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Volumn 15, Issue 7, 2006, Pages 1608-1618

Cooperativity and the origins of rapid, single-exponential kinetics in protein folding

Author keywords

Contact order; Misfolded states; Monte Carlo simulation; Native topology; Optimal folding temperature; Two state

Indexed keywords

POLYMER;

EID: 33745698759     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062180806     Document Type: Article
Times cited : (22)

References (60)
  • 1
    • 0029155772 scopus 로고
    • Impact of local and non-local interactions on thermodynamics and kinetics of protein folding
    • Abkevich, V.I., Gutin, A.M., and Shakhnovich, E.I. 1995. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol. 252: 460-471.
    • (1995) J. Mol. Biol. , vol.252 , pp. 460-471
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 2
    • 0030342453 scopus 로고    scopus 로고
    • Improved design of stable and fast-folding model proteins
    • _. 1996. Improved design of stable and fast-folding model proteins. Fold. Des. 1: 221-230.
    • (1996) Fold. Des. , vol.1 , pp. 221-230
  • 3
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • Bryngelson, J.D. and Wolynes, P.G. 1987. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. 84: 7524-7528.
    • (1987) Proc. Natl. Acad. Sci. , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 4
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • _. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93: 6902-6915.
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
  • 5
    • 0028947257 scopus 로고
    • Funnels, pathways and the energy landscape of protein folding: A synthesis
    • Bryngelson, J.D., Onuchic, J.N., Socci, N.D., and Wolynes, P. 1995. Funnels, pathways and the energy landscape of protein folding: A synthesis. Proteins 21: 167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.4
  • 6
    • 0001544150 scopus 로고    scopus 로고
    • Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus
    • Buchler, N.E.G. and Goldstein, R.A. 2000. Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus. J. Chem. Phys. 112: 2533-2547.
    • (2000) J. Chem. Phys. , vol.112 , pp. 2533-2547
    • Buchler, N.E.G.1    Goldstein, R.A.2
  • 7
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Chan, H.S. and Dill, K.A. 1997. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4: 10-19.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Chan, H.S.1    Dill, K.A.2
  • 8
    • 0003166498 scopus 로고    scopus 로고
    • Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
    • _. 1998. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30: 2-33.
    • (1998) Proteins , vol.30 , pp. 2-33
  • 9
    • 1542319916 scopus 로고    scopus 로고
    • Cooperativity principles in protein folding
    • Chan, H.S., Shimizu, S., and Kaya, H. 2004. Cooperativity principles in protein folding. Methods Enzymol. 380: 350-379.
    • (2004) Methods Enzymol. , vol.380 , pp. 350-379
    • Chan, H.S.1    Shimizu, S.2    Kaya, H.3
  • 11
    • 0000239504 scopus 로고    scopus 로고
    • Master equation approach to protein folding and kinetic traps
    • Cieplak, M., Henkel, M., Karbowski, J., and Banavar, J.R. 1998. Master equation approach to protein folding and kinetic traps. Phys. Rev. Lett. 80: 3654-3657.
    • (1998) Phys. Rev. Lett. , vol.80 , pp. 3654-3657
    • Cieplak, M.1    Henkel, M.2    Karbowski, J.3    Banavar, J.R.4
  • 12
    • 0000301323 scopus 로고    scopus 로고
    • Scaling of folding properties in simple models of proteins
    • Cieplack, M., Hoang, T.X., and Li, M.S. 1999. Scaling of folding properties in simple models of proteins. Phys. Rev. Lett. 83: 1684-1687.
    • (1999) Phys. Rev. Lett. , vol.83 , pp. 1684-1687
    • Cieplack, M.1    Hoang, T.X.2    Li, M.S.3
  • 13
    • 0035826032 scopus 로고    scopus 로고
    • Role of explicitly cooperative interactions in protein folding funnels: A simulation study
    • Eastwood, M.P. and Wolynes, P.G. 2001. Role of explicitly cooperative interactions in protein folding funnels: A simulation study. J. Chem. Phys. 114: 4702-4716.
    • (2001) J. Chem. Phys. , vol.114 , pp. 4702-4716
    • Eastwood, M.P.1    Wolynes, P.G.2
  • 14
    • 4644259872 scopus 로고    scopus 로고
    • Three-body interactions improve the prediction of rate and mechanism in protein folding models
    • Ejtehadi, M.R., Avall, S.P., and Plotkin, S.S. 2004. Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc. Natl. Acad. Sci. 101: 15088-15093.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 15088-15093
    • Ejtehadi, M.R.1    Avall, S.P.2    Plotkin, S.S.3
  • 15
    • 0037156117 scopus 로고    scopus 로고
    • Thermodynamic control and dynamical regimes in protein folding
    • Faísca, P.F.N. and Ball, R.C. 2002a. Thermodynamic control and dynamical regimes in protein folding. J. Chem. Phys. 116: 7231-7238.
    • (2002) J. Chem. Phys. , vol.116 , pp. 7231-7238
    • Faísca, P.F.N.1    Ball, R.C.2
  • 16
    • 0037044965 scopus 로고    scopus 로고
    • Topological complexity, contact order, and protein folding rates
    • _. 2002b. Topological complexity, contact order, and protein folding rates. J. Chem. Phys. 117: 8587-8591.
    • (2002) J. Chem. Phys. , vol.117 , pp. 8587-8591
  • 17
    • 24644503109 scopus 로고    scopus 로고
    • The Gō model revisited: Native structure and the geometric coupling between local and long-range contacts
    • Faísca, P.F.N., da Gama, M.M., and Nunes, A. 2005. The Gō model revisited: Native structure and the geometric coupling between local and long-range contacts. Proteins 60: 712-722.
    • (2005) Proteins , vol.60 , pp. 712-722
    • Faísca, P.F.N.1    Da Gama, M.M.2    Nunes, A.3
  • 19
    • 0037091023 scopus 로고    scopus 로고
    • Three-body correlations in protein folding: The origin of cooperativity
    • Fernandez, A., Colubri, A., and Berry, R.S. 2002. Three-body correlations in protein folding: The origin of cooperativity. Physica A (Amsterdam) 307: 235-259.
    • (2002) Physica A (Amsterdam) , vol.307 , pp. 235-259
    • Fernandez, A.1    Colubri, A.2    Berry, R.S.3
  • 20
    • 0034710944 scopus 로고    scopus 로고
    • Non-glassy kinetics in the folding of a simple, single domain protein
    • Gillespie, B. and Plaxco, K.W. 2000. Non-glassy kinetics in the folding of a simple, single domain protein. Proc. Natl. Acad. Sci. 97: 12014-12019.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 12014-12019
    • Gillespie, B.1    Plaxco, K.W.2
  • 21
    • 3943113660 scopus 로고    scopus 로고
    • Using protein folding rates to test protein folding theories
    • _. 2004. Using protein folding rates to test protein folding theories. Annu. Rev. Biochem. 73: 837-859.
    • (2004) Annu. Rev. Biochem. , vol.73 , pp. 837-859
  • 22
    • 0041530316 scopus 로고    scopus 로고
    • NMR and Temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics
    • Gillespie, B., Vu, D., Shah, P.S., Marshall, S., Dyer, R.B., Mayo, S.L., and Plaxco, K.W. 2003. NMR and Temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics. J. Mol. Biol. 330: 813-819.
    • (2003) J. Mol. Biol. , vol.330 , pp. 813-819
    • Gillespie, B.1    Vu, D.2    Shah, P.S.3    Marshall, S.4    Dyer, R.B.5    Mayo, S.L.6    Plaxco, K.W.7
  • 23
    • 0028999105 scopus 로고
    • Searching for foldable protein structures using optimized energy functions
    • Govindarajan, S. and Goldstein, R.A. 1995. Searching for foldable protein structures using optimized energy functions. Biopolymers 36: 43-51.
    • (1995) Biopolymers , vol.36 , pp. 43-51
    • Govindarajan, S.1    Goldstein, R.A.2
  • 24
    • 0035967862 scopus 로고    scopus 로고
    • Comparison between long-range interactions and contact order in determining the folding rate of two-state folders: Application of long-range order to folding rate prediction
    • Gromiha, M.M. and Selvaraj, S. 2001. Comparison between long-range interactions and contact order in determining the folding rate of two-state folders: Application of long-range order to folding rate prediction. J. Mol. Biol. 310: 27-32.
    • (2001) J. Mol. Biol. , vol.310 , pp. 27-32
    • Gromiha, M.M.1    Selvaraj, S.2
  • 26
    • 0031746226 scopus 로고    scopus 로고
    • A protein engineering analysis of the transition state for protein folding: Simulation in the lattice model
    • _. 1998a. A protein engineering analysis of the transition state for protein folding: Simulation in the lattice model. Fold. Des. 3: 183-194.
    • (1998) Fold. Des. , vol.3 , pp. 183-194
  • 27
    • 0001229818 scopus 로고    scopus 로고
    • Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition
    • Gutin, A., Sali, A., Abkevich, V., Karplus, M., and Shakhnovich, E.I. 1998b. Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition. J. Chem. Phys. 108: 6466-6483.
    • (1998) J. Chem. Phys. , vol.108 , pp. 6466-6483
    • Gutin, A.1    Sali, A.2    Abkevich, V.3    Karplus, M.4    Shakhnovich, E.I.5
  • 28
    • 0037423710 scopus 로고    scopus 로고
    • Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates
    • Jewett, A., Pande, V.S., and Plaxco, K.W. 2003. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J. Mol. Biol. 326: 247-253.
    • (2003) J. Mol. Biol. , vol.326 , pp. 247-253
    • Jewett, A.1    Pande, V.S.2    Plaxco, K.W.3
  • 29
    • 0034310589 scopus 로고    scopus 로고
    • Energetic components of cooperative protein folding
    • Kaya, H. and Chan, H.S. 2000. Energetic components of cooperative protein folding. Phys. Rev. Lett. 85: 4823-4826.
    • (2000) Phys. Rev. Lett. , vol.85 , pp. 4823-4826
    • Kaya, H.1    Chan, H.S.2
  • 30
    • 0042130544 scopus 로고    scopus 로고
    • Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity
    • _. 2003a. Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity. Proteins 52: 510-523.
    • (2003) Proteins , vol.52 , pp. 510-523
  • 31
    • 0042631521 scopus 로고    scopus 로고
    • Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences
    • _. 2003b. Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins 52: 524-533.
    • (2003) Proteins , vol.52 , pp. 524-533
  • 32
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamic and kinetics cooperativity: How adequate is native-centric topological modeling?
    • _. 2003c. Solvation effects and driving forces for protein thermodynamic and kinetics cooperativity: How adequate is native-centric topological modeling? J. Mol. Biol. 326: 911-931.
    • (2003) J. Mol. Biol. , vol.326 , pp. 911-931
  • 33
    • 19444381093 scopus 로고    scopus 로고
    • Chevron behaviour and isostable enthalpic barriers in protein folding: Successes and limitations of simple Go-like modeling
    • Kaya, H., Liu, Z., and Chan, H.S. 2005. Chevron behaviour and isostable enthalpic barriers in protein folding: Successes and limitations of simple Go-like modeling. Biophys. J. 89: 520-535.
    • (2005) Biophys. J. , vol.89 , pp. 520-535
    • Kaya, H.1    Liu, Z.2    Chan, H.S.3
  • 34
    • 1342324030 scopus 로고    scopus 로고
    • Exploring folding free energy landscapes using computational protein design
    • Kuhlman, B. and Baker, D. 2004. Exploring folding free energy landscapes using computational protein design. Curr. Opin. Struct. Biol. 14: 89-95.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 89-95
    • Kuhlman, B.1    Baker, D.2
  • 36
    • 0037215268 scopus 로고    scopus 로고
    • The topomer search model: A quantitative, first-principles description of two-state protein folding kinetics
    • Makarov, D.E. and Plaxco, K.W. 2003. The topomer search model: A quantitative, first-principles description of two-state protein folding kinetics. Protein Sci. 12: 17-26.
    • (2003) Protein Sci. , vol.12 , pp. 17-26
    • Makarov, D.E.1    Plaxco, K.W.2
  • 39
    • 0036606863 scopus 로고    scopus 로고
    • Emergence of highly designable protein-backbone conformations in an off-lattice model
    • Miller, J., Zeng, C., Wingreen, N.S., and Tang, C. 2002. Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins 47: 506-512.
    • (2002) Proteins , vol.47 , pp. 506-512
    • Miller, J.1    Zeng, C.2    Wingreen, N.S.3    Tang, C.4
  • 40
    • 0030334626 scopus 로고    scopus 로고
    • Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model
    • Mirny, L.A., Abkevich, V., and Shakhnovich, E.I. 1996. Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model. Fold. Des. 1: 103-116.
    • (1996) Fold. Des. , vol.1 , pp. 103-116
    • Mirny, L.A.1    Abkevich, V.2    Shakhnovich, E.I.3
  • 41
    • 0032574769 scopus 로고    scopus 로고
    • How evolution makes proteins fold quickly
    • _. 1998. How evolution makes proteins fold quickly. Proc. Natl. Acad. Sci. 95: 4976-4981.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 4976-4981
  • 42
    • 33845377127 scopus 로고
    • Estimation of effective inter-residue contact energies from protein crystal-structures-quasi-chemical approximation
    • Miyazawa, S. and Jernigan, R.L. 1985. Estimation of effective inter-residue contact energies from protein crystal-structures-quasi-chemical approximation. Macromolecules 18: 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 43
    • 0000329743 scopus 로고    scopus 로고
    • Symmetry and kinetic optimization of proteinlike heteropolymers
    • Nelson, E.D., Teneyck, L.F., and Onuchic, J.N. 1997. Symmetry and kinetic optimization of proteinlike heteropolymers. Phys. Rev. Lett. 79: 3534-3537.
    • (1997) Phys. Rev. Lett. , vol.79 , pp. 3534-3537
    • Nelson, E.D.1    Teneyck, L.F.2    Onuchic, J.N.3
  • 44
    • 0032568599 scopus 로고    scopus 로고
    • Folding funnels and frustration in off-lattice minimalist protein landscapes
    • Nymeyer, H., Garca, A.E., and Onuchic, J.N. 1998. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl. Acad. Sci. 95: 5921-5928.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 5921-5928
    • Nymeyer, H.1    Garca, A.E.2    Onuchic, J.N.3
  • 46
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco, K.W., Simmons, K.T., and Baker, D. 1998a. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 985-994.
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simmons, K.T.2    Baker, D.3
  • 48
    • 0007463680 scopus 로고    scopus 로고
    • Statistical mechanics of a correlated energy landscape model for protein folding funnels
    • Plotkin, S.S., Wang, J., and Wolynes, P.G. 1997. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J. Chem. Phys. 106: 2932-2948.
    • (1997) J. Chem. Phys. , vol.106 , pp. 2932-2948
    • Plotkin, S.S.1    Wang, J.2    Wolynes, P.G.3
  • 49
    • 0027409570 scopus 로고
    • A geometrical constraint approach for reproducing the native backbone conformation of a protein
    • Saitoh, S., Nakai, T., and Nishikawa, K. 1993. A geometrical constraint approach for reproducing the native backbone conformation of a protein. Proteins 15: 191-204.
    • (1993) Proteins , vol.15 , pp. 191-204
    • Saitoh, S.1    Nakai, T.2    Nishikawa, K.3
  • 51
    • 1842635571 scopus 로고    scopus 로고
    • Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection
    • Scalley-Kim, M. and Baker, D. 2004. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J. Mol. Biol. 338: 573-583.
    • (2004) J. Mol. Biol. , vol.338 , pp. 573-583
    • Scalley-Kim, M.1    Baker, D.2
  • 52
    • 4243392673 scopus 로고
    • Proteins with selected sequences fold into unique native conformation
    • Shakhnovich, E.I. 1994. Proteins with selected sequences fold into unique native conformation. Phys. Rev. Lett. 72: 3907-3910.
    • (1994) Phys. Rev. Lett. , vol.72 , pp. 3907-3910
    • Shakhnovich, E.I.1
  • 53
    • 0027234766 scopus 로고
    • Engineering of stable and fast-folding sequences of model proteins
    • Shakhnovich, E.I. and Gutin, A.M. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. 90: 7195-7199.
    • (1993) Proc. Natl. Acad. Sci. , vol.90 , pp. 7195-7199
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 54
    • 0000630681 scopus 로고
    • Protein folding bottlenecks: A lattice Monte Carlo simulation
    • Shakhnovich, E., Farztdinov, G., Gutin, A.M., and Karplus, M. 1991. Protein folding bottlenecks: A lattice Monte Carlo simulation. Phys. Rev. Lett. 67: 1665-1667.
    • (1991) Phys. Rev. Lett. , vol.67 , pp. 1665-1667
    • Shakhnovich, E.1    Farztdinov, G.2    Gutin, A.M.3    Karplus, M.4
  • 55
    • 0033607208 scopus 로고    scopus 로고
    • Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
    • Shea, J.E., Onuchic, J.N., and Brooks, C.L. 1999. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A. Proc. Natl. Acad. Sci. 96: 12512-12517.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 12512-12517
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 56
    • 0036643497 scopus 로고    scopus 로고
    • Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins
    • Shimizu, S. and Chan, H.S. 2002. Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins. Proteins 48: 15-30.
    • (2002) Proteins , vol.48 , pp. 15-30
    • Shimizu, S.1    Chan, H.S.2
  • 57
    • 0032147243 scopus 로고    scopus 로고
    • Protein folding mechanisms and the multidimensional folding funnel
    • Socci, N.D., Onuchic, J.N., and Wolynes, P.G. 1998. Protein folding mechanisms and the multidimensional folding funnel. Proteins 32: 136-158.
    • (1998) Proteins , vol.32 , pp. 136-158
    • Socci, N.D.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 58
    • 0032606941 scopus 로고    scopus 로고
    • Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
    • Takada, S., Luthey-Schulten, Z.A., and Wolynes, P.G. 1999. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer. J. Chem. Phys. 110: 11616-11629.
    • (1999) J. Chem. Phys. , vol.110 , pp. 11616-11629
    • Takada, S.1    Luthey-Schulten, Z.A.2    Wolynes, P.G.3
  • 59
    • 0000095559 scopus 로고
    • The problem of the heme interactions in hemoglobin and the basis of the Bohr effect
    • Wyman, J. and Allen, D.W. 1951. The problem of the heme interactions in hemoglobin and the basis of the Bohr effect. J. Polym. Sci. 7: 499-518.
    • (1951) J. Polym. Sci. , vol.7 , pp. 499-518
    • Wyman, J.1    Allen, D.W.2


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