Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2014, Article ID 573936, 16 pages
http://dx.doi.org/10.1155/2014/573936
Research Article

C-Terminal Domain Swapping of SSB Changes the Size of the ssDNA Binding Site

1School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
2Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan

Received 26 May 2014; Accepted 9 July 2014; Published 4 August 2014

Academic Editor: Huangen Ding

Copyright © 2014 Yen-Hua Huang and Cheng-Yang Huang. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. Reyes-Lamothe, D. J. Sherratt, and M. C. Leake, “Stoichiometry and architecture of active DNA replication machinery in escherichia coli,” Science, vol. 328, no. 5977, pp. 498–501, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. D. J. Richard, E. Bolderson, and K. K. Khanna, “Multiple human single-stranded DNA binding proteins function in genome maintenance: structural, biochemical and functional analysis,” Critical Reviews in Biochemistry and Molecular Biology, vol. 44, no. 2-3, pp. 98–116, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. R. D. Shereda, A. G. Kozlov, T. M. Lohman, M. M. Cox, and J. L. Keck, “SSB as an organizer/mobilizer of genome maintenance complexes,” Critical Reviews in Biochemistry and Molecular Biology, vol. 43, no. 5, pp. 289–318, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. D. J. Richard, E. Bolderson, L. Cubeddu et al., “Single-stranded DNA-binding protein hSSB1 is critical for genomic stability,” Nature, vol. 453, no. 7195, pp. 677–681, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. R. R. Meyer and P. S. Laine, “The single-stranded DNA-binding protein of Escherichia coli,” Microbiological Reviews, vol. 54, no. 4, pp. 342–380, 1990. View at Google Scholar · View at Scopus
  6. C. Yang, U. Curth, C. Urbanke, and C. Kang, “Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 Å resolution,” Nature Structural Biology, vol. 4, no. 2, pp. 153–157, 1997. View at Publisher · View at Google Scholar · View at Scopus
  7. G. Webster, J. Genschel, U. Curth, C. Urbanke, C. Kang, and R. Hilgenfeld, “A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria,” FEBS Letters, vol. 411, pp. 313–316, 1997. View at Google Scholar
  8. R. L. Flynn and L. Zou, “Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians,” Critical Reviews in Biochemistry and Molecular Biology, vol. 45, no. 4, pp. 266–275, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. K. Chan, Y. Lee, C. Wang, H. Huang, and Y. Sun, “Single-Stranded DNA-Binding Protein Complex from Helicobacter pylori Suggests an ssDNA-Binding Surface,” Journal of Molecular Biology, vol. 388, no. 3, pp. 508–519, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. D. L. Theobald, R. M. Mitton-Fry, and D. S. Wuttke, “Nucleic acid recognition by OB-fold proteins,” Annual Review of Biophysics and Biomolecular Structure, vol. 32, pp. 115–133, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Raghunathan, A. G. Kozlov, T. M. Lohman, and G. Waksman, “Structure of the DNA binding domain of E. coli SSB bound to ssDNA,” Nature Structural Biology, vol. 7, no. 8, pp. 648–652, 2000. View at Publisher · View at Google Scholar · View at Scopus
  12. A. G. Murzin, “OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences,” EMBO Journal, vol. 12, no. 3, pp. 861–867, 1993. View at Google Scholar · View at Scopus
  13. N. P. George, K. V. Ngo, S. Chitteni-Pattu et al., “Structure and cellular dynamics of deinococcus radiodurans single-stranded DNA (ssDNA)-binding protein (SSB)-DNA complexes,” The Journal of Biological Chemistry, vol. 287, no. 26, pp. 22123–22132, 2012. View at Publisher · View at Google Scholar · View at Scopus
  14. P. Filipkowski and J. Kur, “Identification and properties of the Deinococcus grandis and Deinococcus proteolyticus single-stranded DNA binding proteins (SSB),” Acta Biochimica Polonica, vol. 54, no. 1, pp. 79–87, 2007. View at Google Scholar · View at Scopus
  15. P. Filipkowski, A. Duraj-Thatte, and J. Kur, “Identification, cloning, expression, and characterization of a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi,” Protein Expression and Purification, vol. 53, no. 1, pp. 201–208, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. P. Filipkowski, M. Koziatek, and J. Kur, “A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans,” Extremophiles, vol. 10, no. 6, pp. 607–614, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. P. Filipkowski, A. Duraj-Thatte, and J. Kur, “Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis,” Archives of Microbiology, vol. 186, no. 2, pp. 129–137, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. G. Witte, C. Urbanke, and U. Curth, “Single-stranded DNA-binding protein of Deinococcus radiodurans: a biophysical characterization,” Nucleic Acids Research, vol. 33, no. 5, pp. 1662–1670, 2005. View at Publisher · View at Google Scholar · View at Scopus
  19. D. A. Bernstein, J. M. Eggingtont, M. P. Killoran, A. M. Misic, M. M. Cox, and J. L. Keck, “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 Sciences of the United States of America, vol. 101, no. 23, pp. 8575–8580, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Dabrowski, M. Olszewski, R. Piatek, A. Brillowska-Dabrowska, G. Konopa, and J. Kur, “Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus—new arrangement of binding domains,” Microbiology, vol. 148, no. 10, pp. 3307–3315, 2002. View at Google Scholar · View at Scopus
  21. R. Gamsjaeger, R. Kariawasam, C. Touma, A. H. Kwan, M. F. White, and L. Cubeddu, “Backbone and side-chain 1H, 13C and 15N resonance assignments of the OB domain of the single stranded DNA binding protein from Sulfolobus solfataricus and chemical shift mapping of the DNA-binding interface,” Biomolecular NMR Assignments, 2013. View at Publisher · View at Google Scholar
  22. M. L. Rolfsmeier and C. A. Haseltine, “The single-stranded DNA binding protein of Sulfolobus solfataricus acts in the presynaptic step of homologous recombination,” Journal of Molecular Biology, vol. 397, no. 1, pp. 31–45, 2010. View at Publisher · View at Google Scholar · View at Scopus
  23. I. D. Kerr, R. I. M. Wadsworth, L. Cubeddu, W. Blankenfeldt, J. H. Naismith, and M. F. White, “Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein,” EMBO Journal, vol. 22, no. 11, pp. 2561–2570, 2003. View at Publisher · View at Google Scholar · View at Scopus
  24. C. A. Haseltine and S. C. Kowalczykowski, “A distinctive single-stranded DNA-binding protein from the Archaeon Sulfolobus solfataricus,” Molecular Microbiology, vol. 43, no. 6, pp. 1505–1515, 2002. View at Publisher · View at Google Scholar · View at Scopus
  25. R. I. M. Wadsworth and M. F. White, “Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus,” Nucleic Acids Research, vol. 29, no. 4, pp. 914–920, 2001. View at Publisher · View at Google Scholar · View at Scopus
  26. S. Sugiman-Marangos and M. S. Junop, “The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding proteins,” Nucleic Acids Research, vol. 38, no. 10, Article ID gkq036, pp. 3432–3440, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. H. Ghalei, H. V. Moeller, D. Eppers et al., “Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein,” Nucleic Acids Research, vol. 42, no. 10, pp. 6698–6708, 2014. View at Publisher · View at Google Scholar
  28. S. Paytubi, S. A. McMahon, S. Graham et al., “Displacement of the canonical single-stranded DNA-binding protein in the thermoproteales,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 7, pp. E398–E405, 2012. View at Publisher · View at Google Scholar · View at Scopus
  29. T. H. Dickey, S. E. Altschuler, and D. S. Wuttke, “Single-stranded DNA-binding proteins: multiple domains for multiple functions,” Structure, vol. 21, no. 7, pp. 1074–1084, 2013. View at Publisher · View at Google Scholar · View at Scopus
  30. D. Vujaklija and B. Macek, “Detecting posttranslational modifications of bacterial SSB proteins,” Methods in Molecular Biology, vol. 922, pp. 205–218, 2012. View at Publisher · View at Google Scholar · View at Scopus
  31. I. Mijakovic, D. Petranovic, B. Macek et al., “Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine,” Nucleic Acids Research, vol. 34, no. 5, pp. 1588–1596, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. M. Olszewski, A. Grot, M. Wojciechowski, M. Nowak, M. Mickiewicz, and J. Kur, “Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana,” BMC Microbiology, vol. 10, article 260, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. U. Curth, J. Genschel, C. Urbanke, and J. Greipel, “In vitro and in vivo function of the C-terminus of Escherichia coil single-stranded DNA binding protein,” Nucleic Acids Research, vol. 24, no. 14, pp. 2706–2711, 1996. View at Publisher · View at Google Scholar · View at Scopus
  34. G. Witte, C. Urbanke, and U. Curth, “DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery,” Nucleic Acids Research, vol. 31, pp. 4434–4440, 2003. View at Google Scholar
  35. D. Shishmarev, Y. Wang, C. E. Mason et al., “Otting, Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy,” Nucleic Acids Research, vol. 42, pp. 2750–2757, 2014. View at Google Scholar
  36. A. G. Kozlov, M. M. Cox, and T. M. Lohman, “Regulation of single-stranded DNA binding by the C termini of Escherichia coli single-stranded DNA-binding (SSB) protein,” Journal of Biological Chemistry, vol. 285, no. 22, pp. 17246–17252, 2010. View at Publisher · View at Google Scholar · View at Scopus
  37. M. Nowak, M. Olszewski, M. Spibida, and J. Kur, “Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, Flavobacterium psychrophilum, Psychrobacter arcticus, Psychrobacter cryohalolentis, Psychromonas ingrahamii, Psychroflexus torquis, and Photobacterium profundum,” BMC Microbiology, vol. 14, article 91, 2014. View at Google Scholar
  38. T. Paradzik, N. Ivic, Z. Filic et al., “Structure-function relationships of two paralogous single-stranded DNA-binding proteins from Streptomyces coelicolor: implication of SsbB in chromosome segregation during sporulation,” Nucleic Acids Research, vol. 41, no. 6, pp. 3659–3672, 2013. View at Publisher · View at Google Scholar · View at Scopus
  39. S. Jain, M. Zweig, E. Peeters et al., “Characterization of the single stranded DNA binding protein SsbB encoded in the gonoccocal genetic island,” PLoS ONE, vol. 7, no. 4, Article ID e35285, 2012. View at Publisher · View at Google Scholar · View at Scopus
  40. Y. H. Huang and C. Y. Huang, “Characterization of a single-stranded DNA-binding protein from Klebsiella pneumoniae: mutation at either Arg73 or Ser76 causes a less cooperative complex on DNA,” Genes to Cells, vol. 17, no. 2, pp. 146–157, 2012. View at Publisher · View at Google Scholar · View at Scopus
  41. E. Antony, E. A. Weiland, S. Korolev, and T. M. Lohman, “Plasmodium falciparum SSB tetramer wraps single-stranded DNA with similar topology but opposite polarity to E. Coli SSB,” Journal of Molecular Biology, vol. 420, no. 4-5, pp. 269–283, 2012. View at Publisher · View at Google Scholar · View at Scopus
  42. H. Jan, Y. L. Lee, and C. Y. Huang, “Characterization of a single-stranded DNA-binding protein from pseudomonas aeruginosa PAO1,” Protein Journal, vol. 30, no. 1, pp. 20–26, 2011. View at Publisher · View at Google Scholar · View at Scopus
  43. Y.-H. Huang, Y.-L. Lee, and C.-Y. Huang, “Characterization of a single-stranded DNA binding protein from Salmonella enterica serovar typhimurium LT2,” Protein Journal, vol. 30, no. 2, pp. 102–108, 2011. View at Publisher · View at Google Scholar · View at Scopus
  44. S. K. Bharti, K. Rex, P. Sreedhar, N. Krishnan, and U. Varshney, “Chimeras of Escherichia coli and Mycobacterium tuberculosis single-stranded DNA binding proteins: characterization and function in Escherichia coli,” PLoS ONE, vol. 6, no. 12, Article ID e27216, 2011. View at Publisher · View at Google Scholar · View at Scopus
  45. M. T. Oliveira and L. S. Kaguni, “Functional roles of the N- and C-terminal regions of the human mitochondrial single-stranded DNA-binding protein,” PLoS ONE, vol. 5, no. 10, Article ID e15379, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. A. G. Kozlov, J. M. Eggington, M. M. Cox, and T. M. Lohman, “Binding of the dimeric Deinococcus radiodurans single-stranded DNA binding protein to single-stranded DNA,” Biochemistry, vol. 49, no. 38, pp. 8266–8275, 2010. View at Publisher · View at Google Scholar · View at Scopus
  47. T. M. Lohman and M. E. Ferrari, “Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperatives,” Annual Review of Biochemistry, vol. 63, pp. 527–570, 1994. View at Publisher · View at Google Scholar · View at Scopus
  48. R. Zhou, A. G. Kozlov, R. Roy et al., “SSB functions as a sliding platform that migrates on DNA via reptation,” Cell, vol. 146, pp. 222–232, 2011. View at Google Scholar
  49. R. Roy, A. G. Kozlov, T. M. Lohman, and T. Ha, “SSB protein diffusion on single-stranded DNA stimulates RecA filament formation,” Nature, vol. 461, pp. 1092–1097, 2009. View at Google Scholar
  50. R. Roy, A. G. Kozlov, T. M. Lohman, and T. Ha, “Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein,” Journal of Molecular Biology, vol. 369, no. 5, pp. 1244–1257, 2007. View at Publisher · View at Google Scholar · View at Scopus
  51. T. J. Kelly, P. Simancek, and G. S. Brush, “Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 25, pp. 14634–14639, 1998. View at Publisher · View at Google Scholar · View at Scopus
  52. C. Y. Huang, Determination of the Binding Site-Size of the Protein-DNA Complex by Use of the Electrophoretic Mobility Shift Assay, InTech Press, Rijeka, Croatia, 2012.
  53. A. Kornberg, “Ten commandments of enzymology, amended,” Trends in Biochemical Sciences, vol. 28, no. 10, pp. 515–517, 2003. View at Publisher · View at Google Scholar · View at Scopus
  54. W. Zhang, X. Lü, and J. Shen, “EMSA and single-molecule force spectroscopy study of interactions between bacillus subtilis single-stranded DNA-binding protein and single-stranded DNA,” Langmuir, vol. 27, no. 24, pp. 15008–15015, 2011. View at Publisher · View at Google Scholar · View at Scopus
  55. M. Ostermeier and S. J. Benkovic, “Evolution of protein function by domain swapping,” Advances in Protein Chemistry, vol. 55, pp. 29–77, 2000. View at Google Scholar · View at Scopus
  56. W. F. Peng and C. Y. Huang, “Allantoinase and dihydroorotase binding and inhibition by flavonols and the substrates of cyclic amidohydrolases,” Biochimie, vol. 101, pp. 113–122, 2014. View at Publisher · View at Google Scholar
  57. Y. H. Huang, M. J. Lin, and C. Y. Huang, “DnaT is a single-stranded DNA binding protein,” Genes to Cells, vol. 18, no. 11, pp. 1007–1019, 2013. View at Publisher · View at Google Scholar
  58. Y. Y. Ho, Y. H. Huang, and C. Y. Huang, “Chemical rescue of the post-translationally carboxylated lysine mutant of allantoinase and dihydroorotase by metal ions and short-chain carboxylic acids,” Amino Acids, vol. 44, no. 4, pp. 1181–1191, 2013. View at Publisher · View at Google Scholar · View at Scopus
  59. Y. H. Huang, Y. Lo, W. Huang, and C. Y. Huang, “Crystal structure and DNA-binding mode of Klebsiella pneumoniae primosomal PriB protein,” Genes to Cells, vol. 17, no. 10, pp. 837–849, 2012. View at Publisher · View at Google Scholar · View at Scopus
  60. C. Y. Huang, C. Y. Hsu, Y. Sun, H. Wu, and C. Hsiao, “Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA-binding mode,” Nucleic Acids Research, vol. 34, no. 14, pp. 3878–3886, 2006. View at Publisher · View at Google Scholar · View at Scopus
  61. T. Kinebuchi, H. Shindo, H. Nagai, N. Shimamoto, and M. Shimizu, “Functional domains of Escherichia coli single-stranded DNA binding protein as assessed by analyses of the deletion mutants,” Biochemistry, vol. 36, no. 22, pp. 6732–6738, 1997. View at Publisher · View at Google Scholar · View at Scopus
  62. N. Shimamoto, N. Ikushima, H. Utiyama, H. Tachibana, and K. Horie, “Specific and cooperative binding of E. coli single-stranded DNA binding protein to mRNA,” Nucleic Acids Research, vol. 15, no. 13, pp. 5241–5250, 1987. View at Publisher · View at Google Scholar · View at Scopus
  63. H. Lin and C. Y. Huang, “Characterization of flavonol inhibition of DnaB helicase: Real-time monitoring, structural modeling, and proposed mechanism,” Journal of Biomedicine and Biotechnology, vol. 2012, Article ID 735368, 2012. View at Publisher · View at Google Scholar · View at Scopus
  64. Y. H. Huang, H. H. Lin, and C. Y. Huang, “A single residue determines the cooperative binding property of a primosomal DNA replication protein, PriB, to single-stranded DNA,” Bioscience, Biotechnology and Biochemistry, vol. 76, no. 6, pp. 1110–1115, 2012. View at Publisher · View at Google Scholar · View at Scopus
  65. H. C. Hsieh and C. Y. Huang, “Identification of a novel protein, PriB, in Klebsiella pneumoniae,” Biochemical and Biophysical Research Communications, vol. 404, no. 1, pp. 546–551, 2011. View at Publisher · View at Google Scholar · View at Scopus
  66. J. H. Liu, T. W. Chang, C. Y. Huang et al., “Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli,” The Journal of Biological Chemistry, vol. 279, no. 48, pp. 50465–50471, 2004. View at Publisher · View at Google Scholar · View at Scopus
  67. Y. H. Huang and C. Y. Huang, “The N-terminal domain of DnaT, a primosomal DNA replication protein, is crucial for PriB binding and self-trimerization,” Biochemical and Biophysical Research Communications, vol. 442, pp. 147–152, 2013. View at Publisher · View at Google Scholar
  68. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  69. S. N. Savvides, S. Raghunathan, K. Fütterer, A. G. Kozlov, T. M. Lohman, and G. Waksman, “The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA,” Protein Science, vol. 13, no. 7, pp. 1942–1947, 2004. View at Publisher · View at Google Scholar · View at Scopus
  70. C.-C. Chen, J.-K. Hwang, and J.-M. Yang, “(PS)2-v2: template-based protein structure prediction server,” BMC Bioinformatics, vol. 10, article 366, 2009. View at Publisher · View at Google Scholar · View at Scopus
  71. C. Chen, J. Hwang, and J. Yang, “(PS)2: protein structure prediction server,” Nucleic Acids Research, vol. 34, pp. W152–W157, 2006. View at Publisher · View at Google Scholar · View at Scopus
  72. K. Bush and J. F. Fisher, “Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria,” Annual Review of Microbiology, vol. 65, pp. 455–478, 2011. View at Publisher · View at Google Scholar · View at Scopus
  73. K. K. Kumarasamy, M. A. Toleman, T. R. Walsh et al., “Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study,” The Lancet Infectious Diseases, vol. 10, no. 9, pp. 597–602, 2010. View at Publisher · View at Google Scholar · View at Scopus
  74. K. Bush and M. J. MacIelag, “New β-lactam antibiotics and β-lactamase inhibitors,” Expert Opinion on Therapeutic Patents, vol. 20, no. 10, pp. 1277–1293, 2010. View at Publisher · View at Google Scholar · View at Scopus
  75. K. Bush, “Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae,” Current Opinion in Microbiology, vol. 13, no. 5, pp. 558–564, 2010. View at Publisher · View at Google Scholar · View at Scopus
  76. A. Srivastava, M. Talaue, S. Liu et al., “New target for inhibition of bacterial RNA polymerase: “switch region”,” Current Opinion in Microbiology, vol. 14, no. 5, pp. 532–543, 2011. View at Publisher · View at Google Scholar · View at Scopus
  77. K. Chono, K. Katsumata, T. Kontani et al., “ASP2151, a novel helicase-primase inhibitor, possesses antiviral activity against varicella-zoster virus and herpes simplex virus types 1 and 2,” Journal of Antimicrobial Chemotherapy, vol. 65, no. 8, pp. 1733–1741, 2010. View at Publisher · View at Google Scholar · View at Scopus
  78. M. T. Black and K. Coleman, “New inhibitors of bacterial topoisomerase GyrA/ParC subunits,” Current Opinion in Investigational Drugs, vol. 10, no. 8, pp. 804–810, 2009. View at Google Scholar · View at Scopus
  79. A. H. Marceau, D. A. Bernstein, B. W. Walsh, W. Shapiro, L. A. Simmons, and J. L. Keck, “Protein interactions in genome maintenance as novel antibacterial targets,” PLoS ONE, vol. 8, no. 3, Article ID e58765, 2013. View at Publisher · View at Google Scholar · View at Scopus
  80. D. Lu, D. A. Bernstein, K. A. Satyshur, and J. L. Keck, “Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 2, pp. 633–638, 2010. View at Publisher · View at Google Scholar · View at Scopus
  81. I. Wong and T. M. Lohman, “A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions,” Proceedings of the National Academy of Sciences of the United States of America, vol. 90, no. 12, pp. 5428–5432, 1993. View at Publisher · View at Google Scholar · View at Scopus
  82. M. Mitas, J. Y. Chock, and M. Christy, “The binding-site sizes of Escherichia coli single-stranded-DNA-binding protein and mammalian replication protein A are 65 and ≥ 54 nucleotides respectively,” Biochemical Journal, vol. 324, no. 3, pp. 957–961, 1997. View at Google Scholar · View at Scopus
  83. C. Urbanke, G. Witte, and U. Curth, “Sedimentation velocity method in the analytical ultracentrifuge for the study of protein-protein interactions,” Methods in Molecular Biology, vol. 305, pp. 101–114, 2005. View at Google Scholar · View at Scopus
  84. S. Chrysogelos and J. Griffith, “Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units,” Proceedings of the National Academy of Sciences of the United States of America, vol. 79, no. 19, pp. 5803–5807, 1982. View at Publisher · View at Google Scholar · View at Scopus
  85. J. R. Casas-Finet, K. R. Fischer, and R. L. Karpel, “Structural basis for the nucleic acid binding cooperativity of bacteriophage T4 gene 32 protein: the (Lys/Arg)3(Ser/Thr)2 (LAST) motif,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, pp. 1050–1054, 1992. View at Google Scholar
  86. G. Witte, R. Fedorov, and U. Curth, “Biophysical analysis of Thermus aquaticus single-stranded DNA binding protein,” Biophysical Journal, vol. 94, no. 6, pp. 2269–2279, 2008. View at Publisher · View at Google Scholar · View at Scopus
  87. R. Fedorov, G. Witte, C. Urbanke, D. J. Manstein, and U. Curth, “3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins,” Nucleic Acids Research, vol. 34, no. 22, pp. 6708–6717, 2006. View at Publisher · View at Google Scholar · View at Scopus
  88. K. L. Tsai, C. Y. Huang, C. H. Chang, Y. J. Sun, W. J. Chuang, and C. D. Hsiao, “Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins,” Journal of Biological Chemistry, vol. 281, no. 25, pp. 17400–17409, 2006. View at Publisher · View at Google Scholar · View at Scopus
  89. A. H. Mao, N. Lyle, and R. V. Pappu, “Describing sequence-ensemble relationships for intrinsically disordered proteins,” Biochemical Journal, vol. 449, no. 2, pp. 307–318, 2013. View at Publisher · View at Google Scholar · View at Scopus
  90. R. Wetzel, “Physical chemistry of polyglutamine: Intriguing tales of a monotonous sequence,” Journal of Molecular Biology, vol. 421, no. 4-5, pp. 466–490, 2012. View at Publisher · View at Google Scholar · View at Scopus
  91. H. T. Orr, “Polyglutamine neurodegeneration: expanded glutamines enhance native functions,” Current Opinion in Genetics and Development, vol. 22, no. 3, pp. 251–255, 2012. View at Publisher · View at Google Scholar · View at Scopus
  92. M. Figiel, W. J. Szlachcic, P. M. Switonski, A. Gabka, and W. J. Krzyzosiak, “Mouse models of polyglutamine diseases: review and data table. Part I,” Molecular Neurobiology, vol. 46, no. 2, pp. 393–429, 2012. View at Publisher · View at Google Scholar · View at Scopus
  93. J. Nasica-Labouze and N. Mousseau, “Kinetics of amyloid aggregation: a study of the GNNQQNY prion sequence,” PLoS Computational Biology, vol. 8, no. 11, Article ID e1002782, 2012. View at Publisher · View at Google Scholar · View at Scopus
  94. J. Nasica-Labouze, M. Meli, P. Derreumaux, G. Colombo, and N. Mousseau, “A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide gnnqqny from the yeast prion sup-35,” PLoS Computational Biology, vol. 7, no. 5, Article ID e1002051, 2011. View at Publisher · View at Google Scholar · View at Scopus
  95. J. R. Lewandowski, P. C. A. van der Wel, M. Rigney, N. Grigorieff, and R. G. Griffin, “Structural complexity of a composite amyloid fibril,” Journal of the American Chemical Society, vol. 133, no. 37, pp. 14686–14698, 2011. View at Publisher · View at Google Scholar · View at Scopus