메뉴 건너뛰기




Volumn 105, Issue 29, 2008, Pages 9999-10004

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

Author keywords

Double mutant cycles; Fyn SH3 domain; G models; HP model; Langevin dynamics

Indexed keywords

PROTEIN SH3;

EID: 48249138078     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0801874105     Document Type: Article
Times cited : (120)

References (50)
  • 1
    • 0037686252 scopus 로고    scopus 로고
    • The present view of the mechanism of protein folding
    • Daggett V, Fersht A (2003) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4:497-502.
    • (2003) Nat Rev Mol Cell Biol , vol.4 , pp. 497-502
    • Daggett, V.1    Fersht, A.2
  • 2
    • 1342281633 scopus 로고    scopus 로고
    • Kubelka J, Hofrichter J, Eaton WA (2004) The protein folding speed limit. Curr Opin Struct Biol 14:76-88.
    • Kubelka J, Hofrichter J, Eaton WA (2004) The protein folding "speed limit." Curr Opin Struct Biol 14:76-88.
  • 3
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson SE (1998) How do small single-domain proteins fold? Folding Des 3:R81-R91.
    • (1998) Folding Des , vol.3
    • Jackson, S.E.1
  • 4
    • 1542319916 scopus 로고    scopus 로고
    • Cooperativity principles in protein folding
    • Chan HS, Shimizu S, 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
  • 5
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill KA, Chan HS (1997) From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 6
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (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.G.4
  • 7
    • 0042093787 scopus 로고    scopus 로고
    • Origins of chevron rollovers in non-two-state protein folding kinetics
    • Kaya H, Chan HS (2003) Origins of chevron rollovers in non-two-state protein folding kinetics. Phys Rev Lett 90:258104.
    • (2003) Phys Rev Lett , vol.90 , pp. 258104
    • Kaya, H.1    Chan, H.S.2
  • 8
    • 33846708445 scopus 로고    scopus 로고
    • The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection
    • Watters AL, et al. (2007) The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell 128:613-624.
    • (2007) Cell , vol.128 , pp. 613-624
    • Watters, A.L.1
  • 9
    • 0024358426 scopus 로고
    • Mapping the transition state and pathway of protein folding by protein engineering
    • Matouschek A, Kellis JT, Serrano L, Fersht AR (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340:122-126.
    • (1989) Nature , vol.340 , pp. 122-126
    • Matouschek, A.1    Kellis, J.T.2    Serrano, L.3    Fersht, A.R.4
  • 10
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco KW, Simons KT, Baker D (1998) 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    Simons, K.T.2    Baker, D.3
  • 11
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
    • Taketomi H, Ueda Y, Gō N (1975) Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 7:445-459.
    • (1975) Int J Pept Protein Res , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Gō, N.3
  • 12
    • 18344391877 scopus 로고    scopus 로고
    • Protein structures and optimal folding from a geometrical variational principle
    • Micheletti C, Banavar JR, Maritan A, Seno F (1999) Protein structures and optimal folding from a geometrical variational principle. Phys Rev Lett 82:3372-3375.
    • (1999) Phys Rev Lett , vol.82 , pp. 3372-3375
    • Micheletti, C.1    Banavar, J.R.2    Maritan, A.3    Seno, F.4
  • 13
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • Clementi C, Nymeyer H, Onuchic JN (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298:937-953.
    • (2000) J Mol Biol , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 14
    • 0037117477 scopus 로고    scopus 로고
    • Unspecific hydrophobic stabilization of folding transition states
    • Viguera AR, Vega C, Serrano L (2002) Unspecific hydrophobic stabilization of folding transition states. Proc Natl Acad Sci USA 99:5349-5354.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5349-5354
    • Viguera, A.R.1    Vega, C.2    Serrano, L.3
  • 15
    • 33750004434 scopus 로고    scopus 로고
    • Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy
    • Neudecker P, et al. (2006) Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy. J Mol Biol 363:958-976.
    • (2006) J Mol Biol , vol.363 , pp. 958-976
    • Neudecker, P.1
  • 16
    • 34447261443 scopus 로고    scopus 로고
    • The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9
    • Morton VL, Friel CT, Allen LR, Paci E, Radford SE (2007) The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9. J Mol Biol 371:554-568.
    • (2007) J Mol Biol , vol.371 , pp. 554-568
    • Morton, V.L.1    Friel, C.T.2    Allen, L.R.3    Paci, E.4    Radford, S.E.5
  • 17
    • 2542619154 scopus 로고    scopus 로고
    • Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation
    • Di Nardo AA, et al. (2004) Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Proc Natl Acad Sci USA 101:7954-7959.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7954-7959
    • Di Nardo, A.A.1
  • 18
    • 0034112774 scopus 로고    scopus 로고
    • Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
    • Li L, Mirny LA, Shakhnovich EI (2000) Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 7:336-342.
    • (2000) Nat Struct Biol , vol.7 , pp. 336-342
    • Li, L.1    Mirny, L.A.2    Shakhnovich, E.I.3
  • 19
    • 0036836534 scopus 로고    scopus 로고
    • Non-native interactions, effective contact order, and protein folding: A mutational investigation with the energetically frustrated hydrophobic model
    • Treptow WL, Barbosa MA, Garcia LG, Pereira de Araujo AF (2002) Non-native interactions, effective contact order, and protein folding: A mutational investigation with the energetically frustrated hydrophobic model. Proteins 49:167-180.
    • (2002) Proteins , vol.49 , pp. 167-180
    • Treptow, W.L.1    Barbosa, M.A.2    Garcia, L.G.3    Pereira de Araujo, A.F.4
  • 20
    • 3042677501 scopus 로고    scopus 로고
    • The effects of nonnative interactions on protein folding rates: Theory and simulation
    • Clementi C, Plotkin SS (2004) The effects of nonnative interactions on protein folding rates: Theory and simulation. Protein Sci 13:1750-1766.
    • (2004) Protein Sci , vol.13 , pp. 1750-1766
    • Clementi, C.1    Plotkin, S.S.2
  • 21
    • 0043094427 scopus 로고    scopus 로고
    • Folding of lattice protein chains with modified Gō potential
    • Fan K, Wang J, Wang W (2002) Folding of lattice protein chains with modified Gō potential. Eur Phys J B 30:381-391.
    • (2002) Eur Phys J B , vol.30 , pp. 381-391
    • Fan, K.1    Wang, J.2    Wang, W.3
  • 22
    • 0036870910 scopus 로고    scopus 로고
    • The range of the contact interactions and the kinetics of the Go models of proteins
    • Cieplak M, Hoang TX (2002) The range of the contact interactions and the kinetics of the Go models of proteins. Int J Mod Phys C 13:1231-1242.
    • (2002) Int J Mod Phys C , vol.13 , pp. 1231-1242
    • Cieplak, M.1    Hoang, T.X.2
  • 23
    • 0035576033 scopus 로고    scopus 로고
    • Speeding protein folding beyond the Gō model: How a little frustration sometimes helps
    • Plotkin SS (2001) Speeding protein folding beyond the Gō model: How a little frustration sometimes helps. Proteins 45:337-345.
    • (2001) Proteins , vol.45 , pp. 337-345
    • Plotkin, S.S.1
  • 24
  • 25
    • 33645294148 scopus 로고    scopus 로고
    • Conformational entropic barriers in topology-dependent protein folding: Perspectives from a simple native-centric polymer model
    • Wallin S, Chan HS (2006) Conformational entropic barriers in topology-dependent protein folding: Perspectives from a simple native-centric polymer model. J Phys Condens Matter 18:S307-S328.
    • (2006) J Phys Condens Matter , vol.18
    • Wallin, S.1    Chan, H.S.2
  • 26
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
    • Kaya H, Chan HS (2003) Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling? J Mol Biol 326:911-931.
    • (2003) J Mol Biol , vol.326 , pp. 911-931
    • Kaya, H.1    Chan, H.S.2
  • 27
    • 0028929556 scopus 로고
    • Principles of protein folding - A perspective from simple exact models
    • Dill KA, et al. (1995) Principles of protein folding - A perspective from simple exact models. Protein Sci 4:561-602.
    • (1995) Protein Sci , vol.4 , pp. 561-602
    • Dill, K.A.1
  • 28
    • 0036172116 scopus 로고    scopus 로고
    • Hydrophobic core packing in the SH3 domain folding transition state
    • Northey JG, Di Nardo AA, Davidson AR (2002) Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Biol 9:126-130.
    • (2002) Nat Struct Biol , vol.9 , pp. 126-130
    • Northey, J.G.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 29
    • 0036296248 scopus 로고    scopus 로고
    • Protein folding kinetics beyond the Φ value: Using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state
    • Northey JG, Maxwell KL, Davidson AR (2002) Protein folding kinetics beyond the Φ value: Using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J Mol Biol 320:389-402.
    • (2002) J Mol Biol , vol.320 , pp. 389-402
    • Northey, J.G.1    Maxwell, K.L.2    Davidson, A.R.3
  • 30
    • 34748838920 scopus 로고    scopus 로고
    • Protein folding kinetics provides a context-independent assessment of β-strand propensity in the Fyn SH3 domain
    • Zarrine-Afsar A, Dahesh S, Davidson AR (2007) Protein folding kinetics provides a context-independent assessment of β-strand propensity in the Fyn SH3 domain. J Mol Biol 373:764-774.
    • (2007) J Mol Biol , vol.373 , pp. 764-774
    • Zarrine-Afsar, A.1    Dahesh, S.2    Davidson, A.R.3
  • 31
    • 0034284366 scopus 로고    scopus 로고
    • Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity
    • Chan HS (2000) Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity. Proteins 40:543-571.
    • (2000) Proteins , vol.40 , pp. 543-571
    • Chan, H.S.1
  • 32
    • 33749027499 scopus 로고    scopus 로고
    • Criteria for downhill protein folding: Calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity
    • Knott M, Chan HS (2006) Criteria for downhill protein folding: Calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity. Proteins 65:373-391.
    • (2006) Proteins , vol.65 , pp. 373-391
    • Knott, M.1    Chan, H.S.2
  • 33
    • 0000484499 scopus 로고
    • Hydrophobic parameters Π of amino-acid side-chains from the partitioning of N-acetyl-amino-acid amides
    • Fauchère JL, Pliška V (1983) Hydrophobic parameters Π of amino-acid side-chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem 18:369-375.
    • (1983) Eur J Med Chem , vol.18 , pp. 369-375
    • Fauchère, J.L.1    Pliška, V.2
  • 34
    • 0028820703 scopus 로고
    • Denaturant m-values and heat capacity changes - Relation to changes in accessible surface areas of protein unfolding
    • Myers JK, Pace CN, Scholtz JM (1995) Denaturant m-values and heat capacity changes - Relation to changes in accessible surface areas of protein unfolding. Protein Sci 4:2138-2148.
    • (1995) Protein Sci , vol.4 , pp. 2138-2148
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 35
    • 0035970299 scopus 로고    scopus 로고
    • Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states
    • Mok YK, Elisseeva EL, Davidson AR, Forman-Kay JD (2001) Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states. J Mol Biol 307:913-928.
    • (2001) J Mol Biol , vol.307 , pp. 913-928
    • Mok, Y.K.1    Elisseeva, E.L.2    Davidson, A.R.3    Forman-Kay, J.D.4
  • 38
    • 0032734515 scopus 로고    scopus 로고
    • Experiment and theory highlight role of native state topology in SH3 folding
    • Riddle DS, et al. (1999) Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 6:1016-1024.
    • (1999) Nat Struct Biol , vol.6 , pp. 1016-1024
    • Riddle, D.S.1
  • 40
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
    • Martinez JC, Serrano L (1999) The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol 6:1010-1016.
    • (1999) Nat Struct Biol , vol.6 , pp. 1010-1016
    • Martinez, J.C.1    Serrano, L.2
  • 41
    • 35648945863 scopus 로고    scopus 로고
    • Φ-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy
    • Neudecker P, Zarrine-Afsar A, Davidson AR, Kay LE (2007) Φ-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy. Proc Natl Acad Sci USA 104:15717-15722.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 15717-15722
    • Neudecker, P.1    Zarrine-Afsar, A.2    Davidson, A.R.3    Kay, L.E.4
  • 42
    • 0021530861 scopus 로고
    • Characterization of the transition state of lysozyme unfolding. II. Effects of the intrachain crosslinking and the inhibitor binding on the transition state
    • Segawa S, Sugihara M (1984) Characterization of the transition state of lysozyme unfolding. II. Effects of the intrachain crosslinking and the inhibitor binding on the transition state. Biopolymers 23:2489-2498.
    • (1984) Biopolymers , vol.23 , pp. 2489-2498
    • Segawa, S.1    Sugihara, M.2
  • 43
    • 0042130544 scopus 로고    scopus 로고
    • Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity
    • Kaya H, Chan HS (2003) Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity. Proteins 52:510-523.
    • (2003) Proteins , vol.52 , pp. 510-523
    • Kaya, H.1    Chan, H.S.2
  • 44
    • 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
    • Kaya H, Chan HS (2003) 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
    • Kaya, H.1    Chan, H.S.2
  • 45
    • 4644259872 scopus 로고    scopus 로고
    • Three-body interactions improve the prediction of rate and mechanism in protein folding models
    • Ejtehadi MR, Avall SP, Plotkin SS (2004) Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc Natl Acad Sci USA 101:15088-15093.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 15088-15093
    • Ejtehadi, M.R.1    Avall, S.P.2    Plotkin, S.S.3
  • 46
    • 34547516861 scopus 로고    scopus 로고
    • Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding
    • MacCallum JL, Moghaddam MS, Chan HS, Tieleman DP (2007) Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding. Proc Natl Acad Sci USA 104:6206-6210.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 6206-6210
    • MacCallum, J.L.1    Moghaddam, M.S.2    Chan, H.S.3    Tieleman, D.P.4
  • 47
    • 34547466590 scopus 로고    scopus 로고
    • Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates
    • Qi X, Portman JJ (2007) Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates. Proc Natl Acad Sci USA 104:10841-10846.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 10841-10846
    • Qi, X.1    Portman, J.J.2
  • 48
    • 24344449144 scopus 로고    scopus 로고
    • The cooperative nature of hydrophobic forces and protein folding kinetics
    • Wang J, Lee C, Stell G (2005) The cooperative nature of hydrophobic forces and protein folding kinetics. Chem Phys 316:53-60.
    • (2005) Chem Phys , vol.316 , pp. 53-60
    • Wang, J.1    Lee, C.2    Stell, G.3
  • 49
    • 24644490546 scopus 로고    scopus 로고
    • Experimental investigation of the frequency and substitution dependence of negative Φ-values in two-state proteins
    • de los Rios MA, Daneshi M, Plaxco KW (2005) Experimental investigation of the frequency and substitution dependence of negative Φ-values in two-state proteins. Biochemistry 44:12160-12167.
    • (2005) Biochemistry , vol.44 , pp. 12160-12167
    • de los1    Rios, M.A.2    Daneshi, M.3    Plaxco, K.W.4
  • 50
    • 0032542018 scopus 로고    scopus 로고
    • Mutagenesis of a buried polar interaction in an SH3 domain: Sequence conservation provides the best prediction of stability effects
    • Maxwell KL, Davidson AR (1998) Mutagenesis of a buried polar interaction in an SH3 domain: Sequence conservation provides the best prediction of stability effects. Biochemistry 37:16172-16182.
    • (1998) Biochemistry , vol.37 , pp. 16172-16182
    • Maxwell, K.L.1    Davidson, A.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.