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The VES hypothesis and protein misfolding

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  • Proteins function by changing conformation. These conformational changes, which involve the concerted motion of a large number of atoms are classical events but, in many cases, the triggers are quantum mechanical events such as chemical reactions. Here the initial quantum states after the chemical reaction are assumed to be vibrational excited states, something that has been designated as the VES hypothesis. While the dynamics under classical force fields fail to explain the relatively lower structural stability of the proteins associated with misfolding diseases, the application of the VES hypothesis to two cases can provide a new explanation for this phenomenon. This explanation relies on the transfer of vibrational energy from water molecules to proteins, a process whose viability is also examined.
    Mathematics Subject Classification: Primary: 92C05, 82C10; Secondary: 92C37.


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  • [1]

    J. Abrahams, A. Leslie, R. Lutter and J. Walker, Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria, Nature, 370 (1994), 621-628.doi: 10.1038/370621a0.


    P. W. Anderson, Absence of diffusion in certain random lattices, Phys. Rev., 109 (1958), 1492-1505.doi: 10.1103/PhysRev.109.1492.


    H. C. Berg, The rotary motor of bacterial flagella, Annu. Rev. Biochem., 72 (2003), 19-54.doi: 10.1146/annurev.biochem.72.121801.161737.


    H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne, The protein data bank, Nuc. Acids Res., 28 (2000), 235-242.doi: 10.1093/nar/28.1.235.


    P. F. Bernath, "Spectra of Atoms and Molecules," 1st edition, Oxford University Press, New York, Oxford, 1995.


    D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. III Cheatham, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crowley, V. Tsui, R. J. Radmer, Y. Duan, J. Pitera, I. Massova, G. L. Seibel, et al, AMBER 6 (software), University of California, San Francisco, 1999.


    L. Cruzeiro, Why are proteins with glutamine- and asparagine-rich regions associated with protein misfolding diseases?, J. Phys.: Condens. Matter, 17 (2005), 7833-7844.doi: 10.1088/0953-8984/17/50/005.


    L. Cruzeiro, Influence of the nonlinearity and dipole strength on the amide I band of protein $\alpha$-helices, J. Chem. Phys., 123 (2005), 234909-1-7.doi: 10.1063/1.2138705.


    L. Cruzeiro, Protein's multi-funnel energy landscape and misfolding diseases, J. Phys. Org. Chem., 21 (2008), 549-554.doi: 10.1002/poc.1315.


    L. Cruzeiro-Hansson, Dynamics of a mixed quantum-classical system at finite temperature, Europhys. Lett., 33 (1996), 655-659.doi: 10.1209/epl/i1996-00394-5.


    L. Cruzeiro-Hansson and S. Takeno, Davydov model: The quantum, quantum-classical, and full classical model, Phys. Rev. E, 56 (1997), 894-906.doi: 10.1103/PhysRevE.56.894.


    A. S. Davydov, "Solitons in Molecular Systems," 2nd edition, Kluwer Academic Publ., Dordrecht, 1991.


    C. M. Dobson, Protein folding and misfolding, Nature, 426 (2003), 884-890.doi: 10.1038/nature02261.


    J. Edler and P. Hamm, Self-trapping of the amide I band in a peptide model crystal, J. Chem. Phys., 117 (2002), 2415-2424.doi: 10.1063/1.1487376.


    J. C. Eilbeck, P. S. Lomdahl and A. C. Scott, Soliton structure in crystalline acetanilide, Phys. Rev. B, 30 (1984), 4703-4712.doi: 10.1103/PhysRevB.30.4703.


    H. Feddersen, Localization of vibrational-energy in globular protein, Phys. Lett. A, 154 (1991), 391-395.doi: 10.1016/0375-9601(91)90039-B.


    M. Gerstein, A. M. Lesk and C. Chothia, Structural mechanisms for domain movements in proteins, Biochemistry, 33 (1994), 6739-6749.doi: 10.1021/bi00188a001.


    J. F. Gusella and M. E. Macdonald, Molecular genetics: Unmasking polyglutamine triggers in neurodegenerative disease, Nature Rev. Neurosci., 1 (2000), 109-115.doi: 10.1038/35039051.


    J. D. Jackson, "Classical Electrodynamics," 2nd edition, John Wiley & Sons, Inc., New York-Toronto, 1962.


    S. Krimm and J. Bandekar, Vibrational Spectroscopy and conformation of peptides, polypeptides and proteins, Adv. Prot. Chem., 38 (1986), 181-364.doi: 10.1016/S0065-3233(08)60528-8.


    L. Masino and A. Pastore, Glutamine repeats: Structural hypotheses and neurodegeneration, Biochem. Soc. Trans., 30 (2002), 548-551.doi: 10.1042/BST0300548.


    F. Mauri, R. Car and E. Tosatti, Canonical statistical averages of coupled quantum-classical systems, Europhys. Lett., 24 (1993), 431-436.


    C. W. F. McClare, Resonance in bioenergetics, Ann. N. Y. Acad. Sci., 227 (1974), 74-97.doi: 10.1111/j.1749-6632.1974.tb14374.x.


    M. D. Michelitsch and J. S. Weissman, A census of glutamine/asparagine-rich regions: Implications for their conserved function and the prediction of novel prions, Proc. Natl. Acad. Sci. USA, 97 (2000), 11910-11915.doi: 10.1073/pnas.97.22.11910.


    D. Narzi, I. Daidone, A. Amadei and A. Di Nola, Protein folding pathways revealed by essential dynamics sampling, J. Chem. Theory Comput., 4 (2008), 1940-1948.doi: 10.1021/ct800157v.


    N. A. Nevskaya and Yu. N. Chirgadze, Infrared spectra and resonance interactions of amide-I and II vibrations of $\alpha$-helix, Biopolymers, 15 (1976), 637-648.doi: 10.1002/bip.1976.360150404.


    D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. III Cheatham, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comp. Phys. Commun., 91 (1995), 1-41.doi: 10.1016/0010-4655(95)00041-D.


    M. F. Perutz and A. H. Windle, Cause of neural death in neurodegenerative diseases attributable to expansion of glutamine repeats, Nature, 143 (2001), 143-144.doi: 10.1038/35084141.


    S. B. Prusiner, Novel proteinaceous infectious particles cause scrapie, Science, 216 (1982), 136-144.doi: 10.1126/science.6801762.


    S. B. Prusiner, Molecular biology of prion diseases, Science, 252 (1991), 1515-1522.doi: 10.1126/science.1675487.


    S. B. Prusiner, Molecular biology and pathogenesis of prion diseases, TIBS, 21 (1996), 482-487.doi: 10.1016/S0968-0004(96)10063-3.


    S. B. Prusiner, Prion diseases and the BSE crisis, Science, 278 (1997), 245-251.doi: 10.1126/science.278.5336.245.


    J. Schlitter, M. Engels and P. Kruger, Targeted molecular dynamics: a new approach for searching pathways of conformational transitions, J. Mol. Graphics, 12 (1994), 84-89.doi: 10.1016/0263-7855(94)80072-3.


    A. Scott, Davydov's soliton, Phys. Rep., 217 (1992), 1-67.doi: 10.1016/0370-1573(92)90093-F.


    G. Sieler and R. Schweitzer-Stenner, The amide I mode peptides in aqueous solution involves vibrational coupling between the peptide group and water molecules of the hydration shell, J. Am. Chem. Soc., 119 (1997), 1720-1726.doi: 10.1021/ja960889c.


    M. Tirion, Large amplitude elastic motions in proteins from a single parameter, atomic analysis, Phys. Rev. Letters, 77 (1996), 1905-1908.doi: 10.1103/PhysRevLett.77.1905.


    R. Zahn, A. Liu, T. Luhrs, R. Riek, C. Von Schroetter, F. L. Garcia, M. Billeter, L. Calzolai, G. Wider and K. Wuthrich, NMR solution structure of the human prion protein, Proc. Nat. Acad. Sci. USA, 97 (2000), 145-150.doi: 10.1073/pnas.97.1.145.

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