Biochemistry
R. Bentley
J. Brodsky
J. Franzen
P. Grabowski
J. Hempel
L. Jen-Jacobson
K. Kiselyov
C. Peebles
J. Rosenberg
A. Schwacha

Cell Biology
J. Brodsky
A. Chung
J. Hildebrand
L. Jacobson
N. Kaufmann
K. Kiselyov
J. Pipas
M.-T. Sáens-Robles
W. Saunders
C. Walsh

Computational Biology
M. Grabe
J. Lawrence
J. Rosenberg

Developmental Biology
G. Campbell
D. Chapman
J. Hildebrand
B. Roman
S. Shostak
B. Stronach
V. Twombly

Ecology
T.-L. Ashman
W. Carson
W. Coffman
S. Kalisz
T. Katzner
R. Relyea
S. Tonsor
B. Traw

Evolution
T.-L. Ashman
A. Bledsoe
S. Kalisz
J. Lawrence
Z.-X. Luo
R. Relyea
S. Shostak
S. Tonsor
B. Traw

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

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

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

Professional Interests - Publications - Contact Information - Lab Personnel

Professional Interests of John Rosenberg

Dr. Rosenberg's group is investigating the relationship between macromolecular structure and function via X-ray Crystallography, Molecular Dynamics and related techniques. The focus has been on sequence-specific recognition of DNA as exemplified by EcoRI endonuclease.

Structure determinations have been carried out for several cocrystalline complexes of EcoRI endonuclease and cognate DNA; other structure determinations are in progress:

1. Structures have been obtained for complexes of the protein with two oligonucleotides that differ outside the EcoRI recognition site. Final refinement and comparison of these structures is in progress.
2. Soaking enzyme-substrate cocrystals in magnesium and manganese activates the catalytic machinery, and structures of the resulting enzyme-product cocrystals have been determined. Final refinement and comparison to the native structure is in progress.
3. The structure of the protein within the complex suggests that the enzyme changes conformation upon binding DNA. Crystals have also been obtained of EcoRI endonuclease in the absence of DNA and determination of their structure is in progress.
4. Crystals of site-directed mutants of the enzyme and crystals of complexes with base analog-containing oligonucleotides have been obtained. Additional crystallizations and structure determinations are anticipated in an attempt to correlate genetic, functional and structural information.

The Rosenberg group is also using molecular dynamics (MD) because many functional questions are inherently dynamical. For example, the DNA is distorted by the enzyme; the energy surface in the vicinity of this EcoRI kink" was investigated by conducting MD simulations. The kinked structure appears to be an example of molecular strain because it is not near an energy minimum. The most credible simulations also suggest that the kinked DNA and B-DNA are not separated by a thermally significant energy barrier. Control simulations of B-DNA yielded the surprising observation that the B-A transition could be influenced by the distribution of counterions around the molecule.

Current computational efforts focus on completing these MD investigations and extending the efforts to simulations of the entire protein-DNA complex. The long term goal is to obtain calculated values for thermodynamic and kinetic parameters that can be compared with experimental values. Once reasonable agreement is obtained, the computational methods are expected to provide insight into the details of the recognition mechanism. Several new crystallographic projects are at an earlier stage:

1. DNA topoisomerases play critical roles in replication and other aspects of DNA metabolism. Collaborative projects have been initiated with Wai Mun Huang (Univ. of Utah) to determine the structure of selected type II topoisomerases and with Saleem Khan (School of Medicine, Univ. of Pittsburgh) to investigate the structure of the RepC protein. Crystals have been obtained of the p52 subunit of T4 topoisomerase II, including probable DNA-protein cocrystals.
2. Bacteriophage P22, a lambdoid virus that infects Salmonella is a well characterized model system for the study of biological assembly processes. In collaboration with Roger Hendrix (this department), the Rosenberg group has obtained crystals of the virus and are currently investigating their utility for structure determination.
3. A nucleic acid structure project focuses on the connections between sequence and structure in DNA and RNA and between structure and function in catalytic RNA.
4. In collaboration with James Pipas (this department), an effort has been initiated to obtain crystals of SV40 large T antigen and/or crystals of selected domains of this protein.

Publication Archive
37 Citations
24 Abstracts
1 PDFs

Recent Publications of John Rosenberg

Sapienza, P.J., J.M. Rosenberg, and L. Jen-Jacobson (2007) Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease. Structure 15:1368-1382

Gopalakrishnan, V., G. Livingston, D. Hennessy, B. Buchanan, and J.M. Rosenberg (2004) Machine-learning techniques for macromolecular crystallization data. Acta Crystallogr. D 60:1705-1716

Klumpp, L.M., A.T. Mackey, C.M. Farrell, J.M. Rosenberg, and S.P. Gilbert (2003) A kinesin switch I arginine to lysine mutation rescues microtubule function. J. Biol. Chem. 278:39059-39067 (PDF Reprint: 547 kb)

Klumpp, L.M., K.M. Brendza, J.M. Rosenberg, A. Hoenger, and S.P. Gilbert (2003) Motor domain mutation traps kinesin as a microtubule rigor complex. Biochemistry 42:2595-2606

Hennessy, D., B. Buchanan, D. Subramanian, P.A. Wilkosz, and J.M. Rosenberg (2000) Statistical methods for the objective design of screening procedures for macromolecular crystallization. Acta Crystallogr. D. 56:817-827

Gopalakrishnan, V., B.G. Buchanan, and J.M. Rosenberg (2000) Intelligent aids for parallel experiment planning and macromolecular crystallization. ISMB 8:171-182

How to Contact John Rosenberg

 
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