Bob Duda's Publications - Bacteriophage HK97 capsid studies:

Functional domains of the HK97 capsid maturation protease and the mechanisms of protein encapsidation.
Duda, R. L., B. Oh, and R. W. Hendrix.
2013. J Mol Biol 425:2765-81.
The Prohead-I structure of bacteriophage HK97: implications for scaffold-mediated control of particle assembly and maturation.
Huang, R. K., R. Khayat, K. K. Lee, I. Gertsman, R. L. Duda, R. W. Hendrix, and J. E. Johnson.
2011. J Mol Biol 408:541-54.
An unexpected twist in viral capsid maturation.
Gertsman, I., L. Gan, M. Guttman, K. Lee, J. A. Speir, R. L. Duda, R. W. Hendrix, E. A. Komives, and J. E. Johnson.
2009. Nature 458:646-50.
Structure and energetics of encapsidated DNA in bacteriophage HK97 studied by scanning calorimetry and cryo-electron microscopy.
Duda, R. L., P. D. Ross, N. Cheng, B. A. Firek, R. W. Hendrix, J. F. Conway, and A. C. Steven.
2009. J Mol Biol 391:471-83.
Mutational analysis of a conserved glutamic acid required for self-catalyzed cross-linking of bacteriophage HK97 capsids.
Dierkes, L. E., C. L. Peebles, B. A. Firek, R. W. Hendrix, and R. L. Duda.
2009. J Virol 83:2088-98.
Virus capsid expansion driven by the capture of mobile surface loops.
Lee, K. K., L. Gan, H. Tsuruta, C. Moyer, J. F. Conway, R. L. Duda, R. W. Hendrix, A. C. Steven, and J. E. Johnson.
2008. Structure 16:1491-502.
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.
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.
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 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.
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.
Bacteriophage HK97: assembly of the capsid and evolutionary connections.
Hendrix, R. W.
2005. Adv Virus Res 64:1-14.
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.
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.
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.
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 55:763-71.
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.
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.

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



Chaperone-Protein Interactions That Mediate Assembly of the Bacteriophage Lambda Tail to the Correct Length.
Xu, J., R. W. Hendrix, and R. L. Duda.
2013. J Mol Biol.
A Balanced Ratio of Proteins from Gene G and Frameshift-Extended Gene GT Is Required for Phage Lambda Tail Assembly.
Xu, J., R. W. Hendrix, and R. L. Duda.
2013. J Mol Biol 425:3476-87.
Xu, J., Hendrix, R. W. & Duda, R. L.
Conserved translational frameshift in dsDNA bacteriophage tail assembly genes
(2004) Mol Cell 16, 11-21
Vianelli, A., Wang, G. R., Gingery, M., Duda, R. L., Eiserling, F. A. & Goldberg, E. B.
Bacteriophage T4 self-assembly: localization of gp3 and its role in determining tail length
(2000) J Bacteriol 182, 680-8
Hendrix, R. W. & Duda, R. L.
Bacteriophage lambda PaPa: not the mother of all lambda phages
(1992) Science 258, 1145-8
Duda, R. L., Gingery, M., Ishimoto, L. K. & Eiserling, F. A.
Expression of plasmid-encoded structural proteins permits engineering of bacteriophage T4 assembly
(1990) Virology 179, 728-37
Duda, R. L., Gingery, M. & Eiserling, F. A.
Potential length determiner and DNA injection protein is extruded from bacteriophage T4 tail tubes in vitro
(1986) Virology 151, 296-314
Duda, R. L., Wall, J. S., Hainfeld, J. F., Sweet, R. M. & Eiserling, F. A.
Mass distribution of a probable tail-length-determining protein in bacteriophage T4
(1985) Proc Natl Acad Sci U S A 82, 5550-4
Duda, R. L. & Eiserling, F. A.
Evidence for an internal component of the bacteriophage T4D tail core: a possible length-determining template
(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



Functional domains of the HK97 capsid maturation protease and the mechanisms of protein encapsidation.
Duda, R. L., B. Oh, and R. W. Hendrix.
2013. J Mol Biol 425:2765-81.
Maturation in action: CryoEM study of a viral capsid caught during expansion.
Veesler, D., J. Quispe, N. Grigorieff, C. S. Potter, B. Carragher, and J. E. Johnson.
2012. Structure 20:1384-90.
Mechanics of bacteriophage maturation.
Roos, W. H., I. Gertsman, E. R. May, C. L. Brooks, 3rd, J. E. Johnson, and G. J. Wuite.
2012. Proc Natl Acad Sci U S A 109:2342-7.
fSUB: normal mode analysis with flexible substructures.
Lu, M., D. Ming, and J. Ma.
2012. J Phys Chem B 116:8636-45.
Bacteriophage HK97 capsid assembly and maturation.
Hendrix, R. W., and J. E. Johnson.
2012. Adv Exp Med Biol 726:351-63.
Transferrin-mediated targeting of bacteriophage HK97 nanoparticles into tumor cells.
Huang, R. K., N. F. Steinmetz, C. Y. Fu, M. Manchester, and J. E. Johnson.
2011. Nanomedicine (Lond) 6:55-68.
The Prohead-I structure of bacteriophage HK97: implications for scaffold-mediated control of particle assembly and maturation.
Huang, R. K., R. Khayat, K. K. Lee, I. Gertsman, R. L. Duda, R. W. Hendrix, and J. E. Johnson.
2011. J Mol Biol 408:541-54.
Virus particle maturation: insights into elegantly programmed nanomachines.
Johnson, J. E.
2010. Curr Opin Struct Biol 20:210-6.
HK97 maturation studied by crystallography and H/2H exchange reveals the structural basis for exothermic particle transitions.
Gertsman, I., E. A. Komives, and J. E. Johnson.
2010. J Mol Biol 397:560-74.
Critical salt bridges guide capsid assembly, stability, and maturation behavior in bacteriophage HK97.
Gertsman, I., C. Y. Fu, R. Huang, E. A. Komives, and J. E. Johnson.
2010. Mol Cell Proteomics 9:1752-63.
Unfolding thermodynamics of the Delta-domain in the prohead I subunit of phage HK97: determination by factor analysis of Raman spectra.
Nemecek, D., S. A. Overman, R. W. Hendrix, and G. J. Thomas, Jr.
2009. J Mol Biol 385:628-41.
An unexpected twist in viral capsid maturation.
Gertsman, I., L. Gan, M. Guttman, K. Lee, J. A. Speir, R. L. Duda, R. W. Hendrix, E. A. Komives, and J. E. Johnson.
2009. Nature 458:646-50.
Structure and energetics of encapsidated DNA in bacteriophage HK97 studied by scanning calorimetry and cryo-electron microscopy.
Duda, R. L., P. D. Ross, N. Cheng, B. A. Firek, R. W. Hendrix, J. F. Conway, and A. C. Steven.
2009. J Mol Biol 391:471-83.
Mutational analysis of a conserved glutamic acid required for self-catalyzed cross-linking of bacteriophage HK97 capsids.
Dierkes, L. E., C. L. Peebles, B. A. Firek, R. W. Hendrix, and R. L. Duda.
2009. J Virol 83:2088-98.
Virus capsid expansion driven by the capture of mobile surface loops.
Lee, K. K., L. Gan, H. Tsuruta, C. Moyer, J. F. Conway, R. L. Duda, R. W. Hendrix, A. C. Steven, and J. E. Johnson.
2008. Structure 16:1491-502.
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.
Crosslinking in viral capsids via tiling theory.
Twarock, R., and R. W. Hendrix.
2006. J Theor Biol 240:419-24.
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.
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.
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 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.
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 55:763-71.
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.
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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