Department of Biomolecular Chemistry, UW School of Medicine and Public Health

Publications

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Peer-Reviewed Research Manuscripts

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2020

  1. Voter, AF, Callaghan, MM, Tippana, R, Myong, S, Dillard, JP & Keck, JL (2020) “Antigenic variation in Neisseria gonorrheae occurs independently of RecQ-mediated unwinding of the pilE G-quadruplex” Journal of Bacteriology 202 (3), e00607-19.
  2. Dubiel K, Henry C, Spenkelink LM, Kozlov AG, Wood EA, Jergic S, Dixon NE, van Oijen AM, Cox MM, Lohman TM, Sandler SJ, Keck JL (2020) “Development of a Single-Stranded DNA-binding Protein Fluorescent Fusion Toolbox” Nucleic Acids Research 48 (11), 6053-6067.

2019

  1. Anderson BW, Liu K, Wolak C, Dubiel K, She F, Satyshur KA, Keck JL, Wang JD (2019) “Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction” ELife.
  2. Windgassen, TA, Leroux, M, Sandler, SJ, Keck, JL (2019) “Function of a strand-separation pin element in the PriA DNA replication restart helicase” Journal of Biological Chemistry 294, 2801-2814.
  3. Liu, S, Alnammi, M, Ericksen, SS, Voter, AF, Ananiev GE, Keck JL, Hoffman, FM, Wildman SA, Gitter A (2019) “Practical Model Selection for Prospective Virtual Screening” Journal of Chemical Information and Modeling 59, 282-293.
  4. Dubiel, K, Myers, AR, Kozlov, AG, Yang, O, Zhang, J, Ha, T, Lohman, TM, Keck, JL (2019) “Structural mechanisms of cooperative DNA binding by bacterial single-stranded DNA-binding proteins” Journal of Molecular Biology 431, 282-293.

2018

  1. Voter, AF, Qui, Y, Tippana, R, Myong, S, Keck, JL (2018) “A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases” Nature Communications 9.
  2. Windgassen, TA, Leroux, M, Satyshur, KA, Sandler, SJ, Keck, JL (2018) “Structure-specific DNA replication fork recognition directs helicase and replication restart activities of the PriA DNA helicase” Proceedings of the National Academy of Sciences 115, E9075-E9084.
  3. Bagchi, D, Manosas, M, Zhang, W, Manthei, KA, Hodeib, S, Ducos, B, Keck, JL, Croquette, V (2018) “Single molecule kinetics uncover roles for E. coli RecQ DNA helicase domains and interactions with SSB” Nucleic Acids Research 46, 8500-8515.
  4. Voter, AF, Killoran, MP, Anavive, GE, Wildman, S, Hoffmann, FM & Keck, JL (2018) “A high-throughput screening strategy to identify inhibitors of SSB protein-protein interactions in an academic screening facility” SLAS Discovery 23, 94-101.

2016

  1. Windgassen, TA, Keck, JL (2016) “An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase” Nucleic Acids Research 44, 9745-9757.
  2. Leite, WC, Galvao, CW, Saab, SC, Iulek, J, Etto, RM, Steffens, MBR, Chitteni-Pattu, S, Stanage, T, Keck, JL & Cox, MM (2016) “Structural and functional studies of H. seropedicae RecA protein – insights into the polymerization of RecA protein as nucleoprotein filament” PLOS ONE 11, e0159871.
  3. Wessel, SR, Cornilescu, CC, Cornilescu, G, Sandler, SJ, Markley, JL & Keck, JL (2016) “Structure and function of the PriC DNA replication restart protein” Journal of Biological Chemistry 291, 18384-18396.
  4. Voter, AF, Manthei, KA & Keck, JL (2016) “A high throughput screening strategy to identify protein-protein interaction inhibitors that block the Fanconi anemia DNA repair pathway” Journal of Biomolecular Screening 21, 626-633.

2015

  1. Petzold, C, Marceau, AH, Miller, KH, Marqusee, S & Keck, JL (2015) “Interaction with single-stranded DNA-binding protein stimulates Escherichia coli ribonuclease HI enzymatic activity” Journal of Biological Chemistry 290, 14626-14636.
  2. Manthei, KA, Hill, MC, Burke, JE, Butcher, SE & Keck, JL (2015) “Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases” Proceedings of the National Academy of Sciences 114, 4292-4297.
  3. Liu, K, Krasny, K, Myers, AR, Satyshur, KA, Keck, JL & Wang, JD (2015) “Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp” Molecular Cell 57, 735-749.

2014

  1. Walsh, BW, Bolz, SA, Wessel, SR, Schroeder, JW, Keck, JL & Simmons, LA (2014) “RecD2 helicase limits replication fork stress in Bacillus subtilis” Journal of Bacteriology 196, 1359-1368.
  2. Bhattacharyya, B, George, NP, Zhou, R, Jani, N, Wessel, SR, Sandler, SJ, Ha, T & Keck, JL (2014) “Structural mechanisms of PriA-mediated DNA replication restart” Proceedings of the National Academy of Sciences 111, 1373-1378.

2013

  1. Wessel, SR, Marceau, AH, Massoni, SC, Zhou, R, Ha, T, Sandler, SJ & Keck, JL (2013) “PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein” Journal of Biological Chemistry 288, 17569-17578.
  2. Cahoon, LA, Manthei, KA, Rotman, E, Keck, JL & Seifert HS (2013) “Neisseria gonorrhoeae RecQ helicase HRDC domains are essential for efficient binding and unwinding of the pilE guanine quartet structure required for pilin antigenic variation” Journal of Bacteriology 195, 2255-2261.
  3. Marceau, AH, Bernstein, DA, Walsh, BW, Shapiro, W, Simmons, LA & Keck, JL (2013) “Protein interactions in genome maintenance as novel antibacterial targets” PLOS ONE 8, e58765.
  4. Norais, C, Servant, P, Bouthier-de-la-Tour, C, Coureux, PD, Guerin, P, Dulberger, CL, Satyshur, KA, Keck, JL, Armengaud, J, Cox, MM & Sommer, S (2013) “The Deinococcus radiodurans DR1245, a DdrB partner homologous to YbjN proteins and reminiscent of Type III secretion system chaperones” PLOS ONE 8, e56558.

2012

  1. Rymer, RU, Solorio, FA, Tehanchi, AK, Chu, C, Keck, JL, Corn, JE, Wang, JD & Berger, JM (2012) “Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to bacterial DnaG-type primases” Structure 20, 1478-1489.
  2. George, NP, Ngo, KV, Chitteni-Pattu, S, Norais, CA, Battista, JR, Cox, MM & Keck, JL (2012) “Structure and cellular dynamics of Deinococcus radiodurans Single-stranded DNA (ssDNA)-binding Protein (SSB)-DNA complexes” Journal of Biological Chemistry 287, 22123-22132.
  3. Yadav T, Carrasco, B, Myers, AR, George, NP, Keck, JL & Alanso, JC (2012) “Genetic recombination in Bacillus subtilis: a division of labor between two single-strand DNA-binding proteins” Nucleic Acids Research 40, 5546-5559.
  4. Hoadley, KA, Xue, Y, Ling, C, Takata, M, Wang, W & Keck JL (2012) “Defining the molecular interface that connects the Fanconi Anemia protein FANCM to the Bloom Syndrome dissolvasome” Proceedings of the National Academy of Sciences 109, 4437-4442.
  5. Smith, BC, Anderson, MA, Hoadley, KA, Cleland, WW, Keck, JL & Denu, JM (2012) “Structural and kinetic isotope effects studies of Nicotinamidase (Pnc1) from Saccharomyces cerevisiae” Biochemistry 51, 243-256.

2011

  1. Lindner, SE, Llinas, M, Keck JL & Kappe, SHI (2011) “The primase domain of PfPrex is a proteolytically matured, essential enzyme of the apicoplast” Molecular and Biochemical Parasitology 180, 69-75.
  2. Marceau, AH, Massoni, SC, Soon, B, George, NP, Marians, KJ, Sandler, SJ & Keck, JL (2011) “Structure of the SSB-DNA polymerase III interface and its role in DNA replication” EMBO Journal 30, 4236-4247.
  3. Lu, D, Myers, AR, George, NP & Keck, JL (2011) “Mechanism of Exonuclease I stimulation by the single-stranded DNA-binding protein” Nucleic Acids Research 39, 6536-6545.
  4. Page, AN, George, NP, Marceau, AH, Cox, MM & Keck, JL (2011) “Structure and biochemical activities of Escherichia coli MgsA” Journal of Biological Chemistry 286, 12075-12085.
  5. Gruenig, MC, Lu, D, Won, SJ, Byers, NM, Manlick, AC, Keck, JL & Cox, MM (2011) “Creating double strand breaks with a novel RecA-dependent nuclease from bacteriophage P1” Journal of Biological Chemistry 286, 8240-8251.

2010

  1. Kolonko, EM, Albaugh, BN, Lindner, SE, Chen, Y, Satyshur, KA, Arnold, KM, Kaufman, PD, Keck, JL & Denu, JM (2010) “Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone” Proceedings of the National Academy of Sciences 107, 20275-20280.
  2. Hoadley, KA, Xu, Y, Xue, D, Satyshur, KA, Wang, W & Keck, JL (2010) “Structure and cellular roles of the RMI core complex from the Bloom syndrome dissolvasome” Structure 18, 1149-1158.
  3. Petrova, V, Satyshur, KA, George, NP, McCaslin, D, Cox, MM & Keck, JL (2010) “X-ray crystal structure of the bacterial conjugation factor PsiB, a negative regulator of RecA” Journal of Biological Chemistry 285, 30615-30621.
  4. Lu, D, Bernstein, DA, Satyshur, KA & Keck, JL (2010) “Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance” Proceedings of the National Academy of Sciences 107, 633-638.
  5. Lindner, SE, De Silva, E., Keck, JL & Llinás, M (2010) “Structural determinants of DNA binding by a P. falciparum ApiAP2 transcriptional regulator” Journal of Molecular Biology 395, 558-567.

2009

  1. Lu, D, Windsor, MA, Gellman, SH & Keck, JL (2009) “Peptide inhibitors identify roles for SSB C-terminal residues in SSB/Exonuclease I complex formation” Biochemistry 48, 6764-6771.
  2. Shereda, RD, Reiter, NJ, Butcher, SE & Keck, JL (2009) “Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB’s C terminus” Journal of Molecular Biology 386, 612-625.
  3. Killoran, MP, Kohler, PL, Dillard, JP & Keck, JL (2009) “RecQ DNA helicase HRDC domains are critical determinants in Neisseria gonorrhoeae pilin antigenic variation and DNA repair” Molecular Microbiology 71, 158-171.

2008

  1. Berndsen, CE, Tsubota, T, Lindner, SE, Holton, JC, Kaufman, PD, Keck, JL & Denu, JM (2008) “Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75” Nature Structural and Molecular Biology 15, 948-956.
  2. Carlson, CB, Keck, JL & Mosher, DF (2008) “The thrombospondin-1 polymorphism Asn700Ser associated with coronary artery disease causes local and long-range changes in protein structure” Journal of Biological Chemistry 283, 20069-20076.
  3. Lu, D & Keck, JL (2008) “Structural basis of E. coli single-stranded DNA-binding protein stimulation of Exonuclease I” Proceedings of the National Academy of Science 105, 9169-9174.
  4. Killoran, MP & Keck, JL (2008) “Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ” Nucleic Acids Research 36, 3139-3149.

2007

  1. Lopper, M, Boonsombat, R, Sandler, SJ & Keck, JL (2007) “A hand-off mechanism for primosome assembly in replication restart” Molecular Cell 26, 781-793.
  2. Shereda, RD, Bernstein, DA & Keck, JL (2007) “A central role for SSB in E. coli RecQ DNA helicase function” Journal of Biological Chemistry 282, 19247-19258.
  3. Horne, WS, Price, JL, Keck, JL & Gellman, SH (2007) “Helix-bundle quaternary structure from α/β-peptide foldamers” Journal of the American Chemical Society 129, 4178-4180.

2006

  1. Hou, Z, Danzer, JR, Fox, CA & Keck, JL (2006) “Structure of the Sir-3 bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 Å resolution” Protein Science 15, 1182-1186.
  2. Killoran, MP & Keck, JL (2006) “Three HRDC domains differentially modulate Deinococcus radiodurans RecQ DNA helicase biochemical activity” Journal of Biological Chemistry 281, 12849-12857.

2005

  1. Zittel, MC & Keck, JL (2005) “Coupling DNA binding and ATP hydrolysis in Escherichia coli RecQ: role of a highly conserved aromatic-rich sequence” Nucleic Acids Research 33, 6982-6991.
  2. Cadman, CJ, Lopper, M, Moon, PB, Keck, JL & McGlynn, P (2005) “PriB stimulates PriA helicase via an interaction with single-stranded DNA” Journal of Biological Chemistry 280, 39693-39700.
  3. Carlson, CB, Bernstein, DA, Annis, DS, Misenheimer, TM, Hannah, BA, Mosher, DF & Keck, JL (2005) “Structure of the calcium-rich signature domain of human thrombospondin-2” Nature Structural and Molecular Biology 12, 910-914.
  4. Bernstein, DA & Keck, JL (2005) “Conferring substrate specificity to DNA helicases – role of the RecQ HRDC domain” Structure 13, 1173-1182.
  5. Wu, L, Chan, KL, Ralf, C, Bernstein, DA, Garcia, PL, Bohr, VA, Vindigni, A, Janscak, P, Keck, JL & Hickson, ID (2005) “The HRDC domain of BLM is required for dissolution of double Holliday junctions” EMBO Journal 24, 2679-2687.
  6. Hou, Z, Bernstein, DA, Fox, CA & Keck, JL (2005) “Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing” Proceedings of the National Academy of Science 102, 8489-8494.

2004

  1. Lopper, M, Holton, JM & Keck, JL (2004) “Crystal structure of PriB, a component of the Escherichia coli primosome” Structure 12, 1967-1975.
  2. Bernstein, DA, Eggington, JM, Killoran, MP, Misic, AM, Cox, MM & Keck, JL (2004) “Crystal structure of the Deinococcus radiodurans single-stranded DNA binding protein suggests a mechanism for coping with DNA damage” Proceedings of the National Academy of Science 101, 8575-8580.
  3. Bose, ME, McConnell, KH, Gardner-Aukema, KA, Muller, U, Weinreich, M, Keck, JL & Fox, CA (2004) “The Origin Recognition Complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain” Molecular and Cell Biology 24, 774-786.

2003

  1. Bernstein, DA, Zittel, MC & Keck, JL (2003) “High-resolution structure of the E. coli RecQ helicase catalytic core” EMBO Journal 22, 4910-4921.
  2. Bernstein, DA & Keck, JL (2003) “Domain mapping of Escherichia coli RecQ defines the roles of conserved amino- and carboxyl-terminal regions in the RecQ family” Nucleic Acids Research 31, 2778-2785.

Pre-UW-Madison

  1. Keck JL, Berger JM. (2001) “Primus inter pares (first among equals)” Nat Struct Biol 8, 2-4.
  2. Goedken ER, Keck JL, Berger JM, Marqusee S. (2000) “Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI” Protein Sci 9, 1914-1921.
  3. Keck JL, Roche DD, Lynch AS, Berger JM. (2000) “Structure of the RNA polymerase domain of E. coli primase” Science 287, 2482-2486.
  4. Keck JL, Berger JM. (2000) “DNA replication at high resolution” Chem Biol. 7, R63-71
  5. Nichols MD, DeAngelis K, Keck JL, Berger JM. (1999) “Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11” EMBO 18, 6177-6188.
  6. Keck JL, Berger JM. (1999) “Enzymes that push DNA around” Nat Struct Biol 6, 900-902.
  7. Bennett RJ, Keck JL, Wang JC. (1999) “Binding specificity determines polarity of DNA unwinding by the Sgs1 protein of S. cerevisiae” J Mol Biol 289, 235-248.
  8. Keck JL, Goedken ER, Marqusee S. (1998) “Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition” J Biol Chem 273, 34128-34133.
  9. Keck JL, Marqusee S. (1996) “The putative substrate recognition loop of Escherichia coli ribonuclease H is not essential for activity” J Biol Chem 271, 19883-19887.
  10. Keck JL, Marqusee S. (1996) “Substitution of a highly basic helix/loop sequence into the RNase H domain of human immunodeficiency virus reverse transcriptase restores its Mn(2+)-dependent RNase H activity” Proc Natl Acad Sci 92, 2740-2744.

Reviews and Book Chapters

  1. Windgassen, TA, Wessel, SR, Bhattacharyya, B & Keck, JL (2018) “Mechanisms of bacterial DNA replication restart” Nucleic Acids Research 46, 504-519.
  2. Voter, AV & Keck, JL (2018) “Development of protein-protein interaction inhibitors for the treatment of infectious diseases” Advances in Protein Chemistry and Structural Biology: Protein-protein interactions in human disease, Part B. 111,197-217, (Elsevier Press, Rossen Donev, editor). ISBN: 978-0-12-814342-1.
  3. Bhattacharyya, B & Keck, JL (2014) “Grip it and rip it: structural mechanisms of DNA helicase binding and unwinding” Protein Science 23, 1498-1507. (peer reviewed)
    -Selected by the editor as a featured article.
  4. Manthei, KA & Keck, JL (2013) “The BLM dissolvasome in DNA replication and repair” Cellular and Molecular Life Sciences 70, 4067-4084. (peer reviewed)
  5. Hoadley, KA & Keck, JL (2010) “Werner helicase wings DNA binding” Structure (Preview) 18, 149-151.
  6. Cox, MM, Keck, JL & Battista, JR (2010) “Rising from the ashes: DNA repair in Deinococcus radiodurans” PLOS Genetics (Perspective) 6, e1000815.
  7. George, NP & Keck, JL (2009) “SSB slips and slides on DNA” Nature (News & Views) 461, 1067-1068.
  8. Shereda, RD, Kozlov, AG, Lohman, TM, Cox, MM & Keck, JL (2008) “SSB as an organizer/mobilizer of genome maintenance complexes” Critical Reviews in Biochemistry and Molecular Biology 43, 289-318. (peer reviewed)
  9. Lopper, M & Keck, JL (2007) “Protein-protein interactions: identification” Encyclopedia of Life Sciences (available on-line).
  10. Gourse, RL & Keck, JL (2007) “Magic spot casts a spell on replication by inhibiting DNA primase” Cell, 128, 833-834.
  11. Killoran, MP & Keck, JL (2006) “Sit down, relax, and unwind: structural and functional mechanisms of RecQ DNA helicases” Nucleic Acids Research 34, 4098-4105. (peer reviewed)
  12. Bennett, RJ & Keck, JL (2004) “Structure and Function of RecQ DNA Helicases” Critical Reviews in Biochemistry and Molecular Biology 39, 79-97. (peer reviewed)
  13. Keck, JL & Berger, JM (2001) “Primus inter pares (First among equals)” Nature Structural Biology 10, 2-4.
  14. Keck, JL & Berger, JM (2000) “DNA replication at high resolution” Chemistry & Biology 7, R63-R71. (peer reviewed)
  15. Keck, JL & Berger, JM (1999) “Enzymes that push DNA around” Nature Structural Biology 8, 900-902.

Books

  1. “Single-Stranded DNA Binding Proteins: Methods and Protocols” (2012) James L. Keck, volume editor, Methods in Molecular Biology, 922 (Humana Press, John Walker, series editor). ISBN: 978-1-62703-031-1.

Patents

  1. US 8,785,157. Gruenig, MC, Keck, JL & Cox, MM “Method for using Ref protein as a targeted RecA-dependent nuclease” (July 22, 2014).
  2. US 8,415,393. Bernstein, DA & Keck, JL “Antibacterial drug targeting of genome maintenance interfaces” (April 9, 2013).