The VES KM: a pathway for protein folding in vivo

  • 1 CCMAR and Physics, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
Leonor CruzeiroORCID iD: https://orcid.org/0000-0001-7958-6435

Abstract

While according to the thermodynamic hypothesis, protein folding reproducibility is ensured by the assumption that the native state corresponds to the minimum of the free energy in normal cellular conditions, here, the VES kinetic mechanism for folding in vivo is described according to which the nascent chain of all proteins is helical and the first and structure defining step in the folding pathway is the bending of that initial helix around a particular amino acid site. Molecular dynamics simulations are presented which indicate both the viability of this mechanism for folding and its limitations in the presence of a Markovian thermal bath. An analysis of a set of protein structures formed only of helices and loops suggests that bending sites are correlated with regions bounded, on the N-side, by positively charged amino acids like Lysine and Histidine and on the C-side by negatively charged amino acids like Aspartic acid.

  • [1]

    P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan. Proc. Natl. Acad. Sci. USA106, 21149 (2009).

    • Crossref
    • Export Citation
  • [2]

    A. Amadei, A. Linssen, H. Berendsen. Proteins: Struct. Funct. Genet.17, 412 (1993).

    • Crossref
    • Export Citation
  • [3]

    C. Anfinsen. Science181, 223 (1973).

  • [4]

    J. Aramini, S. Sharma, Y. Huang, G. Swapna, C. Ho, K. Shetty, K. Cunningham, L. Ma, L. Zhao, L. Owens, M. Jiang, R. Xiao, J. Liu, M. Baran, T. Acton, B. Rost, G. Montelione. Proteins72, 526 (2008).

    • Crossref
    • PubMed
    • Export Citation
  • [5]

    R. Aurora, G. Rose. Prot. Sci.7, 21 (1998).

  • [6]

    R. H. Austin, A. Xie, L. van der Meer, M. Shinn, G. Neild. J. Phys.-Cond. Matt.15, S1693 (2003).

    • Crossref
    • Export Citation
  • [7]

    H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, P. Bourne. Nuc. Acid. Res.28, 235 (2000).

    • Crossref
    • Export Citation
  • [8]

    D. M. Bishop. J. Chem. Phys.98, 3179 (1993).

  • [9]

    G. Careri, U. Buontempo, F. Galluzzi, A. Scott, E. Gratton, E. Shyamsunder. Phys. Rev. B30, 4689 (1984).

    • Crossref
    • Export Citation
  • [10]

    D. Case, T. I. Cheatham, T. Darden, H. Gohlke, R. Luo, K. J. Merz, A. Onufriev, C. Simmerling, B. Wang, R. Woods. J. Computat. Chem.26, 1668 (2005).

    • Crossref
    • Export Citation
  • [11]

    P. Y. Chou, G. D. Fasman. Biochemistry13, 222 (1974).

  • [12]

    P. Y. Chou, G. D. Fasman. Biophys. J.26, 385 (1979).

  • [13]

    H. S. Chung, K. McHale, J. M. Louis, W. A. Eaton. Science335, 981 (2012).

  • [14]

    P. Cossio, A. Trovato, F. Pietrucci, F. Seno, A. Maritan, A. Laio. PLoS Comput. Biol.6, e1000957, 1 (2010).

  • [15]

    L. Cruzeiro. J. Phys. Org. Chem.21, 549 (2008).

  • [16]

    L. Cruzeiro. “Protein folding”, in Chemical Modelling, M. Springborg (Ed.), p. 89, Royal Society of Chemistry, London, UK 7 (2010).

  • [17]

    L. Cruzeiro. Bio-Algorithms and Med-Systems10, 117 (2014).

  • [18]

    L. Cruzeiro. Z. Phys. Chem230, 743 (2016).

  • [19]

    L. Cruzeiro. “Protein folding in vivo: from Anfinsen back to Levinthal”, in Nonlinear Systems, Vol. 2. Understanding Complex Systems, J. Archilla, F. Palmero, M. Lemos, B. Sánchez-Rey, J. Casado-Pascual (Eds.), pp. 3–38, Springer, Cham (2018).

  • [20]

    L. Cruzeiro, L. Degrève. J. Biomol. Struct. Dyn.33, 1539 (2015).

  • [21]

    L. Cruzeiro, L. Degrève. J. Biol. Phys.43, 15 (2016).

  • [22]

    L. Cruzeiro, P. A. Lopes. Mol. Phys.107, 1485 (2009).

  • [23]

    L. Cruzeiro-Hansson. Europhys. Lett.33, 655 (1996).

  • [24]

    L. Cruzeiro-Hansson. Phys. Lett. A223, 383 (1996).

  • [25]

    L. Cruzeiro-Hansson, S. Takeno. Phys. Rev. E56, 894 (1997).

  • [26]

    A. Davydov. J. Theor. Biol.38, 559 (1973).

  • [27]

    K. A. Dill. Biochemistry29, 7133 (1990).

  • [28]

    C. M. Dobson. Nature426, 884 (2009).

  • [29]

    J. Edler, P. Hamm. J. Chem. Phys.117, 2415 (2002).

  • [30]

    J. P. Ellis, C. K. Bakke, R. N. Kirchdoerfer, L. M. Jungbauer, S. Cavagnero. ACS Chem. Biol.3, 555 (2008).

    • Crossref
    • PubMed
    • Export Citation
  • [31]

    M. S. Evans, I. M. Sander, P. L. Clark. J. Mol. Biol.383, 683 (2008).

  • [32]

    M. Fändrich, M. A. Fletcher, C. M. Dobson. Nature410, 165 (2001).

  • [33]

    A. Fersht. Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding, W. H. Freeman and Company, New York (1999).

  • [34]

    P. Gettins. Chem. Rev.102, 4751 (2002).

  • [35]

    B. Gutte, R. B. Merrifield. J. Biol. Chem.246, 1922 (1971).

  • [36]

    F. U. Hartl, M. Hayer-Hartl. Nature Struc. Mol. Biol.16, 574 (2009).

    • Crossref
    • Export Citation
  • [37]

    B. L. d. G. Jochen S. Hub. PLoS Comput. Biol.5, e1000480 (2009).

  • [38]

    C. R. K. Gunasekaran, H. A. Nagarajaram, P. Balaram. J. Mol. Biol.275, 917 (1998).

    • Crossref
    • PubMed
    • Export Citation
  • [39]

    W. Kabsch, C. Sander. Biopolymers22, 2577 (1983).

  • [40]

    C. M. Kaiser, D. H. Goldman, J. D. Chodera, I. Tinoco Jr., C. Bustamante. Science334, 1723 (2011).

    • Crossref
    • PubMed
    • Export Citation
  • [41]

    C. Kimchi-Sarfaty, J. M. Oh, I. W. Kim, Z. E. Sauna, A. M. Calcagno, S. V. Ambudkar, M. M. Gottesman. Science315, 525 (2007).

    • Crossref
    • PubMed
    • Export Citation
  • [42]

    S. Krimm, J. Bandekar. Adv. Prot. Chem.22, 181 (1986).

  • [43]

    J. Kyte, R. Doolittle. J. Mol. Biol.157, 105, 1982.

  • [44]

    C. Levinthal. J. Chim. Phys.65, 44 (1968).

  • [45]

    C. Levinthal. In Mossbauer Spectroscopy in Biological Systems: Proceedings of a meeting held at Allerton House, J. T. P. DeBrunner, E. Munck (eds.), Monticello, Illinois, volume 22, 22 (1969).

  • [46]

    M. Levitt, C. Sander, P. Stern. Int. J. Quant. Chem.10, 181 (1983).

  • [47]

    C. McClare. Ann. N.Y. Acad. Sci.227, 74 (1974).

  • [48]

    R. B. Merrifield. Protein Sci.5, 1947 (1996).

  • [49]

    L. Meyerguz, J. Kleinberg, R. Elber. P. Natl. Acad. Sci. USA104, 11627 (2007).

    • Crossref
    • Export Citation
  • [50]

    R. K. Mitra, S. S. Sinha, S. K. Pal. Langmuir23, 10224 (2007).

  • [51]

    L. Presta, G. Rose. Science240, 1632 (1988).

  • [52]

    S. B. Prusiner. Science216, 136 (1982).

  • [53]

    J. S. Richardson, D. C. Richardson. Science240, 1648 (1988).

  • [54]

    J. M. Sanchez-Ruiz. Biophys. Chem.148, 1 (2010).

  • [55]

    A. Scott. Phys. Rep.217, 1 (1992).

  • [56]

    P. A. S. Silva, L. Cruzeiro-Hansson. Phys. Lett. A315, 447 (2003).

    • Crossref
    • Export Citation
  • [57]

    P. A. S. Silva, L. Cruzeiro-Hansson. Phys. Rev. E74, 021920 (2006).

    • Crossref
    • Export Citation
  • [58]

    J. Sohl, S. Jaswal, D. Agard. Nature395, 817 (1998).

  • [59]

    R. L. Tuinstra, F. C. Peterson, S. Kutlesa, E. S. Elgin, M. A. Kron, B. F. Volkman. P. Natl. Acad. Sci. U.S.A.105, 5057 (2008).

    • Crossref
    • Export Citation
  • [60]

    K. G. Ugrinov, P. L. Clark. Biophys J.98, 1312 (2010).

  • [61]

    N. R. Voss, M. Gerstein, T. A. Steitz, P. B. Moore. J. Mol. Biol.360, 893 (2006).

    • Crossref
    • PubMed
    • Export Citation
  • [62]

    D. N. Wilson, R. Beckmann. Curr. Opin. Struc. Biol.21, 274 (2011).

    • Crossref
    • Export Citation
  • [63]

    A. Xie, L. van der Meer, W. Hoff, R. H. Austin. Phys. Rev. Lett.84, 5435 (2000).

    • Crossref
    • PubMed
    • Export Citation
  • [64]

    G. Zhang, Z. Ignatova. Curr. Opin. Struc. Biol.21, 25 (2011).

    • Crossref
    • Export Citation
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