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 and 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), 621-628. doi: 10.1038/370621a0.

[2]

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

[3]

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

[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), 235-242. doi: 10.1093/nar/28.1.235.

[5]

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

[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, San Francisco, 1999.

[7]

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.

[8]

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

[9]

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

[10]

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.

[11]

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.

[12]

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

[13]

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

[14]

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.

[15]

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.

[16]

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

[17]

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

[18]

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.

[19]

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

[20]

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.

[21]

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

[22]

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

[23]

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.

[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), 11910-11915. doi: 10.1073/pnas.97.22.11910.

[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), 1940-1948. doi: 10.1021/ct800157v.

[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), 637-648. doi: 10.1002/bip.1976.360150404.

[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), 1-41. doi: 10.1016/0010-4655(95)00041-D.

[28]

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

[29]

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

[30]

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

[31]

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

[32]

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

[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), 84-89. doi: 10.1016/0263-7855(94)80072-3.

[34]

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

[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), 1720-1726. doi: 10.1021/ja960889c.

[36]

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.

[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), 145-150. doi: 10.1073/pnas.97.1.145.

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), 621-628. doi: 10.1038/370621a0.

[2]

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

[3]

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

[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), 235-242. doi: 10.1093/nar/28.1.235.

[5]

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

[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, San Francisco, 1999.

[7]

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.

[8]

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

[9]

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

[10]

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.

[11]

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.

[12]

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

[13]

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

[14]

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.

[15]

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.

[16]

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

[17]

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

[18]

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.

[19]

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

[20]

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.

[21]

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

[22]

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

[23]

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.

[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), 11910-11915. doi: 10.1073/pnas.97.22.11910.

[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), 1940-1948. doi: 10.1021/ct800157v.

[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), 637-648. doi: 10.1002/bip.1976.360150404.

[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), 1-41. doi: 10.1016/0010-4655(95)00041-D.

[28]

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

[29]

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

[30]

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

[31]

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

[32]

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

[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), 84-89. doi: 10.1016/0263-7855(94)80072-3.

[34]

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

[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), 1720-1726. doi: 10.1021/ja960889c.

[36]

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.

[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), 145-150. doi: 10.1073/pnas.97.1.145.

[1]

Yining Cao, Chuck Jia, Roger Temam, Joseph Tribbia. Mathematical analysis of a cloud resolving model including the ice microphysics. Discrete and Continuous Dynamical Systems, 2021, 41 (1) : 131-167. doi: 10.3934/dcds.2020219

[2]

James Walsh, Christopher Rackauckas. On the Budyko-Sellers energy balance climate model with ice line coupling. Discrete and Continuous Dynamical Systems - B, 2015, 20 (7) : 2187-2216. doi: 10.3934/dcdsb.2015.20.2187

[3]

Pavel Krejčí, Elisabetta Rocca. Well-posedness of an extended model for water-ice phase transitions. Discrete and Continuous Dynamical Systems - S, 2013, 6 (2) : 439-460. doi: 10.3934/dcdss.2013.6.439

[4]

Keisuke Matsuya, Mikio Murata. Spatial pattern of discrete and ultradiscrete Gray-Scott model. Discrete and Continuous Dynamical Systems - B, 2015, 20 (1) : 173-187. doi: 10.3934/dcdsb.2015.20.173

[5]

Yuncheng You. Dynamics of three-component reversible Gray-Scott model. Discrete and Continuous Dynamical Systems - B, 2010, 14 (4) : 1671-1688. doi: 10.3934/dcdsb.2010.14.1671

[6]

Berat Karaagac. Numerical treatment of Gray-Scott model with operator splitting method. Discrete and Continuous Dynamical Systems - S, 2021, 14 (7) : 2373-2386. doi: 10.3934/dcdss.2020143

[7]

Hongbin Guo, Michael Yi Li. Global dynamics of a staged progression model for infectious diseases. Mathematical Biosciences & Engineering, 2006, 3 (3) : 513-525. doi: 10.3934/mbe.2006.3.513

[8]

M. H. A. Biswas, L. T. Paiva, MdR de Pinho. A SEIR model for control of infectious diseases with constraints. Mathematical Biosciences & Engineering, 2014, 11 (4) : 761-784. doi: 10.3934/mbe.2014.11.761

[9]

Ivo Siekmann, Horst Malchow, Ezio Venturino. An extension of the Beretta-Kuang model of viral diseases. Mathematical Biosciences & Engineering, 2008, 5 (3) : 549-565. doi: 10.3934/mbe.2008.5.549

[10]

Shuo Zhang, Guo Lin. Propagation dynamics in a diffusive SIQR model for childhood diseases. Discrete and Continuous Dynamical Systems - B, 2022, 27 (6) : 3241-3259. doi: 10.3934/dcdsb.2021183

[11]

Kari Eloranta. Archimedean ice. Discrete and Continuous Dynamical Systems, 2013, 33 (9) : 4291-4303. doi: 10.3934/dcds.2013.33.4291

[12]

Yila Bai, Haiqing Zhao, Xu Zhang, Enmin Feng, Zhijun Li. The model of heat transfer of the arctic snow-ice layer in summer and numerical simulation. Journal of Industrial and Management Optimization, 2005, 1 (3) : 405-414. doi: 10.3934/jimo.2005.1.405

[13]

James Walsh. Diffusive heat transport in Budyko's energy balance climate model with a dynamic ice line. Discrete and Continuous Dynamical Systems - B, 2017, 22 (7) : 2687-2715. doi: 10.3934/dcdsb.2017131

[14]

A. K. Misra, Anupama Sharma, Jia Li. A mathematical model for control of vector borne diseases through media campaigns. Discrete and Continuous Dynamical Systems - B, 2013, 18 (7) : 1909-1927. doi: 10.3934/dcdsb.2013.18.1909

[15]

Martin Luther Mann Manyombe, Joseph Mbang, Jean Lubuma, Berge Tsanou. Global dynamics of a vaccination model for infectious diseases with asymptomatic carriers. Mathematical Biosciences & Engineering, 2016, 13 (4) : 813-840. doi: 10.3934/mbe.2016019

[16]

Markus Thäter, Kurt Chudej, Hans Josef Pesch. Optimal vaccination strategies for an SEIR model of infectious diseases with logistic growth. Mathematical Biosciences & Engineering, 2018, 15 (2) : 485-505. doi: 10.3934/mbe.2018022

[17]

Jean-Baptiste Burie, Arnaud Ducrot, Abdoul Aziz Mbengue. Asymptotic behaviour of an age and infection age structured model for the propagation of fungal diseases in plants. Discrete and Continuous Dynamical Systems - B, 2017, 22 (7) : 2879-2905. doi: 10.3934/dcdsb.2017155

[18]

Hiroshi Ito. Input-to-state stability and Lyapunov functions with explicit domains for SIR model of infectious diseases. Discrete and Continuous Dynamical Systems - B, 2021, 26 (9) : 5171-5196. doi: 10.3934/dcdsb.2020338

[19]

Steven G. Krantz and Marco M. Peloso. New results on the Bergman kernel of the worm domain in complex space. Electronic Research Announcements, 2007, 14: 35-41. doi: 10.3934/era.2007.14.35

[20]

Meng Zhang, Kaiyuan Liu, Lansun Chen, Zeyu Li. State feedback impulsive control of computer worm and virus with saturated incidence. Mathematical Biosciences & Engineering, 2018, 15 (6) : 1465-1478. doi: 10.3934/mbe.2018067

2020 Impact Factor: 2.425

Metrics

  • PDF downloads (46)
  • HTML views (0)
  • Cited by (5)

Other articles
by authors

[Back to Top]