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Erratum: Investigation of the photochemistry of the poly {p-phenylenevinylene} precursor system: Implications for nanolithography [J. Chem. Phys. 126, 174703 (2007)]

Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper

J. Chem. Phys. 128, 045106 (2008); doi:10.1063/1.2831513

Published 31 January 2008 | See: Publisher's Note

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Yanxin Liu, Prem P. Chapagain, Jose L. Parra, and Bernard S. Gerstman
Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
The highest level in the hierarchy of protein structure and folding is the formation of protein complexes through protein-protein interactions. We have made modifications to a well established computer lattice model to expand its applicability to two-protein dimerization and aggregation. Based on Brownian dynamics, we implement translation and rotation moves of two peptide chains relative to each other, in addition to the intrachain motions already present in the model. We use this two-chain model to study the folding dynamics of the yeast transcription factor GCN4 leucine zipper. The calculated heat capacity curves agree well with experimental measurements. Free energy landscapes and median first passage times for the folding process are calculated and elucidate experimentally measured characteristics such as the multistate nature of the dimerization process. ©2008 American Institute of Physics
History: Received 4 October 2007; accepted 11 December 2007; published 31 January 2008; corrected 1 February 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/045106/1
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ERRATUM

  1. Publisher's Note: “Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper” [J. Chem. Phys. 128, 045106 (2008)]
    Yanxin Liu et al.
    J. Chem. Phys. 128, 129901 (2008)

KEYWORDS and PACS

Keywords
PACS
  • 87.15.K-
    Biomolecular interactions; membrane-protein interactions
  • 87.15.hp
    Conformational changes of biomolecules
  • 87.14.E-
    Proteins
  • 82.30.Nr
    Association, addition, insertion, cluster formation (chemical reactions)
  • 36.20.Hb
    Macromolecular configuration (bonds, dimensions)
  • 87.10.-e
    General theory and mathematical aspects (biological/medical physics)
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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REFERENCES (50)
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For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. M. Oliveberg and E. Shakhnovich, Curr. Opin. Struct. Biol. 16, 68 (2006).
  2. P. G. Wolynes, Q. Rev. Biophys. 38, 405 (2005).
  3. L. Mirny and E. Shakhnovich, Annu. Rev. Biophys. Biomol. Struct. 30, 361 (2001).
  4. J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 94, 7129 (1997).
  5. K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10 (1997).
  6. A. G. Ladurner, L. S. Itzhaki, V. Daggett, and A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 95, 8473 (1998).
  7. V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. 100, 3555 (2003).
  8. S. Jones and J. M. Thornton, Proc. Natl. Acad. Sci. U.S.A. 93, 13 (1996).
  9. E. D. Levy, J. B. Pereira-Leal, C. Chothia, and S. A. Teichmann, PLOS Comput. Biol. 2, e155 (2006).
  10. E. K. O'Shea, J. D. Klemm, P. S. Kim, and T. Alber, Science 254, 539 (1991).
  11. D. Mohanty, A. Kolinski, and J. Skolnick, Biophys. J. 77, 54 (1999).
  12. X. Zeng, H. Zhu, H. A. Lashuel, and J. C. Hu, Protein Sci. 6, 2218 (1997).
  13. O. D. Monera, N. E. Zhou, P. Lavigne, C. M. Kay, and R. S. Hodges, J. Biol. Chem. 271, 3995 (1996).
  14. C. A. Ross and M. A. Poirier, Nat. Med. 10, S10 (2004).
  15. R. I. Dima and D. Thirumalai, Protein Sci. 11, 1036 (2002).
  16. G. Tiana and R. A. Broglia, Proteins: Struct., Funct., Genet. 49, 82 (2002).
  17. T. Cellmer, D. Bratko, J. M. Prausnitz, and H. Blanch, Proc. Natl. Acad. Sci. U.S.A. 102, 11692 (2005);
  18. T. Cellmer, D. Bratko, J. M. Prausnitz, and H. W. Blanch, Trends Biotechnol. 25, 254 (2007).
  19. D. Bratko and H. W. Blanch, J. Chem. Phys. 118, 5185 (2003).
  20. G. Giugliarelli, C. Micheletti, J. M. Banavar, and A. Maritan, J. Chem. Phys. 113, 5072 (2000).
  21. P. Gupta, C. K. Hall, and A. Voegler, Fluid Phase Equilib. 160, 87 (1999).
  22. L. Toma and S. Toma, Biomacromolecules 1, 232 (2000).
  23. M. Vieth, A. Kolinski, and J. Skolnick, Biochemistry 35, 955 (1996).
  24. S. Miyazawa and R. L. Jernigan, Macromolecules 18, 534 (1985).
  25. J. Skolnick and A. Kolinski, Annu. Rev. Phys. Chem. 40, 207 (1989).
  26. H. S. Chan and K. A. Dill, Annu. Rev. Biophys. Biophys. Chem. 20, 447 (1991).
  27. D. A. Hinds and M. Levitt, Proc. Natl. Acad. Sci. U.S.A. 89, 2536 (1992).
  28. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, Protein Sci. 4, 561 (1995).
  29. A. Sali, E. Shakhnovich, and M. Karplus, Nature (London) 369, 248 (1994);
    30. J. Mol. Biol. 235, 1614 (1994).
  30. A. Kolinski, P. Rotkiewicz, B. Ilkowski, and J. Skolnick, Proteins 37, 592 (1999).
  31. V. S. Pande and D. S. Rokhsar, Proc. Natl. Acad. Sci. U.S.A. 96, 1273 (1999).
  32. D. Thirumalai, J. Phys. (Paris) 5, 1457 (1995).
  33. B. S. Gerstman and P. P. Chapagain, J. Chem. Phys. 123, 054901 (2005).
  34. K. K. Yapa and D. L. Weaver, J. Phys. Chem. 100, 2498 (1996).
  35. J. Skolnick and A. Kolinski, Science 250, 1121 (1990).
  36. A. Kolinski, M. Milik, and J. Skolnick, J. Chem. Phys. 94, 3978 (1991).
  37. J. Skolnick and A. Kolinski, J. Mol. Biol. 221, 499 (1991).
  38. A. Kolinski and J. Skolnick, Proteins 18, 338 (1994).
  39. P. P. Chapagain and B. S. Gerstman, J. Chem. Phys. 120, 2475 (2004).
  40. P. P. Chapagain and B. S. Gerstman, Biopolymers 81, 167 (2006).
  41. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953).
  42. F. Reif, Fundamentals of Statistical and Thermal Physics (McGraw-Hill, Singapore, 1985).
  43. CRC Handbook of Chemistry and Physics, 87th ed., edited by D. R. Lide (CRC, Baco Raton, 2006).
  44. R. A. Kammerer, T. Schulthess, R. Landwehr, A. Lustig, J. Engel, U. Aebi, and M. O. Steinmetz, Proc. Natl. Acad. Sci. U.S.A. 95, 13419 (1998).
  45. D. L. Lee, P. Lavigne, and R. S. Hodges, J. Mol. Biol. 306, 539 (2001).
  46. A. N. Lupas and M. Gruber, Adv. Protein Chem. 70, 37 (2005).
  47. P. P. Chapagain, J. L. Parra, B. S. Gerstman, and Y. Liu, J. Chem. Phys. 127, 075103 (2007).
  48. A. I. Dragan and P. L. Privalov, J. Mol. Biol. 321, 891 (2002).
  49. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988).
  50. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
  51. N. D. Socci and J. N. Onuchic, J. Chem. Phys. 103, 4732 (1995).

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