Dr. Robert Duda

Genetics
K. Arndt
T.-L. Ashman
G. Campbell
D. Chapman
G. Hatfull
J. Hildebrand
L. Jacobson
S. Kalisz
J. Martens
W. Saunders
B. Stronach
S. Tonsor
R. Wood

Microbiology
J. Boyle
G. Hatfull
R. Hendrix
J. Lawrence
J. Pipas
M. Popa
R.L. Duda
S. Godfrey
V. Oke

Molecular Biology
K. Arndt
J. Franzen
P. Grabowski
G. Hatfull
R. Hendrix
L. Jen-Jacobson
J. Martens
C. Peebles
J. Pipas
J. Rosenberg
A. Schwacha
C. Walsh

Plant Biology
T.-L. Ashman
W. Carson
S. Kalisz
V. Oke
C. Partanen
S. Tonsor
B. Traw

Science Education
A. Bledsoe
K. Curto
L. Daniels
S. Godfrey
N. Kaufmann
C. LaFave
J. Newman
E. Polinko
M. Popa
L. Roberts
T. Seiflein
R. Sherwin
A. Slinskey Legg

Structural Biology
M. Grabe
J. Hempel
R. Hendrix
L. Jen-Jacobson
J. Rosenberg
A. VanDemark

Former Faculty

Photo of Dr.
Duda

Structure and Assembly of Bacteriophages

Research Assistant Professor

Dr. Duda received his Ph.D. in 1983 with Fred Eiserling at the University of California, Los Angeles, performed his postdoctoral studies with Roger Hendrix at the University of Pittsburgh, and joined the Department in 2000.

Currently, Dr. Duda is not accepting graduate students in his laboratory. Dr. Duda is accepting undergraduate researchers, and does sponsor students in other laboratories.

Professional Interests - Publications - Contact Information - Lab Personnel

Professional Interests of Robert Duda

My research program has revolved around the use of bacteriophages as model systems to learn how proteins interact with and assemble together with other proteins. We are particularly interested in the genetic regulation of the assembly of the structural components of phages because they large and interesting protein complexes that use covalent and conformational changes to regulate their catalytic activities and assembly interactions.

In 1988 I joined a project with Roger Hendrix to decipher how and why an apparently ordinary, lambda-like bacteriophage called HK97 had covalently cross-linked capsid proteins. Our findings show that the bacteriophage HK97 capsid protein is a remarkable dynamic protein machine that undergoes multiple post-translational conformational changes and covalent modifications during maturation. The end result of these modifications is a monolithic shell composed of protein chainmail, an entirely unanticipated novel protein architecture.

During assembly, the HK97 capsid protein binds to chaperonins, assembles into hexamers and pentamers, co-assembles with additional minor proteins, is cleaved, and finally is topologically interlinked and covalently bonded to its neighbors. We developed a variety of tools to aid these studies, including systems for producing wild-type and mutant structures, protocols for purification of these structures, in vitro protocols for many of the maturation steps, and native and denaturing gel assay systems for monitoring assembly, cleavage, expansion and cross-linking. An important element in bringing the HK97 system to the forefront has been a set of highly successful collaborations.

We collaborate with Alasdair Steven's lab at the NIH, where studies with microscopist Naiqian Cheng and computational biophysicist James Conway have led to important insights into the structural changes during HK97 capsid morphogenesis. A ground-breaking collaboration with virus crystallographers Jack Johnson and William Wikoff at The Scripps Research Institute has produced the first X-ray structure of a capsid of a large dsDNA bacteriophage capsid. A catalog of existing mutations have been mapped onto the new x-ray structure and we are trying to interpret their phenotypes in light of the structure, with some success. Some new mutants have been designed and a few created to test some ideas about the mechanism of formation of the covalent cross-links that form during maturation. In other work, the HK97 maturation protease has just been purified and found to be active in vitro; this represents a good start to a project to determine how the protease is incorporated into the assembling capsid and how its activity is turned on at the right time.

Publication Archive
36 Citations
34 Abstracts
19 PDFs

Recent Publications of Robert Duda

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) Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM. Structure 14:1655-1665 (PDF Reprint: 3.0 MB)

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) Time-resolved molecular dynamics of bacteriophage HK97 capsid maturation interpreted by electron cryo-microscopy and X-ray crystallography. J. Struct. Biol. 153:300-306 (PDF Reprint: 1.0 MB)

Ross, P.D., J.F. Conway, N. Cheng, L. Dierkes, B.A. Firek, R.W. Hendrix, A.C. Steven, and R.L. Duda (2006) A Free Energy Cascade with Locks Drives Assembly and Maturation of Bacteriophage HK97 Capsid. J. Mol. Biol. 364:512-525 (PDF Reprint: 1.8 MB)

Duda, R.L., R.W. Hendrix, W.M. Huang, and J.F. Conway (2006) Shared architecture of bacteriophage SPO1 and herpesvirus capsids. Curr. Biol. 16:440

Ross, P.D., N. Cheng, J.F. Conway, B.A. Firek, R.W. Hendrix, R.L. Duda, and A.C. Steven (2005) Crosslinking renders bacteriophage HK97 capsid maturation irreversible and effects an essential stabilization. EMBO J 24:1352-1363 (PDF Reprint: 645 kb)

Li, Y., J.F. Conway, N. Cheng, A.C. Steven, R.W. Hendrix, and R.L. Duda (2005) Control of virus assembly: HK97 "Whiffleball" mutant capsids without pentons. J. Mol. Biol. 348:167-182 (PDF Reprint: 1.0 MB)

Lee, K.K., H. Tsuruta, R.W. Hendrix, R.L. Duda, and J.E. Johnson (2005) Cooperative reorganization of a 420 subunit virus capsid. J. Mol. Biol. 352:723-735 (PDF Reprint: 400 kb)

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

Lee, K.K., L. Gan, H. Tsuruta, R.W. Hendrix, R.L. Duda, and J.E. Johnson (2004) Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid. J. Mol. Biol. 340:419-433 (PDF Reprint: 627 kb)

Gan, L., J.F. Conway, B.A. Firek, N. Cheng, R.W. Hendrix, A.C. Steven, J.E. Johnson, and R.L. Duda (2004) Control of crosslinking by quaternary structure changes during bacteriophage HK97 maturation. Mol. Cell 14:559-569 (PDF Reprint: 635 kb)

Benevides, J.M., P. Bondre, R.L. Duda, R.W. Hendrix, and G.J. .J.r. Thomas (2004) Domain structures and roles in bacteriophage HK97 capsid assembly and maturation. Biochemistry 43:5428-5436 (PDF Reprint: 8 kb)

Gan, L., J.F. Conway, B.A. Firek, N. Cheng, R.W. Hendrix, A.C. Steven, J.E. Johnson, and R.L. Duda (2004) Control of crosslinking by quaternary structure changes during bacteriophage HK97 maturation. Mol. Cell 14:559-569

Lee, K.K., L. Gan, H. Tsuruta, R.W. Hendrix, R.L. Duda, and J.E. Johnson (2004) Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid. J. Mol. Biol. 340:419-433 (PDF Reprint: 627 kb)

Xu, J., R.W. Hendrix, and R.L. Duda (2004) Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell 16:11-21 (PDF Reprint: 237 kb)

Helgstrand, C., W.R. Wikoff, R.L. Duda, R.W. Hendrix, J.E. Johnson, and L. Liljas (2003) The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution. J. Mol. Biol. 334:885-899 (PDF Reprint: 5.2 MB)

Wikoff, W.R., Z. Che, R.L. Duda, R.W. Hendrix, and J.E. Johnson (2003) Crystallization and preliminary analysis of a dsDNA bacteriophage capsid intermediate: Prohead II of HK97. Acta Crystallogr. D 59:2060-2064 (PDF Reprint: 799 kb)

How to Contact Robert Duda

US Mail
University of Pittsburgh
Department of Biological Sciences
347D Crawford Hall
4249 Fifth Avenue
Pittsburgh, PA 15260

Phone, FAX, Internet
Office : (412) 624-4651
Lab : (412) 624-4651
FAX : (412) 624-4759
Email : duda+@pitt.edu
Web : http://www.pitt.edu/~duda

This Site is maintained by the Bioscience Webmaster; this page was last modified 5 October 2008