromolecular assembly: chainmail stabilization of a viral capsid.: Johnson, J. E., and W. R. Wikoff.; 1998. Curr Biol 8:R914-7.

Bacteriophage HK97 head assembly: a protein ballet.: Hendrix, R. W., and R. L. Duda.; 1998. Adv Virus Res 50:235-88.

Protein chainmail: catenated protein in viral capsids.: Duda, R. L.; 1998. Cell 94:55-60.

Assembly in vitro of bacteriophage HK97 proheads.: Xie, Z., and R. W. Hendrix.; 1995. J Mol Biol 253:74-85.

Bacteriophage HK97 head assembly.: Duda, R. L., K. Martincic, Z. Xie, and R. W. Hendrix.; 1995. FEMS Microbiol Rev 17:41-6.

Genetic basis of bacteriophage HK97 prohead assembly.: Duda, R. L., K. Martincic, and R. W. Hendrix.; 1995. J Mol Biol 247:636-47.

Structural transitions during bacteriophage HK97 head assembly.: Duda, R. L., J. Hempel, H. Michel, J. Shabanowitz, D. Hunt, and R. W. Hendrix.; 1995. J Mol Biol 247:618-35.

Complexes between chaperonin GroEL and the capsid protein of bacteriophage HK97.: Ding, Y., R. L. Duda, R. W. Hendrix, and J. M. Rosenberg.; 1995. Biochemistry 34:14918-31.

Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system.: Conway, J. F., R. L. Duda, N. Cheng, R. W. Hendrix, and A. C. Steven.; 1995. J Mol Biol 253:86-99.

Bacteriophage HK97 structure: wholesale covalent cross-linking between the major head shell subunits.: Popa, M. P., T. A. McKelvey, J. Hempel, and R. W. Hendrix.; 1991. J Virol 65:3227-37.

Host range, immunity and antigenic properties of lambdoid coliphage HK97.: Dhillon, E. K., T. S. Dhillon, A. N. Lai, and S. Linn.; 1980. J Gen Virol 50:217-20.

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