James M. Berger - Publications

Affiliations: 
Biophysics and Biophysical Chemistry Johns Hopkins University, Baltimore, MD 
 University of California, Berkeley, Berkeley, CA 
Area:
Biochemistry, Biophysics and Structural Biology
Website:
http://biophysics.med.jhmi.edu/BIOPHYS/berger.html

158 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A. Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome. Cell Reports. 28: 2673-2688.e8. PMID 31484077 DOI: 10.1016/j.celrep.2019.07.104  0.4
2019 Blower TR, Bandak A, Lee ASY, Austin CA, Nitiss JL, Berger JM. A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents. Nucleic Acids Research. PMID 31287876 DOI: 10.1093/nar/gkz579  0.4
2019 Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q, Berger JM. Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA. Molecular Cell. PMID 30797687 DOI: 10.1016/j.molcel.2019.01.023  0.36
2019 Lawson MR, Berger JM. Tuning the sequence specificity of a transcription terminator. Current Genetics. PMID 30739200 DOI: 10.1007/s00294-019-00939-1  0.32
2018 Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM. Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Molecular Cell. PMID 30122535 DOI: 10.1016/j.molcel.2018.07.014  0.32
2018 Gibson EG, Blower TR, Cacho M, Bax BD, Berger JM, Osheroff N. Mechanism of Action of Mycobacterium tuberculosis Gyrase Inhibitors: A Novel Class of Gyrase Poisons. Acs Infectious Diseases. PMID 29746087 DOI: 10.1021/acsinfecdis.8b00035  0.44
2018 Basu A, Hobson M, Lebel P, Fernandes LE, Tretter EM, Berger JM, Bryant Z. Dynamic coupling between conformations and nucleotide states in DNA gyrase. Nature Chemical Biology. PMID 29662209 DOI: 10.1038/s41589-018-0037-0  1
2018 Wendorff TJ, Berger JM. Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage. Elife. 7. PMID 29595473 DOI: 10.7554/eLife.31724  0.4
2017 Lee JH, Wendorff TJ, Berger JM. Resveratrol: a novel type of topoisomerase II inhibitor. The Journal of Biological Chemistry. PMID 29074616 DOI: 10.1074/jbc.M117.810580  0.4
2017 Ashley RE, Blower TR, Berger JM, Osheroff N. Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase. Biochemistry. PMID 28921956 DOI: 10.1021/acs.biochem.7b00681  0.44
2016 Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM. Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor. Proceedings of the National Academy of Sciences of the United States of America. PMID 27856760 DOI: 10.1073/pnas.1616745113  1
2016 Lawson MR, Dyer K, Berger JM. Ligand-induced and small-molecule control of substrate loading in a hexameric helicase. Proceedings of the National Academy of Sciences of the United States of America. PMID 27821776 DOI: 10.1073/pnas.1616749113  0.32
2016 Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT. IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. Journal of Applied Crystallography. 49: 1057-1064. PMID 27275148 DOI: 10.1107/S1600576716006683  1
2016 Hood IV, Berger JM. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication. Elife. 5. PMID 27244442 DOI: 10.7554/eLife.14158  1
2016 Hauk G, Berger JM. The role of ATP-dependent machines in regulating genome topology. Current Opinion in Structural Biology. 36: 85-96. PMID 26827284 DOI: 10.1016/j.sbi.2016.01.006  1
2016 Blower TR, Williamson BH, Kerns RJ, Berger JM. Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 26792525 DOI: 10.1073/pnas.1525047113  1
2016 Aldred KJ, Blower TR, Kerns RJ, Berger JM, Osheroff N. Fluoroquinolone interactions with Mycobacterium tuberculosis gyrase: Enhancing drug activity against wild-type and resistant gyrase. Proceedings of the National Academy of Sciences of the United States of America. PMID 26792518 DOI: 10.1073/pnas.1525055113  1
2015 Murray TD, Lyubimov AY, Ogata CM, Vo H, Uervirojnangkoorn M, Brunger AT, Berger JM. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. Acta Crystallographica. Section D, Biological Crystallography. 71: 1987-97. PMID 26457423 DOI: 10.1107/S1399004715015011  1
2015 Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna JA, Vance RE. Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling. Molecular Cell. 59: 891-903. PMID 26300263 DOI: 10.1016/j.molcel.2015.07.022  0.6
2015 Arias-Palomo E, Berger JM. An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment. Cell. 162: 860-71. PMID 26276634 DOI: 10.1016/j.cell.2015.07.037  1
2015 Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Acta Crystallographica. Section D, Biological Crystallography. 71: 928-40. PMID 25849403 DOI: 10.1107/S1399004715002308  1
2015 Bleichert F, Botchan MR, Berger JM. Crystal structure of the eukaryotic origin recognition complex. Nature. 519: 321-6. PMID 25762138 DOI: 10.1038/nature14239  1
2015 Petojevic T, Pesavento JJ, Costa A, Liang J, Wang Z, Berger JM, Botchan MR. Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement. Proceedings of the National Academy of Sciences of the United States of America. 112: E249-58. PMID 25561522 DOI: 10.1073/pnas.1422003112  1
2014 Drlica K, Mustaev A, Towle TR, Luan G, Kerns RJ, Berger JM. Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design. Acs Chemical Biology. 9: 2895-904. PMID 25310082 DOI: 10.1021/cb500629k  1
2014 Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE. DNA recognition by a σ(54) transcriptional activator from Aquifex aeolicus. Journal of Molecular Biology. 426: 3553-68. PMID 25158097 DOI: 10.1016/j.jmb.2014.08.009  1
2014 Kranzusch PJ, Lee AS, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA. Structure-guided reprogramming of human cGAS dinucleotide linkage specificity. Cell. 158: 1011-21. PMID 25131990 DOI: 10.1016/j.cell.2014.07.028  0.6
2014 Costa A, Renault L, Swuec P, Petojevic T, Pesavento JJ, Ilves I, MacLellan-Gibson K, Fleck RA, Botchan MR, Berger JM. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome. Elife. 3: e03273. PMID 25117490 DOI: 10.7554/eLife.03273  1
2014 Malik M, Li L, Zhao X, Kerns RJ, Berger JM, Drlica K. Lethal synergy involving bicyclomycin: an approach for reviving old antibiotics. The Journal of Antimicrobial Chemotherapy. 69: 3227-35. PMID 25085655 DOI: 10.1093/jac/dku285  1
2014 Vos SM, Lyubimov AY, Hershey DM, Schoeffler AJ, Sengupta S, Nagaraja V, Berger JM. Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. Genes & Development. 28: 1485-97. PMID 24990966 DOI: 10.1101/gad.241984.114  1
2014 O'Shea VL, Berger JM. Loading strategies of ring-shaped nucleic acid translocases and helicases. Current Opinion in Structural Biology. 25: 16-24. PMID 24878340 DOI: 10.1016/j.sbi.2013.11.006  1
2014 Mustaev A, Malik M, Zhao X, Kurepina N, Luan G, Oppegard LM, Hiasa H, Marks KR, Kerns RJ, Berger JM, Drlica K. Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding. The Journal of Biological Chemistry. 289: 12300-12. PMID 24497635 DOI: 10.1074/jbc.M113.529164  1
2013 Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM. Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Molecular Cell. 52: 844-54. PMID 24373746 DOI: 10.1016/j.molcel.2013.11.016  1
2013 Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM. A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. Elife. 2: e00882. PMID 24137536 DOI: 10.7554/eLife.00882  1
2013 Vos SM, Stewart NK, Oakley MG, Berger JM. Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo. The Embo Journal. 32: 2950-62. PMID 24097060 DOI: 10.1038/emboj.2013.218  1
2013 Vos SM, Lee I, Berger JM. Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV. Journal of Molecular Biology. 425: 3029-45. PMID 23867279 DOI: 10.1016/j.jmb.2013.04.033  1
2013 Costa A, Hood IV, Berger JM. Mechanisms for initiating cellular DNA replication. Annual Review of Biochemistry. 82: 25-54. PMID 23746253 DOI: 10.1146/annurev-biochem-052610-094414  1
2013 Kranzusch PJ, Lee AS, Berger JM, Doudna JA. Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Reports. 3: 1362-8. PMID 23707061 DOI: 10.1016/j.celrep.2013.05.008  0.6
2013 Jude KM, Hartland A, Berger JM. Real-time detection of DNA topological changes with a fluorescently labeled cruciform. Nucleic Acids Research. 41: e133. PMID 23680786 DOI: 10.1093/nar/gkt413  1
2013 Lee I, Dong KC, Berger JM. The role of DNA bending in type IIA topoisomerase function. Nucleic Acids Research. 41: 5444-56. PMID 23580548 DOI: 10.1093/nar/gkt238  1
2013 Arias-Palomo E, O'Shea VL, Hood IV, Berger JM. The bacterial DnaC helicase loader is a DnaB ring breaker. Cell. 153: 438-48. PMID 23562643 DOI: 10.1016/j.cell.2013.03.006  1
2013 Duderstadt KE, Berger JM. A structural framework for replication origin opening by AAA+ initiation factors. Current Opinion in Structural Biology. 23: 144-53. PMID 23266000 DOI: 10.1016/j.sbi.2012.11.012  1
2013 Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM. A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation Elife. 2013. DOI: 10.7554/eLife.00882.001  1
2012 Schmidt BH, Osheroff N, Berger JM. Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nature Structural & Molecular Biology. 19: 1147-54. PMID 23022727 DOI: 10.1038/nsmb.2388  1
2012 Wendorff TJ, Schmidt BH, Heslop P, Austin CA, Berger JM. The structure of DNA-bound human topoisomerase II alpha: conformational mechanisms for coordinating inter-subunit interactions with DNA cleavage. Journal of Molecular Biology. 424: 109-24. PMID 22841979 DOI: 10.1016/j.jmb.2012.07.014  1
2012 Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE, Keck JL, Wang JD, Berger JM. Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure (London, England : 1993). 20: 1478-89. PMID 22795082 DOI: 10.1016/j.str.2012.05.017  1
2012 Lyubimov AY, Costa A, Bleichert F, Botchan MR, Berger JM. ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote. Proceedings of the National Academy of Sciences of the United States of America. 109: 11999-2004. PMID 22778422 DOI: 10.1073/pnas.1209406109  1
2012 Thomsen ND, Berger JM. Crystallization and X-ray structure determination of an RNA-dependent hexameric helicase. Methods in Enzymology. 511: 171-90. PMID 22713320 DOI: 10.1016/B978-0-12-396546-2.00008-5  1
2012 Basu A, Schoeffler AJ, Berger JM, Bryant Z. ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA. Nature Structural & Molecular Biology. 19: 538-46, S1. PMID 22484318 DOI: 10.1038/nsmb.2278  1
2012 Tretter EM, Berger JM. Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity. The Journal of Biological Chemistry. 287: 18636-44. PMID 22457353 DOI: 10.1074/jbc.M112.345678  1
2012 Tretter EM, Berger JM. Mechanisms for defining supercoiling set point of DNA gyrase orthologs: II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency. The Journal of Biological Chemistry. 287: 18645-54. PMID 22457352 DOI: 10.1074/jbc.M112.345736  1
2012 Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization. Plos One. 7: e32498. PMID 22393408 DOI: 10.1371/journal.pone.0032498  1
2012 Zunder RM, Antczak AJ, Berger JM, Rine J. Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. Proceedings of the National Academy of Sciences of the United States of America. 109: E144-53. PMID 22198837 DOI: 10.1073/pnas.1119095109  1
2011 Leonelli L, Pelton J, Schoeffler A, Dahlbeck D, Berger J, Wemmer DE, Staskawicz B. Structural elucidation and functional characterization of the Hyaloperonospora arabidopsidis effector protein ATR13. Plos Pathogens. 7: e1002428. PMID 22194684 DOI: 10.1371/journal.ppat.1002428  1
2011 Vos SM, Tretter EM, Schmidt BH, Berger JM. All tangled up: how cells direct, manage and exploit topoisomerase function. Nature Reviews. Molecular Cell Biology. 12: 827-41. PMID 22108601 DOI: 10.1038/nrm3228  1
2011 Duderstadt KE, Chuang K, Berger JM. DNA stretching by bacterial initiators promotes replication origin opening. Nature. 478: 209-13. PMID 21964332 DOI: 10.1038/nature10455  1
2011 Bates AD, Berger JM, Maxwell A. The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks. Nucleic Acids Research. 39: 6327-39. PMID 21525132 DOI: 10.1093/nar/gkr258  1
2011 Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K. A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature. 472: 238-42. PMID 21441902 DOI: 10.1038/nature09862  1
2011 Costa A, Ilves I, Tamberg N, Petojevic T, Nogales E, Botchan MR, Berger JM. The structural basis for MCM2-7 helicase activation by GINS and Cdc45. Nature Structural & Molecular Biology. 18: 471-7. PMID 21378962 DOI: 10.1038/nsmb.2004  1
2011 Lyubimov AY, Strycharska M, Berger JM. The nuts and bolts of ring-translocase structure and mechanism. Current Opinion in Structural Biology. 21: 240-8. PMID 21282052 DOI: 10.1016/j.sbi.2011.01.002  1
2011 Dueber EC, Costa A, Corn JE, Bell SD, Berger JM. Molecular determinants of origin discrimination by Orc1 initiators in archaea. Nucleic Acids Research. 39: 3621-31. PMID 21227921 DOI: 10.1093/nar/gkq1308  1
2010 Tretter EM, Lerman JC, Berger JM. A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs. Proceedings of the National Academy of Sciences of the United States of America. 107: 22055-9. PMID 21076033 DOI: 10.1073/pnas.1012938107  1
2010 Li Y, Stewart NK, Berger AJ, Vos S, Schoeffler AJ, Berger JM, Chait BT, Oakley MG. Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction. Proceedings of the National Academy of Sciences of the United States of America. 107: 18832-7. PMID 20921377 DOI: 10.1073/pnas.1008678107  1
2010 Schoeffler AJ, May AP, Berger JM. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Research. 38: 7830-44. PMID 20675723 DOI: 10.1093/nar/gkq665  1
2010 Corbett KD, Berger JM. Structure of the ATP-binding domain of Plasmodium falciparum Hsp90. Proteins. 78: 2738-44. PMID 20635416 DOI: 10.1002/prot.22799  1
2010 Duderstadt KE, Mott ML, Crisona NJ, Chuang K, Yang H, Berger JM. Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. The Journal of Biological Chemistry. 285: 28229-39. PMID 20595381 DOI: 10.1074/jbc.M110.147975  1
2010 Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM. A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature. 465: 641-4. PMID 20485342 DOI: 10.1038/nature08974  1
2010 Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC. THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nature Structural & Molecular Biology. 17: 117-23. PMID 20010837 DOI: 10.1038/nsmb.1742  1
2010 Dedeo MT, Duderstadt KE, Berger JM, Francis MB. Nanoscale protein assemblies from a circular permutant of the tobacco mosaic virus. Nano Letters. 10: 181-6. PMID 19924865 DOI: 10.1021/nl9032395  1
2010 Li Y, Schoeffler AJ, Berger JM, Oakley MG. The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB. Journal of Molecular Biology. 395: 11-9. PMID 19853611 DOI: 10.1016/j.jmb.2009.10.040  1
2010 Tretter EM, Schoeffler AJ, Weisfield SR, Berger JM. Crystal structure of the DNA gyrase GyrA N-terminal domain from Mycobacterium tuberculosis. Proteins. 78: 492-5. PMID 19787774 DOI: 10.1002/prot.22600  1
2010 Botchan M, Berger J. DNA Replication: Making Two Forks from One Prereplication Complex Molecular Cell. 40: 860-861. DOI: 10.1016/j.molcel.2010.12.014  1
2009 Wang AY, Schulze JM, Skordalakes E, Gin JW, Berger JM, Rine J, Kobor MS. Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation. Proceedings of the National Academy of Sciences of the United States of America. 106: 21573-8. PMID 19966225 DOI: 10.1073/pnas.0906539106  1
2009 Thomsen ND, Berger JM. Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell. 139: 523-34. PMID 19879839 DOI: 10.1016/j.cell.2009.08.043  1
2009 Dossani ZY, Weirich CS, Erzberger JP, Berger JM, Weis K. Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1. Proceedings of the National Academy of Sciences of the United States of America. 106: 16251-6. PMID 19805289 DOI: 10.1073/pnas.0902251106  1
2009 Hanes MS, Jude KM, Berger JM, Bonomo RA, Handel TM. Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein. Biochemistry. 48: 9185-93. PMID 19731932 DOI: 10.1021/bi9007963  1
2009 Kintzer AF, Thoren KL, Sterling HJ, Dong KC, Feld GK, Tang II, Zhang TT, Williams ER, Berger JM, Krantz BA. The protective antigen component of anthrax toxin forms functional octameric complexes. Journal of Molecular Biology. 392: 614-29. PMID 19627991 DOI: 10.1016/j.jmb.2009.07.037  1
2009 Stuchinskaya T, Mitchenall LA, Schoeffler AJ, Corbett KD, Berger JM, Bates AD, Maxwell A. How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. Journal of Molecular Biology. 385: 1397-408. PMID 19094994 DOI: 10.1016/j.jmb.2008.11.056  1
2008 Mott ML, Erzberger JP, Coons MM, Berger JM. Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell. 135: 623-34. PMID 19013274 DOI: 10.1016/j.cell.2008.09.058  1
2008 Reynolds KA, Hanes MS, Thomson JM, Antczak AJ, Berger JM, Bonomo RA, Kirsch JF, Handel TM. Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface. Journal of Molecular Biology. 382: 1265-75. PMID 18775544 DOI: 10.1016/j.jmb.2008.05.051  1
2008 Berger JM. SnapShot: nucleic acid helicases and translocases. Cell. 134: 888-888.e1. PMID 18775318 DOI: 10.1016/j.cell.2008.08.027  1
2008 Schoeffler AJ, Berger JM. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Quarterly Reviews of Biophysics. 41: 41-101. PMID 18755053 DOI: 10.1017/S003358350800468X  1
2008 Larson MA, Bressani R, Sayood K, Corn JE, Berger JM, Griep MA, Hinrichs SH. Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines. Nucleic Acids Research. 36: 5260-9. PMID 18684998 DOI: 10.1093/nar/gkn461  1
2008 Thomsen ND, Berger JM. Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases. Molecular Microbiology. 69: 1071-90. PMID 18647240 DOI: 10.1111/j.1365-2958.2008.06364.x  1
2008 Duderstadt KE, Berger JM. AAA+ ATPases in the initiation of DNA replication. Critical Reviews in Biochemistry and Molecular Biology. 43: 163-87. PMID 18568846 DOI: 10.1080/10409230802058296  1
2008 Carlson BL, Ballister ER, Skordalakes E, King DS, Breidenbach MA, Gilmore SA, Berger JM, Bertozzi CR. Function and structure of a prokaryotic formylglycine-generating enzyme. The Journal of Biological Chemistry. 283: 20117-25. PMID 18390551 DOI: 10.1074/jbc.M800217200  1
2008 Corn JE, Pelton JG, Berger JM. Identification of a DNA primase template tracking site redefines the geometry of primer synthesis. Nature Structural & Molecular Biology. 15: 163-9. PMID 18193061 DOI: 10.1038/nsmb.1373  1
2007 Dong KC, Berger JM. Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature. 450: 1201-5. PMID 18097402 DOI: 10.1038/nature06396  1
2007 Murillo AC, Li HY, Alber T, Baker EN, Berger JM, Cherney LT, Cherney MM, Cho YS, Eisenberg D, Garen CR, Goulding CW, Hung LW, Ioerger TR, Jacobs WR, James MN, et al. High throughput crystallography of TB drug targets. Infectious Disorders Drug Targets. 7: 127-39. PMID 17970224 DOI: 10.2174/187152607781001853  1
2007 Dueber EL, Corn JE, Bell SD, Berger JM. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science (New York, N.Y.). 317: 1210-3. PMID 17761879 DOI: 10.1126/science.1143690  1
2007 Corn JE, Berger JM. FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies. Structure (London, England : 1993). 15: 773-80. PMID 17637338 DOI: 10.1016/j.str.2007.05.006  1
2007 Corbett KD, Benedetti P, Berger JM. Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Nature Structural & Molecular Biology. 14: 611-9. PMID 17603498 DOI: 10.1038/nsmb1264  1
2007 Mott ML, Berger JM. DNA replication initiation: mechanisms and regulation in bacteria. Nature Reviews. Microbiology. 5: 343-54. PMID 17435790 DOI: 10.1038/nrmicro1640  1
2007 Douglas AE, Corbett KD, Berger JM, McFadden G, Handel TM. Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl-2. Protein Science : a Publication of the Protein Society. 16: 695-703. PMID 17384234 DOI: 10.1110/ps.062720107  1
2007 Berger JM, Müller CW. Protein-nucleic acid interactions: some assembly required Current Opinion in Structural Biology. 17: 77-79. DOI: 10.1016/j.sbi.2007.01.010  1
2006 Antczak AJ, Tsubota T, Kaufman PD, Berger JM. Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics. Bmc Structural Biology. 6: 26. PMID 17166288 DOI: 10.1186/1472-6807-6-26  1
2006 Skordalakes E, Berger JM. Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell. 127: 553-64. PMID 17081977 DOI: 10.1016/j.cell.2006.08.051  1
2006 Corn JE, Berger JM. Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions. Nucleic Acids Research. 34: 4082-8. PMID 16935873 DOI: 10.1093/nar/gkl363  1
2006 Corbett KD, Berger JM. Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drug radicicol. Nucleic Acids Research. 34: 4269-77. PMID 16920739 DOI: 10.1093/nar/gkl567  1
2006 Erzberger JP, Mott ML, Berger JM. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nature Structural & Molecular Biology. 13: 676-83. PMID 16829961 DOI: 10.1038/nsmb1115  1
2006 Clarey MG, Erzberger JP, Grob P, Leschziner AE, Berger JM, Nogales E, Botchan M. Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. Nature Structural & Molecular Biology. 13: 684-90. PMID 16829958 DOI: 10.1038/nsmb1121  1
2006 Reynolds KA, Thomson JM, Corbett KD, Bethel CR, Berger JM, Kirsch JF, Bonomo RA, Handel TM. Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface. The Journal of Biological Chemistry. 281: 26745-53. PMID 16809340 DOI: 10.1074/jbc.M603878200  1
2006 Weirich CS, Erzberger JP, Flick JS, Berger JM, Thorner J, Weis K. Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nature Cell Biology. 8: 668-76. PMID 16783364 DOI: 10.1038/ncb1424  1
2006 Erzberger JP, Berger JM. Evolutionary relationships and structural mechanisms of AAA+ proteins. Annual Review of Biophysics and Biomolecular Structure. 35: 93-114. PMID 16689629 DOI: 10.1146/annurev.biophys.35.040405.101933  1
2006 Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proceedings of the National Academy of Sciences of the United States of America. 103: 6988-93. PMID 16627621 DOI: 10.1073/pnas.0601676103  1
2006 Hansen CL, Classen S, Berger JM, Quake SR. A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination. Journal of the American Chemical Society. 128: 3142-3. PMID 16522084 DOI: 10.1021/ja0576637  1
2006 Akey D, Martins A, Aniukwu J, Glickman MS, Shuman S, Berger JM. Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D. The Journal of Biological Chemistry. 281: 13412-23. PMID 16476729 DOI: 10.1074/jbc.M513550200  1
2006 Mougous JD, Lee DH, Hubbard SC, Schelle MW, Vocadlo DJ, Berger JM, Bertozzi CR. Molecular basis for G protein control of the prokaryotic ATP sulfurylase. Molecular Cell. 21: 109-22. PMID 16387658 DOI: 10.1016/j.molcel.2005.10.034  1
2005 Corn JE, Pease PJ, Hura GL, Berger JM. Crosstalk between primase subunits can act to regulate primer synthesis in trans. Molecular Cell. 20: 391-401. PMID 16285921 DOI: 10.1016/j.molcel.2005.09.004  1
2005 Schoeffler AJ, Berger JM. Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism. Biochemical Society Transactions. 33: 1465-70. PMID 16246147 DOI: 10.1042/BST20051465  1
2005 Akey DL, Berger JM. Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A. Protein Science : a Publication of the Protein Society. 14: 2744-50. PMID 16155207 DOI: 10.1110/ps.051665905  1
2005 Corbett KD, Schoeffler AJ, Thomsen ND, Berger JM. The structural basis for substrate specificity in DNA topoisomerase IV. Journal of Molecular Biology. 351: 545-61. PMID 16023670 DOI: 10.1016/j.jmb.2005.06.029  1
2005 Corbett KD, Berger JM. Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure (London, England : 1993). 13: 873-82. PMID 15939019 DOI: 10.1016/j.str.2005.03.013  1
2005 Fennell-Fezzie R, Gradia SD, Akey D, Berger JM. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. The Embo Journal. 24: 1921-30. PMID 15902272 DOI: 10.1038/sj.emboj.7600680  1
2005 Cunningham EL, Berger JM. Unraveling the early steps of prokaryotic replication. Current Opinion in Structural Biology. 15: 68-76. PMID 15718136 DOI: 10.1016/j.sbi.2005.01.003  1
2005 Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM. Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. Structure (London, England : 1993). 13: 99-109. PMID 15642265 DOI: 10.1016/j.str.2004.10.013  1
2005 Zhang R, Poustovoitov MV, Ye X, Santos HA, Chen W, Daganzo SM, Erzberger JP, Serebriiskii IG, Canutescu AA, Dunbrack RL, Pehrson JR, Berger JM, Kaufman PD, Adams PD. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Developmental Cell. 8: 19-30. PMID 15621527 DOI: 10.1016/j.devcel.2004.10.019  1
2004 Weirich CS, Erzberger JP, Berger JM, Weis K. The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore. Molecular Cell. 16: 749-60. PMID 15574330 DOI: 10.1016/j.molcel.2004.10.032  1
2004 MacDowell AA, Celestre RS, Howells M, McKinney W, Krupnick J, Cambie D, Domning EE, Duarte RM, Kelez N, Plate DW, Cork CW, Earnest TN, Dickert J, Meigs G, Ralston C, ... ... Berger JM, et al. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. Journal of Synchrotron Radiation. 11: 447-55. PMID 15496731 DOI: 10.1107/S0909049504024835  1
2004 Chow MA, McElroy KE, Corbett KD, Berger JM, Kirsch JF. Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase. Biochemistry. 43: 12780-7. PMID 15461450 DOI: 10.1021/bi0487544  1
2004 Capaldi SA, Berger JM. Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus. Nucleic Acids Research. 32: 4821-32. PMID 15358831 DOI: 10.1093/nar/gkh819  1
2004 Abbate EA, Berger JM, Botchan MR. The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Genes & Development. 18: 1981-96. PMID 15289463 DOI: 10.1101/gad.1220104  1
2004 Mougous JD, Petzold CJ, Senaratne RH, Lee DH, Akey DL, Lin FL, Munchel SE, Pratt MR, Riley LW, Leary JA, Berger JM, Bertozzi CR. Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis. Nature Structural & Molecular Biology. 11: 721-9. PMID 15258569 DOI: 10.1038/nsmb802  1
2004 Corbett KD, Berger JM. Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annual Review of Biophysics and Biomolecular Structure. 33: 95-118. PMID 15139806 DOI: 10.1146/annurev.biophys.33.110502.140357  1
2004 Corbett KD, Shultzaberger RK, Berger JM. The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proceedings of the National Academy of Sciences of the United States of America. 101: 7293-8. PMID 15123801 DOI: 10.1073/pnas.0401595101  1
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. Current Biology : Cb. 13: 2148-58. PMID 14680630 DOI: 10.1016/j.cub.2003.11.027  1
2003 Classen S, Olland S, Berger JM. Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proceedings of the National Academy of Sciences of the United States of America. 100: 10629-34. PMID 12963818 DOI: 10.1073/pnas.1832879100  1
2003 Skordalakes E, Berger JM. Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell. 114: 135-46. PMID 12859904 DOI: 10.1016/S0092-8674(03)00512-9  1
2003 Corbett KD, Berger JM. Emerging roles for plant topoisomerase VI. Chemistry & Biology. 10: 107-11. PMID 12618182 DOI: 10.1016/S1074-5521(03)00027-9  1
2003 Corbett KD, Berger JM. Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution. The Embo Journal. 22: 151-63. PMID 12505993 DOI: 10.1093/emboj/cdg008  1
2002 Hansen CL, Skordalakes E, Berger JM, Quake SR. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proceedings of the National Academy of Sciences of the United States of America. 99: 16531-6. PMID 12486223 DOI: 10.1073/pnas.262485199  1
2002 Erzberger JP, Pirruccello MM, Berger JM. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. The Embo Journal. 21: 4763-73. PMID 12234917 DOI: 10.1093/emboj/cdf496  1
2002 Diaz RL, Alcid AD, Berger JM, Keeney S. Identification of residues in yeast Spo11p critical for meiotic DNA double-strand break formation. Molecular and Cellular Biology. 22: 1106-15. PMID 11809802 DOI: 10.1128/MCB.22.4.1106-1115.2002  1
2002 Robic S, Berger JM, Marqusee S. Contributions of folding cores to the thermostabilities of two ribonucleases H. Protein Science : a Publication of the Protein Society. 11: 381-9. PMID 11790848 DOI: 10.1110/ps.38602  1
2001 Keck JL, Berger JM. Primus inter pares (first among equals). Nature Structural Biology. 8: 2-4. PMID 11135655 DOI: 10.1038/82996  1
2000 Goedken ER, Keck JL, Berger JM, Marqusee S. Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI. Protein Science : a Publication of the Protein Society. 9: 1914-21. PMID 11106164 DOI: 10.1110/ps.9.10.1914  1
2000 Liu J, Smith CL, DeRyckere D, DeAngelis K, Martin GS, Berger JM. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Molecular Cell. 6: 637-48. PMID 11030343  1
2000 Minor DL, Lin YF, Mobley BC, Avelar A, Jan YN, Jan LY, Berger JM. The polar T1 interface is linked to conformational changes that open the voltage-gated potassium channel. Cell. 102: 657-70. PMID 11007484  1
2000 Keck JL, Roche DD, Lynch AS, Berger JM. Structure of the RNA polymerase domain of E. coli primase. Science (New York, N.Y.). 287: 2482-6. PMID 10741967 DOI: 10.1126/science.287.5462.2482  1
2000 Keck JL, Berger JM. DNA replication at high resolution. Chemistry & Biology. 7: R63-71. PMID 10712935 DOI: 10.1016/S1074-5521(00)00094-6  1
1999 Nichols MD, DeAngelis K, Keck JL, Berger JM. Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. The Embo Journal. 18: 6177-88. PMID 10545127 DOI: 10.1093/emboj/18.21.6177  1
1999 Keck JL, Berger JM. Enzymes that push DNA around. Nature Structural Biology. 6: 900-2. PMID 10504717 DOI: 10.1038/13260  1
1999 Fass D, Bogden CE, Berger JM. Crystal structure of the N-terminal domain of the DnaB hexameric helicase. Structure (London, England : 1993). 7: 691-8. PMID 10404598 DOI: 10.1016/S0969-2126(99)80090-2  1
1999 Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM. The structural basis for terminator recognition by the Rho transcription termination factor. Molecular Cell. 3: 487-93. PMID 10230401 DOI: 10.1016/S1097-2765(00)80476-1  1
1999 Fass D, Bogden CE, Berger JM. Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nature Structural Biology. 6: 322-6. PMID 10201398 DOI: 10.1038/7556  1
1999 Su L, Chen L, Egli M, Berger JM, Rich A. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nature Structural Biology. 6: 285-92. PMID 10074948 DOI: 10.1038/6722  1
1998 Berger JM. Structure of DNA topoisomerases. Biochimica Et Biophysica Acta. 1400: 3-18. PMID 9748476 DOI: 10.1016/S0167-4781(98)00124-9  1
1998 Berger JM, Fass D, Wang JC, Harrison SC. Structural similarities between topoisomerases that cleave one or both DNA strands. Proceedings of the National Academy of Sciences of the United States of America. 95: 7876-81. PMID 9653108 DOI: 10.1073/pnas.95.14.7876  1
1998 Berger JM. Type II DNA topoisomerases. Current Opinion in Structural Biology. 8: 26-32. PMID 9519293 DOI: 10.1016/S0959-440X(98)80006-7  1
1998 Singh M, Berger B, Kim PS, Berger JM, Cochran AG. Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proceedings of the National Academy of Sciences of the United States of America. 95: 2738-43. PMID 9501159 DOI: 10.1073/pnas.95.6.2738  1
1997 Fass D, Davey RA, Hamson CA, Kim PS, Cunningham JM, Berger JM. Structure of a murine leukemia virus receptor-binding glycoprotein at 2.0 angstrom resolution. Science (New York, N.Y.). 277: 1662-6. PMID 9287219 DOI: 10.1126/science.277.5332.1662  1
1997 Fass D, Blacklow S, Kim PS, Berger JM. Molecular basis of familial hypercholesterolaemia from structure of LDL receptor module. Nature. 388: 691-3. PMID 9262405 DOI: 10.1038/41798  1
1997 Chan DC, Fass D, Berger JM, Kim PS. Core structure of gp41 from the HIV envelope glycoprotein. Cell. 89: 263-73. PMID 9108481  1
1996 Berger JM, Wang JC. Recent developments in DNA topoisomerase II structure and mechanism. Current Opinion in Structural Biology. 6: 84-90. PMID 8696977 DOI: 10.1016/S0959-440X(96)80099-6  1
1996 Roca J, Berger JM, Harrison SC, Wang JC. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proceedings of the National Academy of Sciences of the United States of America. 93: 4057-62. PMID 8633016 DOI: 10.1073/pnas.93.9.4057  1
1996 Berger JM, Gamblin SJ, Harrison SC, Wang JC. Structure and mechanism of DNA topoisomerase II. Nature. 379: 225-32. PMID 8538787 DOI: 10.1038/379225a0  1
1994 Roca J, Ishida R, Berger JM, Andoh T, Wang JC. Antitumor bisdioxopiperazines inhibit yeast DNA topoisomerase II by trapping the enzyme in the form of a closed protein clamp. Proceedings of the National Academy of Sciences of the United States of America. 91: 1781-5. PMID 8127881  1
1993 Roca J, Berger JM, Wang JC. On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices. The Journal of Biological Chemistry. 268: 14250-5. PMID 8390987  1
1992 Goldenberg DP, Berger JM, Laheru DA, Wooden S, Zhang JX. Genetic dissection of pancreatic trypsin inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 89: 5083-7. PMID 1594616  1
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