October  2011, 4(5): 1033-1046. doi: 10.3934/dcdss.2011.4.1033

The VES hypothesis and protein misfolding

1. 

CCMAR and FCT, Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal

Received  September 2009 Revised  October 2009 Published  December 2010

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.
Citation: Leonor Cruzeiro. The VES hypothesis and protein misfolding. Discrete & Continuous Dynamical Systems - S, 2011, 4 (5) : 1033-1046. doi: 10.3934/dcdss.2011.4.1033
References:
[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.  doi: 10.1038/370621a0.  Google Scholar

[2]

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

[3]

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

[4]

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.  doi: 10.1093/nar/28.1.235.  Google Scholar

[5]

P. F. Bernath, "Spectra of Atoms and Molecules,", 1st edition, (1995).   Google Scholar

[6]

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, (1999).   Google Scholar

[7]

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

[8]

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

[9]

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

[10]

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

[11]

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

[12]

A. S. Davydov, "Solitons in Molecular Systems,", 2nd edition, (1991).   Google Scholar

[13]

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

[14]

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

[15]

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

[16]

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

[17]

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

[18]

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

[19]

J. D. Jackson, "Classical Electrodynamics,", 2nd edition, (1962).   Google Scholar

[20]

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

[21]

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

[22]

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

[23]

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

[24]

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.  doi: 10.1073/pnas.97.22.11910.  Google Scholar

[25]

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.  doi: 10.1021/ct800157v.  Google Scholar

[26]

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.  doi: 10.1002/bip.1976.360150404.  Google Scholar

[27]

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.  doi: 10.1016/0010-4655(95)00041-D.  Google Scholar

[28]

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

[29]

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

[30]

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

[31]

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

[32]

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

[33]

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.  doi: 10.1016/0263-7855(94)80072-3.  Google Scholar

[34]

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

[35]

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.  doi: 10.1021/ja960889c.  Google Scholar

[36]

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

[37]

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.  doi: 10.1073/pnas.97.1.145.  Google Scholar

show all references

References:
[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.  doi: 10.1038/370621a0.  Google Scholar

[2]

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

[3]

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

[4]

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.  doi: 10.1093/nar/28.1.235.  Google Scholar

[5]

P. F. Bernath, "Spectra of Atoms and Molecules,", 1st edition, (1995).   Google Scholar

[6]

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, (1999).   Google Scholar

[7]

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

[8]

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

[9]

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

[10]

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

[11]

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

[12]

A. S. Davydov, "Solitons in Molecular Systems,", 2nd edition, (1991).   Google Scholar

[13]

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

[14]

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

[15]

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

[16]

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

[17]

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

[18]

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

[19]

J. D. Jackson, "Classical Electrodynamics,", 2nd edition, (1962).   Google Scholar

[20]

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

[21]

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

[22]

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

[23]

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

[24]

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.  doi: 10.1073/pnas.97.22.11910.  Google Scholar

[25]

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.  doi: 10.1021/ct800157v.  Google Scholar

[26]

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.  doi: 10.1002/bip.1976.360150404.  Google Scholar

[27]

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.  doi: 10.1016/0010-4655(95)00041-D.  Google Scholar

[28]

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

[29]

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

[30]

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

[31]

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

[32]

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

[33]

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.  doi: 10.1016/0263-7855(94)80072-3.  Google Scholar

[34]

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

[35]

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.  doi: 10.1021/ja960889c.  Google Scholar

[36]

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

[37]

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.  doi: 10.1073/pnas.97.1.145.  Google Scholar

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