메뉴 건너뛰기




Volumn 13, Issue 9, 2004, Pages 2446-2457

What can one learn from experiments about the elusive transition state?

Author keywords

Protein engineering; Protein folding; Transition state

Indexed keywords

PROTEIN; RECOMBINANT PROTEIN;

EID: 4344572930     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04713804     Document Type: Article
Times cited : (26)

References (51)
  • 1
    • 0019571422 scopus 로고
    • Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins
    • Abe, H. and Go, N. 1981. Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins. Biopolymers 20: 1013-1031.
    • (1981) Biopolymers , vol.20 , pp. 1013-1031
    • Abe, H.1    Go, N.2
  • 2
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding: Evidence from the lattice model
    • Abkevich, V.I., Gutin, A.M., and Shakhnovich, E.I. 1994. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33: 10026-10036.
    • (1994) Biochemistry , vol.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 3
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C. 1973. Principles that govern the folding of protein chains. Science 181: 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.1
  • 4
    • 0032972986 scopus 로고    scopus 로고
    • Is protein folding hierarchic? I. Local structure and peptide folding
    • Baldwin, R.L. and Rose, G.D. 1999a. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24: 26-33.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 26-33
    • Baldwin, R.L.1    Rose, G.D.2
  • 5
    • 0033080081 scopus 로고    scopus 로고
    • Is protein folding hierarchic? II. Folding intermediates and transition states
    • -. 1999b. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24: 77-83.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 77-83
  • 6
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • Becker, O.M. and Karplus, M. 1997. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics. J. Chem. Phys. 106: 1495-1517.
    • (1997) J. Chem. Phys. , vol.106 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 7
    • 0037166875 scopus 로고    scopus 로고
    • Exact solution of the Munoz-Eaton model for protein folding
    • Bruscolini, P. and Pelizzola, A. 2002. Exact solution of the Munoz-Eaton model for protein folding. Phys. Rev. Lett. 88: 258101.
    • (2002) Phys. Rev. Lett. , vol.88 , pp. 258101
    • Bruscolini, P.1    Pelizzola, A.2
  • 9
    • 0003166498 scopus 로고    scopus 로고
    • Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
    • Chan, H.S., and Dill, K.A. 1998. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30: 2-33.
    • (1998) Proteins , vol.30 , pp. 2-33
    • Chan, H.S.1    Dill, K.A.2
  • 10
    • 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
    • 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., and Onuchic, J.N. 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
  • 13
    • 0032570532 scopus 로고    scopus 로고
    • Folding intermediates of wild-type and mutants of barnase. I. Use of φ-value analysis and m values to probe the cooperative nature of the folding pre-equilibrium
    • Dalby, P.A., Oliveberg, M., and Fersht, A.R. 1998. Folding intermediates of wild-type and mutants of barnase. I. Use of φ-value analysis and m values to probe the cooperative nature of the folding pre-equilibrium. J. Mol. Biol. 276: 625-646.
    • (1998) J. Mol. Biol. , vol.276 , pp. 625-646
    • Dalby, P.A.1    Oliveberg, M.2    Fersht, A.R.3
  • 14
    • 0036927818 scopus 로고    scopus 로고
    • Direct molecular dynamics observation of protein folding transition state ensemble
    • Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.H., and Shakhnovich, E.I. 2002. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83: 3525-3532.
    • (2002) Biophys. J. , vol.83 , pp. 3525-3532
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.H.4    Shakhnovich, E.I.5
  • 16
    • 0344301982 scopus 로고    scopus 로고
    • Protein folding: A perspective from theory and experiment
    • Dobson, C.M., Sali, A., and Karplus, M. 1998. Protein folding: A perspective from theory and experiment. Angew. Chem. Int. Ed. 37: 868-893.
    • (1998) Angew. Chem. Int. Ed. , vol.37 , pp. 868-893
    • Dobson, C.M.1    Sali, A.2    Karplus, M.3
  • 17
    • 0034628914 scopus 로고    scopus 로고
    • Identifying the protein folding nucleus using molecular dynamics simulations
    • Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., and Shakhnovich, E.I. 2000. Identifying the protein folding nucleus using molecular dynamics simulations. J. Mol. Biol. 296: 1183-1188.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1183-1188
    • Dokholyan, N.V.1    Buldyrev, S.V.2    Stanley, H.E.3    Shakhnovich, E.I.4
  • 18
    • 0000346442 scopus 로고
    • The application of the theory of absolute reaction rates to proteins
    • Eyring, H. and Stern, A.E. 1939. The application of the theory of absolute reaction rates to proteins. Chem. Rev. 24: 253-270.
    • (1939) Chem. Rev. , vol.24 , pp. 253-270
    • Eyring, H.1    Stern, A.E.2
  • 19
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht, A.R. 1997. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7: 3-9.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 21
    • 0037062047 scopus 로고    scopus 로고
    • Energy landscape and native-state structure of proteins - A simplified model
    • Flammini, A., Banavar, J.R., and Maritan, A. 2002. Energy landscape and native-state structure of proteins-A simplified model. Europhys. Lett. 58: 623-629.
    • (2002) Europhys. Lett. , vol.58 , pp. 623-629
    • Flammini, A.1    Banavar, J.R.2    Maritan, A.3
  • 22
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
    • Itzhaki, L.S., Otzen, D.E., and Fersht, A.R. 1995. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254: 260-288.
    • (1995) J. Mol. Biol. , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 23
    • 0026345750 scopus 로고
    • Folding of chymoptrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson, S.E. and Fersht, A.R. 1991. Folding of chymoptrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30: 10428-10435.
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 24
    • 0035836687 scopus 로고    scopus 로고
    • Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution
    • Kazmirski, S.L., Wong, K.-B., Freund, S.M.V., Tan, Y.-J., Fersht, A.R., and Daggett, V. 2001. Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proc. Natl. Acad. Sci. 98: 4349-4354.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 4349-4354
    • Kazmirski, S.L.1    Wong, K.-B.2    Freund, S.M.V.3    Tan, Y.-J.4    Fersht, A.R.5    Daggett, V.6
  • 25
    • 0035370662 scopus 로고    scopus 로고
    • Multiple protein folding nuclei and the transition state ensemble in two-state proteins
    • Klimov, D.K. and Thirumalai, D. 2001. Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins 43: 465-475.
    • (2001) Proteins , vol.43 , pp. 465-475
    • Klimov, D.K.1    Thirumalai, D.2
  • 26
    • 0035956901 scopus 로고    scopus 로고
    • Solvent effects on the energy landscapes and folding kinetics of polyalanine
    • Levy, Y., Jortner, J., and Becker, O.M. 2001. Solvent effects on the energy landscapes and folding kinetics of polyalanine. Proc. Natl. Acad. Sci. 98: 2188-2193.
    • (2001) Proc. Natl. Acad. Sci , vol.98 , pp. 2188-2193
    • Levy, Y.1    Jortner, J.2    Becker, O.M.3
  • 27
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
    • Li, A. and Daggett, V. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. 91: 10430-10434.
    • (1994) Proc. Natl. Acad. Sci. , vol.91 , pp. 10430-10434
    • Li, A.1    Daggett, V.2
  • 28
    • 0034112774 scopus 로고    scopus 로고
    • Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
    • Li, L., Mirny, A.L., and Shakhnovich, E.I. 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, A.L.2    Shakhnovich, E.I.3
  • 29
    • 0024358426 scopus 로고
    • Mapping the transition state and pathway of protein folding by protein engineering
    • Matouschek, A., Kellis Jr., J.T., Serrano, L., and Fersht, A.R. 1989. Mapping the transition state and pathway of protein folding by protein engineering. Nature 342: 122-126.
    • (1989) Nature , vol.342 , pp. 122-126
    • Matouschek, A.1    Kellis Jr., J.T.2    Serrano, L.3    Fersht, A.R.4
  • 30
    • 0025698613 scopus 로고
    • Transient folding intermediates characterized by protein engineering
    • Matouschek, A., Kellis Jr., J.T., Serrano, L., Bycroft, M., and Fersht, A.R. 1990. Transient folding intermediates characterized by protein engineering. Nature 346: 440-445.
    • (1990) Nature , vol.346 , pp. 440-445
    • Matouschek, A.1    Kellis Jr., J.T.2    Serrano, L.3    Bycroft, M.4    Fersht, A.R.5
  • 31
    • 0026550397 scopus 로고
    • The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure
    • Matouschek, A., Serrano, L., and Fersht, A.R. 1992. The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure. J. Mol. Biol. 224: 819-835.
    • (1992) J. Mol. Biol. , vol.224 , pp. 819-835
    • Matouschek, A.1    Serrano, L.2    Fersht, A.R.3
  • 32
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • Munoz, V. and Eaton, W.A. 1999. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. 96: 11311-11316.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 11311-11316
    • Munoz, V.1    Eaton, W.A.2
  • 33
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of β-hairpin formation
    • Munoz, V., Thompson, P.A., Hofrichter, J., and Eaton, W.A. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature 390: 196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 35
    • 0035252685 scopus 로고    scopus 로고
    • Characterisation of the transition states for protein folding: Towards a new level of mechanistic detail in protein engineering analysis
    • Oliveberg, M. 2001. Characterisation of the transition states for protein folding: Towards a new level of mechanistic detail in protein engineering analysis. Curr. Op. Str. Biol. 11: 94-100.
    • (2001) Curr. Op. Str. Biol. , vol.11 , pp. 94-100
    • Oliveberg, M.1
  • 36
    • 0028981210 scopus 로고
    • Negative activation enthalpies in the kinetics of protein folding
    • Oliveberg, M., Tan, Y.-J., and Fersht, A.R. 1995. Negative activation enthalpies in the kinetics of protein folding. Proc. Natl. Acad. Sci. 92: 8926-8929.
    • (1995) Proc. Natl. Acad. Sci. , vol.92 , pp. 8926-8929
    • Oliveberg, M.1    Tan, Y.-J.2    Fersht, A.R.3
  • 38
    • 0027948175 scopus 로고
    • The structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding
    • Otzen, D.S., ElMasry, N., Jackson, S.E., and Fersht, A.R. 1994. The structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc. Natl. Acad. Sci. 91: 10422-10425.
    • (1994) Proc. Natl. Acad. Sci. , vol.91 , pp. 10422-10425
    • Otzen, D.S.1    ElMasry, N.2    Jackson, S.E.3    Fersht, A.R.4
  • 40
    • 0034872511 scopus 로고    scopus 로고
    • Transition states and the meaning of φ values in protein folding kinetics
    • Ozkan, S.B., Bahar, I., and Dill, K.A. 2001. Transition states and the meaning of φ values in protein folding kinetics. Nat. Struct. Biol. 8: 765-769.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 765-769
    • Ozkan, S.B.1    Bahar, I.2    Dill, K.A.3
  • 41
    • 0036074173 scopus 로고    scopus 로고
    • Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
    • Ozkan, S.B., Dill, K.A., and Bahar, I. 2002. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Sci. 11: 1971-1977.
    • (2002) Protein Sci. , vol.11 , pp. 1971-1977
    • Ozkan, S.B.1    Dill, K.A.2    Bahar, I.3
  • 42
    • 0037457892 scopus 로고    scopus 로고
    • Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain
    • Paci, E., Clarke, J., Steward, A., Vendruscolo, M., and Karplus, M. 2003. Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain. Proc. Natl. Acad. Sci. 100: 394-399.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 394-399
    • Paci, E.1    Clarke, J.2    Steward, A.3    Vendruscolo, M.4    Karplus, M.5
  • 43
    • 0033574069 scopus 로고    scopus 로고
    • Folding pathway of a lattice model for proteins
    • Pande, V.S. and Rokhsar, D.S. 1999a. Folding pathway of a lattice model for proteins. Proc. Natl. Acad. Sci. 96: 1273-1278.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 1273-1278
    • Pande, V.S.1    Rokhsar, D.S.2
  • 44
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G
    • -. 1999b. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G. Proc. Natl. Acad. Sci. 96: 9062-9067.
    • (1999) Proc. Natl. Acad. Sci , vol.96 , pp. 9062-9067
  • 47
    • 0034321011 scopus 로고    scopus 로고
    • Energetic frustration and the nature of the transition state in protein folding
    • Shea, J.E., Onuchic, J.N., and Brooks, C.L. 2000. Energetic frustration and the nature of the transition state in protein folding. J. Chem. Phys. 113: 7663-7671.
    • (2000) J. Chem. Phys. , vol.113 , pp. 7663-7671
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 48
    • 0033592876 scopus 로고    scopus 로고
    • From snapshot to movie: φ Analysis of protein folding transition states taken one step further
    • Ternstroem, T., Mayor, U., Akke, M., and Oliveberg, M. 1999. From snapshot to movie: φ analysis of protein folding transition states taken one step further. Proc. Natl. Acad. Sci. 96: 14854-14859.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 14854-14859
    • Ternstroem, T.1    Mayor, U.2    Akke, M.3    Oliveberg, M.4
  • 49
    • 0030067976 scopus 로고    scopus 로고
    • Importance of two buried salt bridges in the stability and folding pathway of barnase
    • Tissot, A.C., Vuilleumier, S., and Fersht, A.R. 1996. Importance of two buried salt bridges in the stability and folding pathway of barnase. Biochemistry 35: 6786-6794.
    • (1996) Biochemistry , vol.35 , pp. 6786-6794
    • Tissot, A.C.1    Vuilleumier, S.2    Fersht, A.R.3
  • 50
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo, M., Paci, E., Dobson, C.M., and Karplus, M. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature 409: 641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.