Rugged Free Energy Landscapes pp 269-291

Part of the Lecture Notes in Physics book series (LNP, volume 736) | Cite as

Protein Folding, Unfolding and Aggregation Studied Using an All-Atom Model with~a~Simplified Interaction Potential

  • Anders Irbäck

Abstract

Finding a suitable transferable energy function for modeling of how different proteins fold into their respective native states is a major challenge in biophysics. Here, we discuss an all-atom protein model with implicit water and some studies based on this model. The model has a simplified and computationally convenient energy function. Despite its simplicity, the model has been found to quite successfully describe the structure and melting behavior of several peptides with about 20 amino acids. The same model, with unchanged parameters, has also been used to investigate the aggregation behavior of a fragment of Alzheimer’s Aβ peptide and the mechanical properties of the 76-residue protein ubiquitin.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    C. Brändén, J. Tooze: Introduction to Protein Structure (Garland, New York, 1991)Google Scholar
  2. 2.
    H. J. Dyson, P. E. Wright: Curr. Opin. Struct. Biol. 12, 54 (2002)CrossRefGoogle Scholar
  3. 3.
    A. K. Dunker, J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero, J. S. Oh, C. J. Oldfield, A. M. Campen, C. R. Ratliff, K. W. Hipps, J. Ausio, M. S. Nissen, R. Reeves, C. H. Kang, C. R. Kissinger, R. W. Bailey, M. D. Griswold, M. Chiu, E. C. Garner, Z. Obradovic: J. Mol. Graph. Modell. 19, 26 (2001)CrossRefGoogle Scholar
  4. 4.
    C. M. Dobson: Nat 426, 884 (2003)CrossRefADSGoogle Scholar
  5. 5.
    H. S. Chan, H. Kaya, S. Shimizu: Computational methods for protein folding: scaling a hierarchy of complexities. In Current Topics in Computational Molecular Biology, edited by T. Jiang, Y. Xu, M. Q. Zhang (MIT press, Cambridge, Massachusetts, USA, 2002), pp. 403–447Google Scholar
  6. 6.
    J. M. Wang, P. Cieplak, P. A. Kollman: J. Comput. Chem. 21, 1049 (2000)CrossRefGoogle Scholar
  7. 7.
    A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus: J. Phys. Chem. B 102, 3586 (1998)CrossRefGoogle Scholar
  8. 8.
    U. Stocker, W. F. van Gunsteren: Proteins 40, 145 (2000)CrossRefGoogle Scholar
  9. 9.
    G. Kaminski, W. L. Jorgensen: J. Phys. Chem. 100, 18010 (1996)CrossRefGoogle Scholar
  10. 10.
    T. Yoda, Y. Sugita, Y. Okamoto: Chem. Phys. 307, 269 (2004)CrossRefADSGoogle Scholar
  11. 11.
    A. Irbäck, B. Samuelsson, F. Sjunnesson, S. Wallin: Biophys. J. 85, 1466 (2003)CrossRefGoogle Scholar
  12. 12.
    A. Irbäck, F. Sjunnesson: Proteins 56, 110 (2004)CrossRefGoogle Scholar
  13. 13.
    A. Irbäck, S. Mohanty: Biophys. J. 88, 1560 (2005)CrossRefGoogle Scholar
  14. 14.
    A. G. Cochran, N. J. Skelton, M. A. Starovasnik: Proc. Natl. Acad. Sci. USA 98, 5578 (2001)CrossRefADSGoogle Scholar
  15. 15.
    G. Favrin, A. Irbäck, S. Mohanty: Biophys. J. 87, 3657 (2004); erratum 89, 754 (2005)Google Scholar
  16. 16.
    A. Irbäck, S. Mitternacht, S. Mohanty: Proc. Natl. Acad. Sci. USA 102, 13427 (2005)CrossRefADSGoogle Scholar
  17. 17.
    A. Irbäck, S. Mitternacht: Proteins 65, 759 (2006)CrossRefGoogle Scholar
  18. 18.
    G. Chikenji, Y. Fujitsuka, S. Takada: Proc. Natl. Acad. Sci. USA 103, 3141 (2006)CrossRefADSGoogle Scholar
  19. 19.
    G. N. Ramachandran, V. Sasisekharan: Adv. Protein Chem. 23, 283 (1968)CrossRefGoogle Scholar
  20. 20.
    J. W. Neidigh, R. M. Fesinmeyer, N. H. Andersen: Nat. Struct. Biol. 9, 425 (2002)CrossRefGoogle Scholar
  21. 21.
    L. R. Dodd, T. D. Boone, D. N. Theodorou: Mol. Phys. 78, 961 (1993)CrossRefADSGoogle Scholar
  22. 22.
    G. Favrin, A. Irbäck, F. Sjunnesson: J. Chem. Phys. 114, 8154 (2001)CrossRefADSGoogle Scholar
  23. 23.
    U. H. E. Hansmann, Y. Okamoto: Curr. Opin. Struct. Biol. 9, 177 (1999)CrossRefGoogle Scholar
  24. 24.
    A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, P. N. Vorontsov-Velyaminov: J. Chem. Phys. 96, 1776 (1992)CrossRefADSGoogle Scholar
  25. 25.
    E. Marinari, G. Parisi: Europhys. Lett. 19, 451 (1992)CrossRefADSGoogle Scholar
  26. 26.
    A. Irbäck, F. Potthast: J. Chem. Phys. 103, 10298 (1995)CrossRefADSGoogle Scholar
  27. 27.
    A. Irbäck, S. Mohanty: J. Comput. Chem. 27, 1548 (2006)CrossRefGoogle Scholar
  28. 28.
    D. J. Lockhart, P. S. Kim: Science 260, 198 (1993)CrossRefADSGoogle Scholar
  29. 29.
    F. J. Blanco, G. Rivas, L. Serrano: Nat. Struct. Biol. 1, 584 (1994)CrossRefGoogle Scholar
  30. 30.
    R. M. Fesinmeyer, F. M. Hudson, N. H. Andersen: J. Am. Chem. Soc. 126, 7238 (2004)CrossRefGoogle Scholar
  31. 31.
    T. Kortemme, M. Ramí rez-Alvarado, L. Serrano: Science 281, 253 (1998)CrossRefADSGoogle Scholar
  32. 32.
    M. López de la Paz, E. Lacroix, M. Ramí rez-Alvarado, L. Serrano: J. Mol. Biol. 312, 229 (2001)CrossRefGoogle Scholar
  33. 33.
    R. Sayle, E. J. Milner-White: Trends Biochem. Sci. 20, 374 (1995)CrossRefGoogle Scholar
  34. 34.
    C. D. Snow, B. Zagrovic, V. S. Pande: J. Am. Chem. Soc. 124, 14548 (2002)CrossRefGoogle Scholar
  35. 35.
    C. Simmerling, B. Strockbine, A. E. Roitberg: J. Am. Chem. Soc. 124, 11258 (2002)CrossRefGoogle Scholar
  36. 36.
    J. W. Pitera, W. Swope: Proc. Natl. Acad. Sci. USA 100, 7587 (2003)CrossRefADSGoogle Scholar
  37. 37.
    R. Zhou: Proc. Natl. Acad. Sci. USA 100, 13280 (2003)CrossRefADSGoogle Scholar
  38. 38.
    A. Schug, W. Wenzel, U. H. E. Hansmann: J. Chem. Phys. 122, 194711 (2005)CrossRefADSGoogle Scholar
  39. 39.
    S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, R. B. Dyer: Biochemistry 35, 691 (1996)CrossRefGoogle Scholar
  40. 40.
    P. A. Thompson, W. A. Eaton, J. Hofrichter: Biochemistry 36, 9200 (1997)CrossRefGoogle Scholar
  41. 41.
    J. A. Vila, D. R. Ripoll, H. A. Scheraga: Proc. Natl. Acad. Sci. USA 97, 13075 (2000)CrossRefADSGoogle Scholar
  42. 42.
    A. E. Garcí a, K. Y. Sanbonmatsu: Proc. Natl. Acad. Sci. USA 99, 2782 (2002)CrossRefADSGoogle Scholar
  43. 43.
    H. Nymeyer, A. E. Garcí a: Proc. Natl. Acad. Sci. USA 100, 13934 (2003)CrossRefADSGoogle Scholar
  44. 44.
    D. Roccatano, A. Amadei, A. Di Nola, H. J. C. Berendsen: ProteinsSci 8, 2130 (1999)CrossRefGoogle Scholar
  45. 45.
    V. S. Pande, D. S. Rokhsar: Proc. Natl. Acad. Sci. USA 96, 9062 (1999)CrossRefADSGoogle Scholar
  46. 46.
    A. R. Dinner, T. Lazaridis, M. Karplus: Proc. Natl. Acad. Sci. USA 96, 9068 (1999)CrossRefADSGoogle Scholar
  47. 47.
    A. E. Garcí a, K. Y. Sanbonmatsu: Proteins 42, 345 (2001)CrossRefGoogle Scholar
  48. 48.
    B. Zagrovic, E. J. Sorin, V. Pande: J. Mol. Biol. 313, 151 (2001)CrossRefGoogle Scholar
  49. 49.
    R. Zhou, B. J. Berne, R. Germain: Proc. Natl. Acad. Sci. USA 98, 14931 (2001)CrossRefADSGoogle Scholar
  50. 50.
    E. Kussell, J. Shimada, E. I. Shakhnovich: Proc. Natl. Acad. Sci. USA 99, 5343 (2002)CrossRefADSGoogle Scholar
  51. 51.
    R. Zhou: Proteins 53, 148 (2003)CrossRefGoogle Scholar
  52. 52.
    P. G. Bolhuis: Proc. Natl. Acad. Sci. USA 14, 12129 (2003)CrossRefADSGoogle Scholar
  53. 53.
    G. Wei, N. Mousseau, P. Derreumaux: Proteins 56, 464 (2004)CrossRefGoogle Scholar
  54. 54.
    P. H. Nguyen, G. Stock, E. Mittag, C. K. Hu, M. S. Li: Proteins 61, 795 (2005)CrossRefGoogle Scholar
  55. 55.
    V. Muñoz, P. A. Thompson, J. Hofrichter, W. A. Eaton: Nature 390, 196 (1997)CrossRefADSGoogle Scholar
  56. 56.
    A. M. Gronenborn, D. R. Filpula, N. Z. Essig, A. Achari, M. Whitlow, P. T. Wingfield, G. M. Clore: Science 253, 657 (1991)CrossRefADSGoogle Scholar
  57. 57.
    B. D. Bursulaya, C. L. Brooks III: J. Am. Chem. Soc. 121, 9947 (1999)CrossRefGoogle Scholar
  58. 58.
    G. Colombo, D. Roccatano, A. E. Mark: Proteins 46, 380 (2002)CrossRefGoogle Scholar
  59. 59.
    S. Y. Kim, J. Lee, J. Lee: J. Chem. Phys. 120, 8271 (2004)CrossRefADSGoogle Scholar
  60. 60.
    J. C. Rochet, P. T. Lansbury Jr.: Curr. Opin. Struct. Biol. 10, 60 (2000)CrossRefGoogle Scholar
  61. 61.
    J. J. Balbach, Y. Ishii, O. N. Antzutkin, R. D. Leapman, N. W. Rizzo, F. Dyda, J. Reed, R. Tycko: Biochemistry 39, 13748 (2000)CrossRefGoogle Scholar
  62. 62.
    L. O. Tjernberg, J. Näslund, F. Lindqvist, J. Johansson, A. R. Karlström, J. Thyberg, L. Terenius, C. Nordstedt: J. Biol. Chem. 271, 8545 (1996)CrossRefGoogle Scholar
  63. 63.
    B. Ma, R. Nussinov: Proc. Natl. Acad. Sci. USA 99, 14126 (2002)CrossRefADSGoogle Scholar
  64. 64.
    D. K. Klimov, D. Thirumalai: Structure 11, 295 (2003)CrossRefGoogle Scholar
  65. 65.
    S. Santini, N. Mousseau, P. Derreumaux: J. Am. Chem. Soc. 126, 11509 (2004)CrossRefGoogle Scholar
  66. 66.
    S. Gnanakaran, R. Nussinov, A. E. Garcí a: J. Am. Chem. Soc. 128, 2158 (2006)CrossRefGoogle Scholar
  67. 67.
    M. Sunde, C. Blake: Adv. Protein Chem. 50, 123 (1997)CrossRefGoogle Scholar
  68. 68.
    D. J. Gordon, J. J. Balbach, R. Tycko, S. C. Meredith: Biophys. J. 86, 428 (2004)CrossRefGoogle Scholar
  69. 69.
    M. P. Lambert, A. K. Barlow, B. A. Chromy, C. Edwards, R. Freed, M. Liosatos, T. E. Morgan, I. Rozovsky, B. Trommer, K. L. Viola, P. Wals, C. Zhang, C. E. Finch, G. A. Krafft, W. L. Klein: Proc. Natl. Acad. Sci. USA 95, 6448 (1998)CrossRefADSGoogle Scholar
  70. 70.
    D. M. Walsh, D. M. Hartley, Y. Kusumoto, Y. Fezoui, M. M. Condron, A. Lomakin, G. B. Benedek, D. J. Selkoe, D. B. Teplow: J. Biol. Chem. 274, 25945 (1999)CrossRefGoogle Scholar
  71. 71.
    D. M. Walsh, I. Klyubin, J. V. Fadeeva, W. K. Cullen, R. Anwyl, M. S. Wolfe, M. J. Rowan, D. J. Selkoe: Nature 416, 535 (2002)CrossRefADSGoogle Scholar
  72. 72.
    M. Schlierf, H. Li, J. M. Fernandez: Proc. Natl. Acad. Sci. USA 101, 7299 (2004)CrossRefADSGoogle Scholar
  73. 73.
    G. Cornilescu, J. L. Marquardt, M. Ottiger, A. Bax: J. Am. Chem. Soc. 120, 6836 (1998)CrossRefGoogle Scholar
  74. 74.
    F. Cordier, S. Grzesiek: J. Mol. Biol. 317, 739 (2002)CrossRefGoogle Scholar
  75. 75.
    H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, A. Tokmakoff: Proc. Natl. Acad. Sci. USA 102, 612 (2005)CrossRefADSGoogle Scholar
  76. 76.
    H. M. Went, S. E. Jackson: Protein Eng. Des. Sel. 18, 229 (2005)CrossRefGoogle Scholar
  77. 77.
    B. A. Krantz, R. S. Dothager, T. R. Sosnick: J. Mol. Biol. 337, 463 (2004)CrossRefGoogle Scholar
  78. 78.
    P. C. Li, D. E. Makarov: J. Chem. Phys. 121, 4826 (2004)CrossRefADSGoogle Scholar
  79. 79.
    H. Lu, K. Schulten: Biophys. J. 79, 51 (2000)CrossRefGoogle Scholar
  80. 80.
    S. B. Fowler, R. B. Best, J. L. T. Herrera, T. J. Rutherford, A. Steward, E. Paci, M. Karplus, J. Clarke: J. Mol. Biol. 322, 841 (2002)CrossRefGoogle Scholar
  81. 81.
    R. Rohs, C. Etchebest, R. Lavery: Biophys. J. 76, 2760 (1999)CrossRefGoogle Scholar
  82. 82.
    D. J. Brockwell, E. Paci, R. C. Zinober, G. S. Beddard, P. D. Olmsted, D. A. Smith, R. N. Perham, S. E. Radford: Nat. Struct. Biol. 10, 731 (2003)CrossRefGoogle Scholar
  83. 83.
    M. Cieplak, J. Sulkowska: J. Chem. Phys. 123, 194908 (2005)CrossRefADSGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Anders Irbäck
    • 1
  1. 1.Computational Biology and Biological Physics Group Department of Theoretical PhysicsLund UniversitySölvegatan 14ASweden

Personalised recommendations