Selected Publications

2005
Cunningham E.L. and Berger J.M., "Unraveling the early steps of prokaryotic replication," Current Opinion in Structural Biology, 15: 68-76, 2005.

Skordalakes E., Brogan A.P., Park B.S., Kohn H., and Berger J.M., "Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin," Structure, 13: 99-109, 2005.

Zhang R., Poustovoitov M.V., Ye X., Santos H.A., Chen W., Daganzo, S.M., Erzberger J.P., Serebriiskii I.G., Canutescu A.A., Dunbrack R.L., Pehrson J.R., Berger J.M., Kaufman P.D., and Adams P.D., "Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA," Dev Cell, 8:19-30, 2005.

2004
Weirich C.S., Erzberger J.P., Berger J.M., Weis K.,  "The N-Terminal Domain of Nup159 Forms a β-Propeller that Functions in mRNA Export by Tethering the Helicase Dbp5 to the Nuclear Pore," Mol Cell, 16: 749-760, 2004.

Chow M.A., McElroy K.E., Corbett K.D., Berger J.M., Kirsch J.F., "Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase," Biochemistry, 43: 12780-12787, 2004.

Capaldi, S.A. and Berger, J.M., "Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus," Nucleic Acids Res, 32: 4821-4832, 2004.

Abbate E.A., Berger J.M., Botchan M.R., "The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2," Genes Dev,. 18: 1981-96, 2004.

Mougous J.D., Petzold C.J., Senaratne R.H., Lee D.H., Akey D.L., Lin F.L., Munchel S.E., Pratt M.R., Riley L.W., Leary J.A., Berger J.M., Bertozzi C.R., “Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis,” Nat Struct Mol Biol, 11: 721-729, 2004.

Corbett, K.D. and Berger, J.M., “Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases,” Annu Rev Biophys Biomol Struct, 33: 94-118, 2004.

Corbett, K.D., Schultzaberger, R.K., Berger, J.M., “The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold,” PNAS, 101: 7293-7298, 2004.

2003
Daganzo SM, Erzberger JP, Lam WM, Skordalakes E, Zhang R, Franco AA, Brill SJ, Adams PD, Berger JM, Kaufman PD., “Structure and function of the conserved core of histone deposition protein Asf1,” Curr. Biol., 13: 2148-2158, 2003.

Classen, S., Olland, E., and Berger, J.M., “Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187,” PNAS, 100: 10692-10634, 2003.

Skordalakes, E. and Berger, J.M., “Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading,” Cell, 114: 135-146, 2003.

Corbett, K.D. and Berger, J.M., “Emerging roles for plant topoisomerase VI,” Chemistry & Biology, 10: 107-111, 2003.

Corbett, K.D. and Berger, J.M., “Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution,” EMBO J., 22:151-163, 2003.

2002
Hansen, C.L., Skordalakes, E., Berger, J.M., Quake, S.R., “A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion,” Proc. Natl. Acad. Sci. USA, 99:16531-16536, 2002.

Erzberger, J.P., Pirruccello, M., and Berger, J.M., “The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation”, EMBO J., 21: 4763-4773, 2002.

Diaz RL, Alcid AD, Berger JM, Keeney S., “Identification of residues in yeast spo11p critical for meiotic DNA double-strand break formation”, Mol Cell Biol., 22:1106-15, 2002.

Robic S, Berger JM, and Marqusee S., “Contributions of folding cores to the thermostabilities of two ribonucleases H”, Protein Sci., 11:381-9, 2002.

2001
Keck J.L. and Berger J.M., “Primus inter pares”, News and Views for Nat. Struct. Biol. 8: 2-4, 2001.

2000
Goedken E.R., Keck J.L., Berger J.M., and Marqusee S, “Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI”, Protein Sci., 9: 1914-21, 2000.

Liu, J., Smith, C.L., DeRyckere, D., DeAngelis, K., Martin, G.S., and Berger, J.M., “Structure and Function of Cdc6/Cdc18: Implications for Origin Recognition and Checkpoint Control”, Mol. Cell, 6: 637-648, 2000.

Minor, D.L., Lin, Y.-F., Mobley, B.C., Avelar, A., Jan, Y.N., Jan, L.Y., and Berger, J.M., “The polar T1 interface is linked to conformational changes that open the voltage-gated potassium channel”, Cell, 102: 657–670, 2000.

Keck, J.L., Roche, D.D., Lynch, A.S., and Berger, J.M., “Structure of the RNA polymerase domain of E. coli primase,” Science, 287: 2482-2486, 2000 (Accompanying Commentary, pg. 2435-2436).

Keck,. J.L. and Berger, J.M., “DNA replication at high resolution”, Review for Chemistry & Biology, 7: R63-R71, 2000.

1999
Nichols, M.D., DeAngelis, K., Keck, J.L., and Berger, J.M., "Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11", EMBO J., 18: 6177-6188, 1999.

Keck, J.L. and Berger, J.M., "Enzymes that push DNA around", News and Views for Nature Structural Biology, 6: 900-2, 1999.

Fass, D., Bogden, C. E., and Berger, J. M., "Crystal Structure of the N-Terminal Domain of the DnaB Hexameric Helicase", Structure, 7:691-698, 1999.

Bogden, C.E., Fass D., Bergman, N., Nichols, M.D., and Berger, J.M., "The Structural Basis for Terminator Recognition by the Rho Transcription Termination Factor", Molecular Cell, 3: 487-493,  1999.

Fass, D., Bogden, C.E., and Berger, J.M., "Quaternary Changes in Topoisomerase II may Direct Orthogonal Movement of Two DNA Strands", Nature Structural Biology, 6:322-326, 1999.

Su, L., Chen, L., Egli, M., Berger, J. M., Rich, A., "Minor Groove RNA triplex in the Crystal Structure of a Ribosomal Frameshifting Viral Pseudoknot", Nature Structural Biology, 6: 285-292, 1999. 

1998
Berger, J.M., "Structure of DNA Topoisomerases", in "DNA Topoisomerases and Topoisomerase-Targeted Drugs", Biochemica et Biophysica Acta, 1400: 3-18, 1998.

Berger, J.M., Fass, D., Wang, J.C., and Harrison, S.C., "Structural Similarities Between Topoisomerases that Cleave One or Both Strands of DNA", Proc. Nat. Acad. Sci. USA, 95: 7876-7881, 1998.

Singh, M., Berger, B., Kim, P.S., Berger, J.M., and Cochran, A.G., "Computational Learning Reveals High-Likelihood Coiled Coils in Histidine Kinase Linker Domains", Proc. Nat. Acad. Sci. USA, 95: 2738-2743, 1998. 

Berger, J.M., "Type II DNA Topoisomerases", Curr. Op. Struct. Biol., 8: 26-32, 1998.

1997
Fass, D., Davey, R.A., Hamson, C.A., Kim, P.S., Cunningham, J., and Berger, J.M., "Structure of a Murine Leukemia Virus Receptor-Binding Glycoprotein at 2.0 A Resolution", Science, 277: 1662-1666, 1997.

Fass, D., Blacklow, S., Kim, P.S., and Berger, J.M., "Molecular Basis of Familial Hypercholesterolemia from Structure of LDL Receptor Module", Nature, 388: 691-693, 1997.

Chan, D. C., Fass., D.F., Berger, J. M., Kim, P.S., "Core Structure of gp41 from the HIV Envelope Glycoprotein", Cell, 89: 263-273, 1997.

1996
Roca, J., Berger, J.M., Harrison, S.C., and Wang, J.C., "DNA Transport by a Type II Topoisomerase: Direct Evidence for a Two-Gate Mechanism", Proc. Nat. Acad. Sci. USA, 93: 4057-4062, 1996.

Berger, J.M. and Wang, J.C., "Recent Developments in DNA Topoisomerase II Structure and Mechanism", Curr. Op. Struct. Biol., 6: 84-90, 1996.

Berger, J.M., Gamblin, S.J., Harrison, S.C., and Wang, J.C., "Structure and mechanism of DNA topoisomerase II", Nature, 379: 225-232, 1996.