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    Hammel, Michal

    TitleBiophysicist Research Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CM, Hammel M, Tainer JA, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure. 2017 Jan 03; 25(1):157-166. PMID: 28052235.
        View in: PubMed
      2. Hammel M, Yu Y, Radhakrishnan SK, Chokshi C, Tsai MS, Matsumoto Y, Kuzdovich M, Remesh SG, Fang S, Tomkinson AE, Lees-Miller SP, Tainer JA. An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex. J Biol Chem. 2016 Dec 30; 291(53):26987-27006. PMID: 27875301.
        View in: PubMed
      3. Nikolaienko RM, Hammel M, Dubreuil V, Zalmai R, Hall DR, Mehzabeen N, Karuppan SJ, Harroch S, Stella SL, Bouyain S. Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues. J Biol Chem. 2016 Oct 07; 291(41):21335-21349. PMID: 27539848.
        View in: PubMed
      4. Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S. HU multimerization shift controls nucleoid compaction. Sci Adv. 2016 07; 2(7):e1600650. PMID: 27482541; PMCID: PMC4966879.
      5. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res. 2016 Jul 08; 44(W1):W424-9. PMID: 27151198; PMCID: PMC4987932.
      6. Hashiguchi T, Fusco ML, Bornholdt ZA, Lee JE, Flyak AI, Matsuoka R, Kohda D, Yanagi Y, Hammel M, Crowe JE, Saphire EO. Structural basis for Marburg virus neutralization by a cross-reactive human antibody. Cell. 2015 Feb 26; 160(5):904-12. PMID: 25723165; PMCID: PMC4344967.
      7. Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer JA. Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst). 2014 May; 17:110-20. PMID: 24656613; PMCID: PMC4102006.
      8. Barta ML, Hickey JM, Anbanandam A, Dyer K, Hammel M, Hefty PS. Atypical response regulator ChxR from Chlamydia trachomatis is structurally poised for DNA binding. PLoS One. 2014; 9(3):e91760. PMID: 24646934; PMCID: PMC3960148.
      9. Lin CS, Chao SY, Hammel M, Nix JC, Tseng HL, Tsou CC, Fei CH, Chiou HS, Jeng US, Lin YS, Chuang WJ, Wu JJ, Wang S. Distinct structural features of the peroxide response regulator from group A Streptococcus drive DNA binding. PLoS One. 2014; 9(2):e89027. PMID: 24586487; PMCID: PMC3931707.
      10. Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer JA, Hura GL. High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol. 2014; 1091:245-58. PMID: 24203338; PMCID: PMC4057279.
      11. Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2014 Jan; 42(Database issue):D336-46. PMID: 24271400; PMCID: PMC3965011.
      12. Zhao W, Saro D, Hammel M, Kwon Y, Xu Y, Rambo RP, Williams GJ, Chi P, Lu L, Pezza RJ, Camerini-Otero RD, Tainer JA, Wang HW, Sung P. Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res. 2014 Jan; 42(2):906-17. PMID: 24150939; PMCID: PMC3902922.
      13. Liu X, Hammel M, He Y, Tainer JA, Jeng US, Zhang L, Wang S, Wang X. Structural insights into the interaction of IL-33 with its receptors. Proc Natl Acad Sci U S A. 2013 Sep 10; 110(37):14918-23. PMID: 23980170; PMCID: PMC3773798.
      14. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J. 2013 Aug 20; 105(4):962-74. PMID: 23972848; PMCID: PMC3752106.
      15. Lee BS, Gapud EJ, Zhang S, Dorsett Y, Bredemeyer A, George R, Callen E, Daniel JA, Osipovich O, Oltz EM, Bassing CH, Nussenzweig A, Lees-Miller S, Hammel M, Chen BP, Sleckman BP. Functional intersection of ATM and DNA-dependent protein kinase catalytic subunit in coding end joining during V(D)J recombination. Mol Cell Biol. 2013 Sep; 33(18):3568-79. PMID: 23836881; PMCID: PMC3753869.
      16. Hura GL, Budworth H, Dyer KN, Rambo RP, Hammel M, McMurray CT, Tainer JA. Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat Methods. 2013 Jun; 10(6):453-4. PMID: 23624664; PMCID: PMC3728378.
      17. Mahaney BL, Hammel M, Meek K, Tainer JA, Lees-Miller SP. XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol. 2013 Feb; 91(1):31-41. PMID: 23442139; PMCID: PMC3725335.
      18. Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr. 2013 Feb 01; 46(Pt 1):1-13. PMID: 23396808.
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      19. Duda DM, Olszewski JL, Tron AE, Hammel M, Lambert LJ, Waddell MB, Mittag T, DeCaprio JA, Schulman BA. Structure of a glomulin-RBX1-CUL1 complex: inhibition of a RING E3 ligase through masking of its E2-binding surface. Mol Cell. 2012 Aug 10; 47(3):371-82. PMID: 22748924; PMCID: PMC3477590.
      20. Hammel M. Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J. 2012 Oct; 41(10):789-99. PMID: 22639100; PMCID: PMC3462898.
      21. Taherbhoy AM, Tait SW, Kaiser SE, Williams AH, Deng A, Nourse A, Hammel M, Kurinov I, Rock CO, Green DR, Schulman BA. Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway. Mol Cell. 2011 Nov 04; 44(3):451-61. PMID: 22055190; PMCID: PMC3277881.
      22. Hammel M, Rey M, Yu Y, Mani RS, Classen S, Liu M, Pique ME, Fang S, Mahaney BL, Weinfeld M, Schriemer DC, Lees-Miller SP, Tainer JA. XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J Biol Chem. 2011 Sep 16; 286(37):32638-50. PMID: 21775435; PMCID: PMC3173232.
      23. Williams GJ, Williams RS, Williams JS, Moncalian G, Arvai AS, Limbo O, Guenther G, SilDas S, Hammel M, Russell P, Tainer JA. ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat Struct Mol Biol. 2011 Apr; 18(4):423-31. PMID: 21441914; PMCID: PMC3118400.
      24. Biersmith BH, Hammel M, Geisbrecht ER, Bouyain S. The immunoglobulin-like domains 1 and 2 of the protein tyrosine phosphatase LAR adopt an unusual horseshoe-like conformation. J Mol Biol. 2011 May 13; 408(4):616-27. PMID: 21402080; PMCID: PMC3086351.
      25. Hammel M, Yu Y, Fang S, Lees-Miller SP, Tainer JA. XLF regulates filament architecture of the XRCC4·ligase IV complex. Structure. 2010 Nov 10; 18(11):1431-42. PMID: 21070942; PMCID: PMC3008546.
      26. Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 2011 Mar; 173(3):461-71. PMID: 20920583; PMCID: PMC3040266.
      27. Chen H, Ricklin D, Hammel M, Garcia BL, McWhorter WJ, Sfyroera G, Wu YQ, Tzekou A, Li S, Geisbrecht BV, Woods VL, Lambris JD. Allosteric inhibition of complement function by a staphylococcal immune evasion protein. Proc Natl Acad Sci U S A. 2010 Oct 12; 107(41):17621-6. PMID: 20876141; PMCID: PMC2955122.
      28. Dray E, Etchin J, Wiese C, Saro D, Williams GJ, Hammel M, Yu X, Galkin VE, Liu D, Tsai MS, Sy SM, Schild D, Egelman E, Chen J, Sung P. Enhancement of RAD51 recombinase activity by the tumor suppressor PALB2. Nat Struct Mol Biol. 2010 Oct; 17(10):1255-9. PMID: 20871616; PMCID: PMC2950913.
      29. Classen S, Rodic I, Holton J, Hura GL, Hammel M, Tainer JA. Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system. J Synchrotron Radiat. 2010 Nov; 17(6):774-81. PMID: 20975223; PMCID: PMC2964114.
      30. Cotner-Gohara E, Kim IK, Hammel M, Tainer JA, Tomkinson AE, Ellenberger T. Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states. Biochemistry. 2010 Jul 27; 49(29):6165-76. PMID: 20518483; PMCID: PMC2922849.
      31. Schneidman-Duhovny D, Hammel M, Sali A. FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W540-4. PMID: 20507903; PMCID: PMC2896111.
      32. Hammel M, Yu Y, Mahaney BL, Cai B, Ye R, Phipps BM, Rambo RP, Hura GL, Pelikan M, So S, Abolfath RM, Chen DJ, Lees-Miller SP, Tainer JA. Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J Biol Chem. 2010 Jan 08; 285(2):1414-23. PMID: 19893054; PMCID: PMC2801267.
      33. Zhuang M, Calabrese MF, Liu J, Waddell MB, Nourse A, Hammel M, Miller DJ, Walden H, Duda DM, Seyedin SN, Hoggard T, Harper JW, White KP, Schulman BA. Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases. Mol Cell. 2009 Oct 09; 36(1):39-50. PMID: 19818708; PMCID: PMC2847577.
      34. Jain R, Hammel M, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Structural insights into yeast DNA polymerase delta by small angle X-ray scattering. J Mol Biol. 2009 Dec 04; 394(3):377-82. PMID: 19818796; PMCID: PMC2790408.
      35. Greenstein AE, Hammel M, Cavazos A, Alber T. Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c. J Biol Chem. 2009 Oct 23; 284(43):29828-35. PMID: 19700407; PMCID: PMC2785613.
      36. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL, Tsutakawa SE, Jenney FE, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MW, Tainer JA. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods. 2009 Aug; 6(8):606-12. PMID: 19620974; PMCID: PMC3094553.
      37. Pelikan M, Hura GL, Hammel M. Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys. 2009 Jun; 28(2):174-89. PMID: 19592714; PMCID: PMC3773563.
      38. Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M, Schulman BA. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell. 2008 Sep 19; 134(6):995-1006. PMID: 18805092; PMCID: PMC2628631.
      39. Fan L, Fuss JO, Cheng QJ, Arvai AS, Hammel M, Roberts VA, Cooper PK, Tainer JA. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell. 2008 May 30; 133(5):789-800. PMID: 18510924; PMCID: PMC3055247.
      40. Hammel M, Nemecek D, Keightley JA, Thomas GJ, Geisbrecht BV. The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution. Protein Sci. 2007 Dec; 16(12):2605-17. PMID: 18029416; PMCID: PMC2222813.
      41. Hammel M, Sfyroera G, Pyrpassopoulos S, Ricklin D, Ramyar KX, Pop M, Jin Z, Lambris JD, Geisbrecht BV. Characterization of Ehp, a secreted complement inhibitory protein from Staphylococcus aureus. J Biol Chem. 2007 Oct 12; 282(41):30051-61. PMID: 17699522.
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      42. Putnam CD, Hammel M, Hura GL, Tainer JA. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys. 2007 Aug; 40(3):191-285. PMID: 18078545.
        View in: PubMed
      43. Hammel M, Sfyroera G, Ricklin D, Magotti P, Lambris JD, Geisbrecht BV. A structural basis for complement inhibition by Staphylococcus aureus. Nat Immunol. 2007 Apr; 8(4):430-7. PMID: 17351618.
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      44. Johs A, Hammel M, Waldner I, May RP, Laggner P, Prassl R. Modular structure of solubilized human apolipoprotein B-100. Low resolution model revealed by small angle neutron scattering. J Biol Chem. 2006 Jul 14; 281(28):19732-9. PMID: 16704977.
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      45. Hammel M, Ramyar KX, Spencer CT, Geisbrecht BV. Crystallization and X-ray diffraction analysis of the complement component-3 (C3) inhibitory domain of Efb from Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Mar 01; 62(Pt 3):285-8. PMID: 16511324; PMCID: PMC2197172.
      46. Hammel M, Fierobe HP, Czjzek M, Kurkal V, Smith JC, Bayer EA, Finet S, Receveur-Bréchot V. Structural basis of cellulosome efficiency explored by small angle X-ray scattering. J Biol Chem. 2005 Nov 18; 280(46):38562-8. PMID: 16157599.
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      47. Hammel M, Walther M, Prassl R, Kuhn H. Structural flexibility of the N-terminal beta-barrel domain of 15-lipoxygenase-1 probed by small angle X-ray scattering. Functional consequences for activity regulation and membrane binding. J Mol Biol. 2004 Oct 29; 343(4):917-29. PMID: 15476810.
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      48. Hammel M, Fierobe HP, Czjzek M, Finet S, Receveur-Bréchot V. Structural insights into the mechanism of formation of cellulosomes probed by small angle X-ray scattering. J Biol Chem. 2004 Dec 31; 279(53):55985-94. PMID: 15502162.
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      49. Hammel M, Kriechbaum M, Gries A, Kostner GM, Laggner P, Prassl R. Solution structure of human and bovine beta(2)-glycoprotein I revealed by small-angle X-ray scattering. J Mol Biol. 2002 Aug 02; 321(1):85-97. PMID: 12139935.
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