메뉴 건너뛰기




Volumn 322, Issue 2, 2002, Pages 463-476

Simple physical models connect theory and experiment in protein folding kinetics

Author keywords

Kinetics; Master equation; Protein folding; Transition state; values

Indexed keywords

HYDROGEN;

EID: 0036384269     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00706-4     Document Type: Article
Times cited : (88)

References (46)
  • 1
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • Alm, E. & Baker, D. (1999). Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl Acad. Sci. USA, 96, 11305-11310.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 2
    • 0033613131 scopus 로고    scopus 로고
    • A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
    • Galzitskaya, O. & Finkelstein, A. (1999). A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl Acad. Sci. USA, 96, 11299-11304.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11299-11304
    • Galzitskaya, O.1    Finkelstein, A.2
  • 3
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • Munoz, V. & Eaton, W. (1999). A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl Acad. Sci. USA, 96, 11311-11316.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11311-11316
    • Munoz, V.1    Eaton, W.2
  • 4
    • 0000227308 scopus 로고    scopus 로고
    • Variational theory for site resolved protein folding free energy surfaces
    • Portman, J., Takada, S. & Wolynes, P. (1998). Variational theory for site resolved protein folding free energy surfaces. Phys. Rev. Lett. 81, 5237-5240.
    • (1998) Phys. Rev. Lett. , vol.81 , pp. 5237-5240
    • Portman, J.1    Takada, S.2    Wolynes, P.3
  • 5
    • 0035868476 scopus 로고    scopus 로고
    • Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
    • Portman, J., Takada, S. & Wolynes, P. (2001). Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach. J. Chem. Phys. 114, 5069-5081.
    • (2001) J. Chem. Phys. , vol.114 , pp. 5069-5081
    • Portman, J.1    Takada, S.2    Wolynes, P.3
  • 6
    • 0035868526 scopus 로고    scopus 로고
    • Microscopic theory of protein folding rates. II. Local reaction coordinates and chaindynamics
    • Portman, J., Takada, S. & Wolynes, P. (2001). Microscopic theory of protein folding rates. II. Local reaction coordinates and chaindynamics. J. Chem. Phys. 114, 5082-5096.
    • (2001) J. Chem. Phys. , vol.114 , pp. 5082-5096
    • Portman, J.1    Takada, S.2    Wolynes, P.3
  • 7
    • 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, J. (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.3
  • 8
    • 0035850732 scopus 로고    scopus 로고
    • Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model
    • Koga, N. & Takada, S. (2001). Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. J. Mol. Biol. 313, 171-180.
    • (2001) J. Mol. Biol. , vol.313 , pp. 171-180
    • Koga, N.1    Takada, S.2
  • 9
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco, K., Simons, K. & 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.1    Simons, K.2    Baker, D.3
  • 11
    • 0034685619 scopus 로고    scopus 로고
    • A breakdown of symmetry in the folding transition state of protein L.
    • Kim, D., Fisher, C. & Baker, D. (2000). A breakdown of symmetry in the folding transition state of protein L. J. Mol. Biol. 298, 971-984.
    • (2000) J. Mol. Biol. , vol.298 , pp. 971-984
    • Kim, D.1    Fisher, C.2    Baker, D.3
  • 12
    • 0033871567 scopus 로고    scopus 로고
    • Critical role of beta-hairpin formation in protein g folding
    • McCallister, E., Alm, E. & Baker, D. (2000). Critical role of beta-hairpin formation in protein g folding. Nature Struct. Biol. 7, 669-673.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 669-673
    • McCallister, E.1    Alm, E.2    Baker, D.3
  • 13
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • Nauli, S., Kuhlman, B. & Baker, D. (2001). Computer-based redesign of a protein folding pathway. Nature Struct. Biol. 8, 602-605.
    • (2001) Nature Struct. Biol. , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman, B.2    Baker, D.3
  • 14
    • 0035845509 scopus 로고    scopus 로고
    • Conversion of monomeric protein L to an obligate dimer by computational protein design
    • Kuhlman, B., O'Neill, J., Kim, D., Zhang, K. & Baker, D. (2001). Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc. Natl Acad. Sci. USA, 98, 10687-10691.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10687-10691
    • Kuhlman, B.1    O'Neill, J.2    Kim, D.3    Zhang, K.4    Baker, D.5
  • 15
    • 0034671177 scopus 로고    scopus 로고
    • The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
    • Guerois, R. & Serrano, L. (2000). The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J. Mol. Biol. 304, 967-982.
    • (2000) J. Mol. Biol. , vol.304 , pp. 967-982
    • Guerois, R.1    Serrano, L.2
  • 16
    • 0024358426 scopus 로고
    • Mapping the transition-state and pathway of protein folding by protein engineering
    • Matouschek, A., Kellis, J. T. J., Serrano, L. & Fersht, A. (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.J.2    Serrano, L.3    Fersht, A.4
  • 17
    • 0028500779 scopus 로고
    • A short linear peptide that folds into a native stable beta-hairpin in aqueous solution
    • Blanco, F., Rivas, G. & Serrano, L. (1994). A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nature Struct. Biol. 1, 584-590.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 584-590
    • Blanco, F.1    Rivas, G.2    Serrano, L.3
  • 18
    • 0036300662 scopus 로고    scopus 로고
    • Accurate computer-based design of a new backbone conformation in the second turn of protein L.
    • Kuhlman, B., O'Neill, J., Kim, D., Zhang, K. & Baker, D. (2002). Accurate computer-based design of a new backbone conformation in the second turn of protein L. J. Mol. Biol. 315, 471-477.
    • (2002) J. Mol. Biol. , vol.315 , pp. 471-477
    • Kuhlman, B.1    O'Neill, J.2    Kim, D.3    Zhang, K.4    Baker, D.5
  • 19
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez, J., Pisabarro, M. & Serrano, L. (1998). Obligatory steps in protein folding and the conformational diversity of the transition state. Nature Struct. Biol. 5, 721-729.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 721-729
    • Martinez, J.1    Pisabarro, M.2    Serrano, L.3
  • 20
    • 0028932770 scopus 로고
    • The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics
    • Viguera, A., Blanco, F. & Serrano, L. (1995). The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247, 670-681.
    • (1995) J. Mol. Biol. , vol.247 , pp. 670-681
    • Viguera, A.1    Blanco, F.2    Serrano, L.3
  • 21
    • 0030334834 scopus 로고    scopus 로고
    • Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2
    • Lopez-Hernandez, E. & Serrano, L. (1996). Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold. Des. 1, 43-55.
    • (1996) Fold. Des. , vol.1 , pp. 43-55
    • Lopez-Hernandez, E.1    Serrano, L.2
  • 22
    • 0026579572 scopus 로고
    • The folding of an enzyme. III. Structure of the transition-state for unfolding of barnase analysed by a protein engineering procedure
    • Serrano, L., Matouschek, A. & Fersht, A. (1992). The folding of an enzyme. III. Structure of the transition-state for unfolding of barnase analysed by a protein engineering procedure. J. Mol. Biol. 224, 805-818.
    • (1992) J. Mol. Biol. , vol.224 , pp. 805-818
    • Serrano, L.1    Matouschek, A.2    Fersht, A.3
  • 23
    • 0034984382 scopus 로고    scopus 로고
    • Mapping the folding pathway of an immunoglobulin domain: Structural detail from phi value analysis and movement of the transition state
    • Fowler, S. & Clarke, J. (2001). Mapping the folding pathway of an immunoglobulin domain: structural detail from phi value analysis and movement of the transition state. Structure, 9, 355-366.
    • (2001) Structure , vol.9 , pp. 355-366
    • Fowler, S.1    Clarke, J.2
  • 24
    • 0035793212 scopus 로고    scopus 로고
    • The folding nucleus of a fibronectin type III domain is composed of core residues of the immunoglobulin-like fold
    • Cota, E., Steward, A., Fowler, S. & Clarke, J. (2001). The folding nucleus of a fibronectin type III domain is composed of core residues of the immunoglobulin-like fold. J. Mol. Biol. 305, 1185-1194.
    • (2001) J. Mol. Biol. , vol.305 , pp. 1185-1194
    • Cota, E.1    Steward, A.2    Fowler, S.3    Clarke, J.4
  • 25
    • 0034677663 scopus 로고    scopus 로고
    • The folding of an immunoglobulin-like greek key protein is defined by a common-core nucleus and regions constrained by topology
    • Hamill, S., Steward, A. & Clarke, J. (2000). The folding of an immunoglobulin-like greek key protein is defined by a common-core nucleus and regions constrained by topology. J. Mol. Biol. 297, 165-178.
    • (2000) J. Mol. Biol. , vol.297 , pp. 165-178
    • Hamill, S.1    Steward, A.2    Clarke, J.3
  • 26
    • 0033592876 scopus 로고    scopus 로고
    • From snapshot to movie: phi analysis of protein folding transition states taken one step further
    • Ternstrom, T., Mayor, U., Akke, M. & Oliveberg, M. (1999). From snapshot to movie: phi analysis of protein folding transition states taken one step further. Proc. Natl Acad. Sci. USA, 96, 14854-14859.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 14854-14859
    • Ternstrom, T.1    Mayor, U.2    Akke, M.3    Oliveberg, M.4
  • 27
    • 0032708771 scopus 로고    scopus 로고
    • Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
    • Chiti, F., Taddei, N., White, P. M., Bucciantini, M., Magherini, F., Stefani, M. & Dobson, C. M. (1999). Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Struct. Biol. 6, 1005-1009.
    • (1999) Nature Struct. Biol. , vol.6 , pp. 1005-1009
    • Chiti, F.1    Taddei, N.2    White, P.M.3    Bucciantini, M.4    Magherini, F.5    Stefani, M.6    Dobson, C.M.7
  • 28
    • 0032515105 scopus 로고    scopus 로고
    • Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
    • Villegas, V., Martinez, J., Aviles, F. & Serrano, L. (1998). Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J. Mol. Biol. 283, 1027-1036.
    • (1998) J. Mol. Biol. , vol.283 , pp. 1027-1036
    • Villegas, V.1    Martinez, J.2    Aviles, F.3    Serrano, L.4
  • 29
    • 0032718386 scopus 로고    scopus 로고
    • Salt-induced detour through compact regions of the protein folding landscape
    • Otzen, D. & Oliveberg, M. (1999). Salt-induced detour through compact regions of the protein folding landscape. Proc. Natl Acad. Sci. USA, 96, 11746-11751.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11746-11751
    • Otzen, D.1    Oliveberg, M.2
  • 30
    • 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., Otzen, D. & Fersht, A. (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.1    Otzen, D.2    Fersht, A.3
  • 31
    • 0029041315 scopus 로고
    • Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: Observation of hammond behavior for the gross structure of the transition-state and anti-hammond behavior for structural elements for unfolding/folding of barnase
    • Matthews, J. & Fersht, A. (1995). Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: observation of hammond behavior for the gross structure of the transition-state and anti-hammond behavior for structural elements for unfolding/folding of barnase. Biochemistry, 34, 6805-6814.
    • (1995) Biochemistry , vol.34 , pp. 6805-6814
    • Matthews, J.1    Fersht, A.2
  • 32
    • 0032812796 scopus 로고    scopus 로고
    • Mapping the interactions present in the transition state for unfolding/folding of FKBP12
    • Fulton, K., Main, E., Daggett, V. & Jackson, S. E. (1999). Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J. Mol. Biol. 291, 445-461.
    • (1999) J. Mol. Biol. , vol.291 , pp. 445-461
    • Fulton, K.1    Main, E.2    Daggett, V.3    Jackson, S.E.4
  • 33
    • 0034650515 scopus 로고    scopus 로고
    • The folding pathway of the cell-cycle regulatory protein p13suc1: Clues for the mechanism of domain swapping
    • Schymkowitz, J., Rousseau, F., Irvine, L. & Itzhaki, L. (2000). The folding pathway of the cell-cycle regulatory protein p13suc1: clues for the mechanism of domain swapping. Struct. Fold. Des. 8, 89-100.
    • (2000) Struct. Fold. Des. , vol.8 , pp. 89-100
    • Schymkowitz, J.1    Rousseau, F.2    Irvine, L.3    Itzhaki, L.4
  • 34
    • 0031005061 scopus 로고    scopus 로고
    • The energy landscape of a fast-folding protein mapped by Ala-Gly substitutions
    • Burton, R., Huang, G., Daugherty, M., Calderone, T. & Oas, T. (1997). The energy landscape of a fast-folding protein mapped by Ala-Gly substitutions. Nature Struct. Biol. 4, 305-310.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 305-310
    • Burton, R.1    Huang, G.2    Daugherty, M.3    Calderone, T.4    Oas, T.5
  • 35
    • 0033015989 scopus 로고    scopus 로고
    • The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP
    • Kragelund, B., Osmark, P., Neergaard, T., Schiodt, J., Kristiansen, K., Knudsen, J. & Poulsen, F. M. (1999). The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP. Nature Struct. Biol. 6, 594-601.
    • (1999) Nature Struct. Biol. , vol.6 , pp. 594-601
    • Kragelund, B.1    Osmark, P.2    Neergaard, T.3    Schiodt, J.4    Kristiansen, K.5    Knudsen, J.6    Poulsen, F.M.7
  • 36
    • 0034680627 scopus 로고    scopus 로고
    • Differential stabilization of two hydrophobic cores in the transition state of the villin 14t folding reaction
    • Choe, S., Matsudaira, P., Wagner, G. & Shakhnovich, E. (2000). Differential stabilization of two hydrophobic cores in the transition state of the villin 14t folding reaction. J. Mol. Biol. 304, 99-115.
    • (2000) J. Mol. Biol. , vol.304 , pp. 99-115
    • Choe, S.1    Matsudaira, P.2    Wagner, G.3    Shakhnovich, E.4
  • 37
    • 0000296912 scopus 로고
    • Statistical fluctuations in auto-catalytic reactions
    • Delbrück, M. (1940). Statistical fluctuations in auto-catalytic reactions. J. Chem. Phys. 8, 120-124.
    • (1940) J. Chem. Phys. , vol.8 , pp. 120-124
    • Delbrück, M.1
  • 39
    • 0347193736 scopus 로고
    • Reaction-rate theory: Fifty years after Kramers
    • Hänggi, P., Talkner, P. & Borkovec, M. (1990). Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62, 251-341.
    • (1990) Rev. Mod. Phys. , vol.62 , pp. 251-341
    • Hänggi, P.1    Talkner, P.2    Borkovec, M.3
  • 40
    • 0000239504 scopus 로고    scopus 로고
    • Master equation approach to protein folding and kinetic traps
    • Cieplak, M., Henkel, M., Karbowski, J. & Banavar, J. (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.4
  • 41
    • 0033060613 scopus 로고    scopus 로고
    • Searching for downhill scenarios in protein folding
    • Eaton, W. (1999). Searching for downhill scenarios in protein folding. Proc. Natl Acad. Sci. USA, 96, 5897-5899.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 5897-5899
    • Eaton, W.1
  • 42
    • 84912079256 scopus 로고
    • Rapid approximation to molecular surface area via the use of boolean logic and look-up tables
    • Le Grand, S. & Merz, K. (1993). Rapid approximation to molecular surface area via the use of boolean logic and look-up tables. J. Comput. Chem. 14, 349-352.
    • (1993) J. Comput. Chem. , vol.14 , pp. 349-352
    • Le Grand, S.1    Merz, K.2
  • 43
    • 0034705338 scopus 로고    scopus 로고
    • NMR characterization of residual structure in the denatured state of protein L.
    • Yi, Q., Scalley-Kim, M., Alm, E. & Baker, D. (2000). NMR characterization of residual structure in the denatured state of protein L. J. Mol. Biol. 299, 1341-1351.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1341-1351
    • Yi, Q.1    Scalley-Kim, M.2    Alm, E.3    Baker, D.4
  • 44
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson, H. & Stockmayer, W. (1950). Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 18, 1600-1606.
    • (1950) J. Chem. Phys. , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.2
  • 46
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson, S. (1998). How do small single-domain proteins fold? Fold. Des. 3, R81-R91.
    • (1998) Fold. Des. , vol.3
    • Jackson, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.