메뉴 건너뛰기




Volumn 13, Issue 5, 2004, Pages 1173-1181

Critical nucleation size in the folding of small apparently two-state proteins

Author keywords

Folding rate; Nucleation size; Topology; Total contact distance

Indexed keywords

ARTICLE; CORRELATION ANALYSIS; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FOLDING;

EID: 1942473645     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03587604     Document Type: Article
Times cited : (31)

References (53)
  • 1
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • Alm, E. and Baker, D. 1999. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. 96: 11305-11310.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 2
    • 0036384269 scopus 로고    scopus 로고
    • Simple physical models connect theory and experiment in protein folding kinetics
    • Alm, E., Morozov, A.V., Kortemme, T., and Baker, D. 2002. Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 322: 463-476.
    • (2002) J. Mol. Biol. , vol.322 , pp. 463-476
    • Alm, E.1    Morozov, A.V.2    Kortemme, T.3    Baker, D.4
  • 3
    • 0029643523 scopus 로고
    • Protein folding intermediates: Native-state hydrogen exchange
    • Bai, Y., Sosnick, T.R., Mayne, L., and Englander, S.W. 1995. Protein folding intermediates: Native-state hydrogen exchange. Science 269: 192-197.
    • (1995) Science , vol.269 , pp. 192-197
    • Bai, Y.1    Sosnick, T.R.2    Mayne, L.3    Englander, S.W.4
  • 4
    • 0032972986 scopus 로고    scopus 로고
    • Is protein folding hierarchic? I. Local structure and peptide folding
    • Baldwin, R.L. and Rose, G.D. 1999. 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
    • 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., and Dobson, C.M. 1999. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat. Struct. Biol. 6: 1005-1009.
    • (1999) Nat. 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
  • 6
    • 0037172787 scopus 로고    scopus 로고
    • Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein
    • Chu, R.A., Pei, W.H., Takei, J., and Bai, Y. 2002. Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein. Biochemistry 41: 7998-8003.
    • (2002) Biochemistry , vol.41 , pp. 7998-8003
    • Chu, R.A.1    Pei, W.H.2    Takei, J.3    Bai, Y.4
  • 8
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill, K.A. 1999. Polymer principles and protein folding. Protein Sci. 8: 1166-1180.
    • (1999) Protein Sci. , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 9
    • 0033871781 scopus 로고    scopus 로고
    • Protein folding intermediates and pathways studied by hydrogen exchange
    • Englander, S.W. 2000. Protein folding intermediates and pathways studied by hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29: 213-238.
    • (2000) Annu. Rev. Biophys. Biomol. Struct. , vol.29 , pp. 213-238
    • Englander, S.W.1
  • 10
    • 0242318402 scopus 로고    scopus 로고
    • Specific non-native hydrophobic interactions in a hidden intermediate: Implications for protien folding
    • Feng, H., Takei, J., Lipsitz, R., Tjandra, N., and Bai, Y. 2003. Specific non-native hydrophobic interactions in a hidden intermediate: Implications for protien folding. Biochemistry 42: 12461-12465.
    • (2003) Biochemistry , vol.42 , pp. 12461-12465
    • Feng, H.1    Takei, J.2    Lipsitz, R.3    Tjandra, N.4    Bai, Y.5
  • 11
    • 0034652206 scopus 로고    scopus 로고
    • Transition-state structure as a unifying basis in protein folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
    • Fersht, A.R. 2000. Transition-state structure as a unifying basis in protein folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl. Acad. Sci. 97: 1525-1529.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 1525-1529
    • Fersht, A.R.1
  • 12
    • 0026511656 scopus 로고
    • The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding
    • Fersht, A.R., Matouschek, A., and Serrano, L. 1992. The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224: 771-782.
    • (1992) J. Mol. Biol. , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 13
    • 0037402639 scopus 로고    scopus 로고
    • Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics
    • Galzitskaya, O.V., Garbuzynskiy, S.O., Ivankov, D.N., and Finkelstein, A. 2003. Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins 51: 162-166.
    • (2003) Proteins , vol.51 , pp. 162-166
    • Galzitskaya, O.V.1    Garbuzynskiy, S.O.2    Ivankov, D.N.3    Finkelstein, A.4
  • 14
    • 0032707954 scopus 로고    scopus 로고
    • Finding the right fold
    • Goldenberg, D.P. 1999. Finding the right fold. Nat. Struct. Biol. 6: 987-990.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 987-990
    • Goldenberg, D.P.1
  • 15
    • 0037432567 scopus 로고    scopus 로고
    • Local secondary structure content predicts folding rates for simple, two-state proteins
    • Gong, H., Isom, D.G., Srinivasan, R., and Rose, G.D. 2003. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 327: 1149-1154.
    • (2003) J. Mol. Biol. , vol.327 , pp. 1149-1154
    • Gong, H.1    Isom, D.G.2    Srinivasan, R.3    Rose, G.D.4
  • 16
    • 0035967862 scopus 로고    scopus 로고
    • Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: 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 proteins: 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
  • 17
    • 0034671177 scopus 로고    scopus 로고
    • The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
    • Guerois, R. and 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
  • 18
    • 0032570543 scopus 로고    scopus 로고
    • Folding kinetics of the SH3 domain of PI3 kinase by real-time NMR combined with optical spectroscopy
    • Guijarro, J.I., Morton, C.J., Plaxco, K.W., Campbell, I.D., and Dobson, C.M. 1998. Folding kinetics of the SH3 domain of PI3 kinase by real-time NMR combined with optical spectroscopy. J. Mol. Biol. 276: 657-667.
    • (1998) J. Mol. Biol. , vol.276 , pp. 657-667
    • Guijarro, J.I.1    Morton, C.J.2    Plaxco, K.W.3    Campbell, I.D.4    Dobson, C.M.5
  • 19
    • 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.J., Steward, A., and 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.J.1    Steward, A.2    Clarke, J.3
  • 20
    • 0037470575 scopus 로고    scopus 로고
    • Rapid cooperative two-state folding of a miniature a-b protein and design of a thermostable variant
    • Horng, J.C., Moroz, V., and Raleigh, D.P. 2003. Rapid cooperative two-state folding of a miniature a-b protein and design of a thermostable variant. J. Mol. Biol. 326: 1261-1270.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1261-1270
    • Horng, J.C.1    Moroz, V.2    Raleigh, D.P.3
  • 21
    • 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
  • 22
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson, S.E. 1998. How do small single-domain proteins fold? Fold. Des. 3: R81-R91.
    • (1998) Fold. Des. , vol.3
    • Jackson, S.E.1
  • 24
    • 0017251893 scopus 로고
    • Protein-folding dynamics
    • Karplus, M. and Weaver, D.L. 1976. Protein-folding dynamics. Nature 260: 404-406.
    • (1976) Nature , vol.260 , pp. 404-406
    • Karplus, M.1    Weaver, D.L.2
  • 25
    • 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. and Chan, H.S. 2003. Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Protein Sci. 52: 524-533.
    • (2003) Protein Sci. , vol.52 , pp. 524-533
    • Kaya, H.1    Chan, H.S.2
  • 26
    • 0034685619 scopus 로고    scopus 로고
    • A breakdown of symmetry in the folding transition state of protein L
    • Kim, D.E., Fisher, C., and 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.E.1    Fisher, C.2    Baker, D.3
  • 27
    • 0036440985 scopus 로고    scopus 로고
    • Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding
    • Krantz, B.A., Mayne, L., Rumbley, J., Englander, S.W., and Sosnick, T.R. 2002. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. 324: 1-13.
    • (2002) J. Mol. Biol. , vol.324 , pp. 1-13
    • Krantz, B.A.1    Mayne, L.2    Rumbley, J.3    Englander, S.W.4    Sosnick, T.R.5
  • 28
    • 1442348207 scopus 로고    scopus 로고
    • Discerning the structure and energy of multiple transition states in protein folding using ψ-analysis
    • in press
    • Krantz, B.A., Dothager, R.S., and Sosnick, T.R. 2004. Discerning the structure and energy of multiple transition states in protein folding using ψ-analysis. J. Mol. Biol. (in press)
    • (2004) J. Mol. Biol.
    • Krantz, B.A.1    Dothager, R.S.2    Sosnick, T.R.3
  • 29
    • 0031576337 scopus 로고    scopus 로고
    • Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates
    • Ladurner, A.G. and Fersht, A.R. 1997. Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J. Mol. Biol. 273: 330-337.
    • (1997) J. Mol. Biol. , vol.273 , pp. 330-337
    • Ladurner, A.G.1    Fersht, A.R.2
  • 30
    • 0034674156 scopus 로고    scopus 로고
    • pH-dependent interactions and the stability and folding kinetics of the N-terminal domain of L9. Electrostatic interactions are only weakly formed in the transition state for folding
    • Luisi, D.L. and Raleigh, D.P. 2000. pH-dependent interactions and the stability and folding kinetics of the N-terminal domain of L9. Electrostatic interactions are only weakly formed in the transition state for folding. J. Mol. Biol. 299: 1091-1100.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1091-1100
    • Luisi, D.L.1    Raleigh, D.P.2
  • 31
    • 0037215268 scopus 로고    scopus 로고
    • The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
    • Makarov, D. and Plaxco, K.W. 2003. The topomer search model: A simple, quantitative theory of two-state protein folding kinetics. Protein Sci. 12: 17-26.
    • (2003) Protein Sci. , vol.12 , pp. 17-26
    • Makarov, D.1    Plaxco, K.W.2
  • 32
    • 0037133574 scopus 로고    scopus 로고
    • How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
    • Makarov, D., Keller, D.A., Plaxco, K.W., and Metiu, H. 2002. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc. Natl. Acad. Sci. 99: 3535-3539.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 3535-3539
    • Makarov, D.1    Keller, D.A.2    Plaxco, K.W.3    Metiu, H.4
  • 33
    • 0039726624 scopus 로고    scopus 로고
    • Thermodynamic analysis of α-spectrin SH3 and two of its circular permutants with different loop lengths: Discerning the reasons for rapid folding in proteins
    • Martinez, J.C., Viguera, A.R., Berisio, R., Wilmanns, M., Mateo, P.L., Filimonov, V.V., and Serrano, L. 1999. Thermodynamic analysis of α-spectrin SH3 and two of its circular permutants with different loop lengths: Discerning the reasons for rapid folding in proteins. Biochemistry 38: 549-559.
    • (1999) Biochemistry , vol.38 , pp. 549-559
    • Martinez, J.C.1    Viguera, A.R.2    Berisio, R.3    Wilmanns, M.4    Mateo, P.L.5    Filimonov, V.V.6    Serrano, L.7
  • 35
    • 0033871567 scopus 로고    scopus 로고
    • Critical role of β-hairpin formation in protein G folding
    • McCallister, E.L., Alm, E., and Baker, D. 2000. Critical role of β-hairpin formation in protein G folding. Nat. Struct. Biol. 7: 669-673.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 669-673
    • McCallister, E.L.1    Alm, E.2    Baker, D.3
  • 36
    • 0036678120 scopus 로고    scopus 로고
    • Experimental evaluation of topological parameters determining protein-folding rates
    • Miller, E.J., Fisher, K.F., and Marqusee, S. 2002. Experimental evaluation of topological parameters determining protein-folding rates. Proc. Natl. Acad. Sci. 99: 10359-10363.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 10359-10363
    • Miller, E.J.1    Fisher, K.F.2    Marqusee, S.3
  • 37
    • 0034984144 scopus 로고    scopus 로고
    • Protein folding theory: From lattice to all-atom models
    • Mirny, L. and Shakhnovich, E. 2001. Protein folding theory: From lattice to all-atom models. Annu. Rev. Biophys. Biomol. Struct. 30: 361-396.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 361-396
    • Mirny, L.1    Shakhnovich, E.2
  • 38
    • 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
  • 39
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamic and mechanism of β-hairpin formation
    • Munoz, V., Thompson, P.A., Hofrichter, J., and Eaton, W.A. 1997. Folding dynamic 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
  • 40
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • Myers, J.K. and Oas, T.G. 2001. Preorganized secondary structure as an important determinant of fast protein folding. Nat. Struct. Biol. 8: 552-558.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 41
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • Nauli, S., Kuhlman, B., and Baker, D. 2001. Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 8: 602-605.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman, B.2    Baker, D.3
  • 42
    • 0031214363 scopus 로고    scopus 로고
    • A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules
    • Plaxco, K.W., Spitzfaden, C., Campbell, I.D., and Dobson, C.M. 1997. A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules. J. Mol. Biol. 270: 763-770.
    • (1997) J. Mol. Biol. , vol.270 , pp. 763-770
    • Plaxco, K.W.1    Spitzfaden, C.2    Campbell, I.D.3    Dobson, C.M.4
  • 43
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco, K.W., Simons, K.T., and 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
  • 45
    • 0037305938 scopus 로고    scopus 로고
    • Low free energy cost of very long loop insertions in proteins
    • Scalley-Kim, M., Minard, P., and Baker, D. 2003. Low free energy cost of very long loop insertions in proteins. Protein Sci. 12: 197-206.
    • (2003) Protein Sci. , vol.12 , pp. 197-206
    • Scalley-Kim, M.1    Minard, P.2    Baker, D.3
  • 46
    • 0029940033 scopus 로고    scopus 로고
    • Molecular collapse: The rate-limiting step in two-state cytochrome c folding
    • Sosnick, T.R., Mayne, L., and Englander, S.W. 1996. Molecular collapse: The rate-limiting step in two-state cytochrome c folding. Proteins 24: 413-426.
    • (1996) Proteins , vol.24 , pp. 413-426
    • Sosnick, T.R.1    Mayne, L.2    Englander, S.W.3
  • 47
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues from a critical contact network in a protein folding transition state
    • Vendruscolo, M., Paci, E., Dobson, C.M., and Karplus, M. 2001. Three key residues from 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
  • 48
    • 0030663205 scopus 로고    scopus 로고
    • Loop length, intramolecular diffusion and protein folding
    • Viguera, A.R. and Serrano, L. 1997. Loop length, intramolecular diffusion and protein folding. Nat. Struct. Biol. 4: 939-946.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 939-946
    • Viguera, A.R.1    Serrano, L.2
  • 49
    • 0038288925 scopus 로고    scopus 로고
    • Dynamic NMR line-shape analysis demonstrates that the Villin headpiece subdomain folds on the microsecond time scale
    • Wang, M., Tang, Y., Sato, S., Vugmeyster, L., McKnight, C.J., and Raleigh, D.P. 2003. Dynamic NMR line-shape analysis demonstrates that the Villin headpiece subdomain folds on the microsecond time scale. J. Am. Chem. Soc. 125: 6032-6033.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 6032-6033
    • Wang, M.1    Tang, Y.2    Sato, S.3    Vugmeyster, L.4    McKnight, C.J.5    Raleigh, D.P.6
  • 50
    • 0038630483 scopus 로고    scopus 로고
    • Folding rates and low-entropy-loss routes of two-state proteins
    • Weikl, T. and Dill, K. A. 2003. Folding rates and low-entropy-loss routes of two-state proteins. J. Mol. Biol. 329: 585-598.
    • (2003) J. Mol. Biol. , vol.329 , pp. 585-598
    • Weikl, T.1    Dill, K.A.2
  • 51
    • 0033598375 scopus 로고    scopus 로고
    • Interpreting the folding kinetics of helical proteins
    • Zhou, Y. and Karplus, M. 1999. Interpreting the folding kinetics of helical proteins. Nature 401: 400-403.
    • (1999) Nature , vol.401 , pp. 400-403
    • Zhou, Y.1    Karplus, M.2
  • 52
    • 0036215854 scopus 로고    scopus 로고
    • Folding rate prediction using total contact distance
    • Zhou, H. and Zhou, Y. 2002. Folding rate prediction using total contact distance. Biophys. J. 82: 458-463.
    • (2002) Biophys. J. , vol.82 , pp. 458-463
    • Zhou, H.1    Zhou, Y.2
  • 53
    • 0028882223 scopus 로고
    • Simple model of protein folding kinetics
    • Zwanzig, R. 1995. Simple model of protein folding kinetics. Proc. Natl. Acad. Sci. 92: 9801-9804.
    • (1995) Proc. Natl. Acad. Sci. , vol.92 , pp. 9801-9804
    • Zwanzig, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.