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Volumn 14, Issue 6, 2005, Pages 1643-1660

A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling

Author keywords

Explicit chain modeling; Levinthal search; Protein folding; Topomer search model; Topomer sampling model

Indexed keywords

PROTEIN;

EID: 19444371858     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041317705     Document Type: Article
Times cited : (41)

References (79)
  • 1
    • 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
  • 2
    • 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
  • 3
    • 0029643523 scopus 로고
    • Protein folding intermediates: Native-state hydrogen exchange
    • Bai, Y., Sosnick, T., 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.2    Mayne, L.3    Englander, S.W.4
  • 4
    • 1942473645 scopus 로고    scopus 로고
    • Critical nucleation size in the folding of small apparently two-state proteins
    • Bai, Y.W, Zhou, H.Y., and Zhou, Y.Q. 2004. Critical nucleation size in the folding of small apparently two-state proteins. Protein Sci. 13: 1173-1181.
    • (2004) Protein Sci. , vol.13 , pp. 1173-1181
    • Bai, Y.W.1    Zhou, H.Y.2    Zhou, Y.Q.3
  • 5
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker, D. 2000. A surprising simplicity to protein folding. Nature 405: 39-42.
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 6
    • 0028387381 scopus 로고
    • Folding intermediates in protein folding
    • Baldwin, R.L. 1994. Folding intermediates in protein folding. BioEssays 16: 207-210.
    • (1994) BioEssays , vol.16 , pp. 207-210
    • Baldwin, R.L.1
  • 9
    • 0000870109 scopus 로고
    • Three-dimensional structures of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin
    • Brünger, A.T., Clore, G.M., Gronenborn, A.M., and Karplus, M. 1986. Three-dimensional structures of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin. Proc. Natl. Acad. Sci. 83: 3801-3805.
    • (1986) Proc. Natl. Acad. Sci. , vol.83 , pp. 3801-3805
    • Brünger, A.T.1    Clore, G.M.2    Gronenborn, A.M.3    Karplus, M.4
  • 11
    • 0031005061 scopus 로고    scopus 로고
    • The energy landscape of a fast-folding protein mapped by Ala → Gly substitutions
    • Burton, R.E., Huang, G.S., Daugherty, M.A., Calderone, T.L., and Oas, T.G. 1997. The energy landscape of a fast-folding protein mapped by Ala → Gly substitutions. Nat. Struct. Biol. 4: 305-310.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 305-310
    • Burton, R.E.1    Huang, G.S.2    Daugherty, M.A.3    Calderone, T.L.4    Oas, T.G.5
  • 12
    • 0001510938 scopus 로고
    • Minimum energy compact structures of random sequences of heteropolymers
    • Camacho, C.J. and Thirumalai, D. 1993. Minimum energy compact structures of random sequences of heteropolymers. Phys. Rev. Lett. 71: 2505-2508.
    • (1993) Phys. Rev. Lett. , vol.71 , pp. 2505-2508
    • Camacho, C.J.1    Thirumalai, D.2
  • 13
    • 5244273418 scopus 로고
    • Compact polymers
    • Chan, H.S. and Dill, K.A. 1989. Compact polymers. Macromolecule 22: 4559-4573.
    • (1989) Macromolecule , vol.22 , pp. 4559-4573
    • Chan, H.S.1    Dill, K.A.2
  • 14
    • 0001193711 scopus 로고
    • The effects of internal constraints on the configurations of chain molecules
    • _. 1990. The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92: 3118-3135.
    • (1990) J. Chem. Phys. , vol.92 , pp. 3118-3135
  • 15
    • 0025906282 scopus 로고
    • Polymer principles in protein structure and stability
    • _. 1991. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20: 447-490.
    • (1991) Annu. Rev. Biophys. Biophys. Chem. , vol.20 , pp. 447-490
  • 16
    • 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
  • 17
    • 3142782241 scopus 로고    scopus 로고
    • Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
    • Chavez, L.L., Onuchic, J.N., and Clementi, C. 2004. Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates. J. Am. Chem. Soc. 126: 8426-8432.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 8426-8432
    • Chavez, L.L.1    Onuchic, J.N.2    Clementi, C.3
  • 18
    • 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
  • 19
    • 0035906650 scopus 로고    scopus 로고
    • Calculation of ensembles of structures representing the unfolded state of an SH3 domain
    • Choy, W.Y. and Forman-Kay, J.D. 2001. Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J. Mol. Biol. 308: 1011-1032.
    • (2001) J. Mol. Biol. , vol.308 , pp. 1011-1032
    • Choy, W.Y.1    Forman-Kay, J.D.2
  • 20
    • 0037216990 scopus 로고    scopus 로고
    • Universality classes in folding times of proteins
    • Cieplak, M. and Hoang, T.X. 2003. Universality classes in folding times of proteins. Biophys. J. 84: 475-488.
    • (2003) Biophys. J. , vol.84 , pp. 475-488
    • Cieplak, M.1    Hoang, T.X.2
  • 21
    • 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?
    • 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? 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
  • 22
    • 0037459022 scopus 로고    scopus 로고
    • Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom study of Protein L.
    • Clementi, C., Garcia, A.E., and Onuchic, J.N. 2003. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom study of Protein L. J. Mol. Biol. 326: 933-954.
    • (2003) J. Mol. Biol. , vol.326 , pp. 933-954
    • Clementi, C.1    Garcia, A.E.2    Onuchic, J.N.3
  • 23
    • 0033521194 scopus 로고    scopus 로고
    • First-principles prediction of protein folding rates
    • Debe, D.A. and Goddard, W.A. 1999. First-principles prediction of protein folding rates. J. Mol. Biol. 294: 619-625.
    • (1999) J. Mol. Biol. , vol.294 , pp. 619-625
    • Debe, D.A.1    Goddard, W.A.2
  • 25
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill, K.A. and Chan, H.S. 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
  • 26
    • 0344301982 scopus 로고    scopus 로고
    • Protein folding: A perspective from theory and experiment
    • Dobson, C.M., Šali, A., and Karplus, M. 1998. Protein folding: A perspective from theory and experiment. Angew. Chem. Int. Ed. Engl. 37: 868-893.
    • (1998) Angew. Chem. Int. Ed. Engl. , vol.37 , pp. 868-893
    • Dobson, C.M.1    Šali, A.2    Karplus, M.3
  • 28
    • 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
  • 29
    • 0037044965 scopus 로고    scopus 로고
    • Topological complexity, contact order, and protein folding rates
    • Faisca, P.F.N. and Ball, R.C. 2002. Topological complexity, contact order, and protein folding rates. J. Chem. Phys. 117: 8587-8591.
    • (2002) J. Chem. Phys. , vol.117 , pp. 8587-8591
    • Faisca, P.F.N.1    Ball, R.C.2
  • 30
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg, A.M. and Swendsen, R.H. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63: 1195-1198.
    • (1989) Phys. Rev. Lett. , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 31
    • 0028856785 scopus 로고
    • Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
    • Fersht, A.R. 1995. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. 92: 10869-10873.
    • (1995) Proc. Natl. Acad. Sci. , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 32
    • 5144225084 scopus 로고    scopus 로고
    • Relationship of Leffler (Bronsted) α values and protein folding φ values to position of transition-state structures on reaction coordinates
    • _. 2004. Relationship of Leffler (Bronsted) α values and protein folding φ values to position of transition-state structures on reaction coordinates. Proc. Natl. Acad. Sci. 101: 14338-14342.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 14338-14342
  • 33
    • 0026511656 scopus 로고
    • The folding of an enzyme. I. 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. I. 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
  • 35
    • 0033613131 scopus 로고    scopus 로고
    • A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
    • Galzitskaya, O.V. and Finkelstein, A.V. 1999. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl. Acad. Sci. 96: 11299-11304.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 11299-11304
    • Galzitskaya, O.V.1    Finkelstein, A.V.2
  • 36
    • 3943113660 scopus 로고    scopus 로고
    • Using protein folding rates to test protein folding theories
    • Gillespie, B. and Plaxco, K.W. 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
    • Gillespie, B.1    Plaxco, K.W.2
  • 37
    • 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
  • 38
    • 0842332830 scopus 로고    scopus 로고
    • Commitment and nucleation in the protein G transition state
    • Hubner, I.A., Shimada, J., and Shakhnovich, E.I. 2004. Commitment and nucleation in the protein G transition state. J. Mol. Biol. 336: 745-761.
    • (2004) J. Mol. Biol. , vol.336 , pp. 745-761
    • Hubner, I.A.1    Shimada, J.2    Shakhnovich, E.I.3
  • 39
    • 0000773431 scopus 로고
    • Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature
    • Irbäck, A. and Potthast, F. 1995. Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature. J. Chem. Phys. 103: 10298-10305.
    • (1995) J. Chem. Phys. , vol.103 , pp. 10298-10305
    • Irbäck, A.1    Potthast, F.2
  • 40
    • 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
  • 42
    • 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
  • 43
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson, S.E. and Fersht, A.R. 1991. Folding of chymotrypsin 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
  • 44
    • 0037423710 scopus 로고    scopus 로고
    • Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates
    • Jewett, A.I., 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.I.1    Pande, V.S.2    Plaxco, K.W.3
  • 45
    • 0041624356 scopus 로고    scopus 로고
    • The largest protein observed to fold by two-state kinetic mechanism does not obey contact-order correlation
    • Jones, K. and Wittung-Stafshede, P. 2003. The largest protein observed to fold by two-state kinetic mechanism does not obey contact-order correlation. J. Am. Chem. Soc. 125: 9606-9607.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 9606-9607
    • Jones, K.1    Wittung-Stafshede, P.2
  • 46
    • 0242330738 scopus 로고    scopus 로고
    • The importance of explicit chain representation in protein folding models: An examination of Ising-like models
    • Karanicolas, J. and Brooks, C.L. 2003. The importance of explicit chain representation in protein folding models: An examination of Ising-like models. Proteins Struct. Funct. Genet. 53: 740-747.
    • (2003) Proteins Struct. Funct. Genet. , vol.53 , pp. 740-747
    • Karanicolas, J.1    Brooks, C.L.2
  • 47
    • 0036304480 scopus 로고    scopus 로고
    • Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
    • Kaya, H. and Chan, H.S. 2002. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding? J. Mol. Biol. 315: 899-909.
    • (2002) J. Mol. Biol. , vol.315 , pp. 899-909
    • Kaya, H.1    Chan, H.S.2
  • 48
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
    • Corrigendum 337: 1069-1070
    • _. 2003a. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling? J. Mol. Biol. 326: 911-931. (Corrigendum 337: 1069-1070.)
    • (2003) J. Mol. Biol. , vol.326 , pp. 911-931
  • 49
    • 0042130544 scopus 로고    scopus 로고
    • Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity
    • _. 2003b. Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity. Proteins Struct. Funct. Genet. 52: 510-523.
    • (2003) Proteins Struct. Funct. Genet. , vol.52 , pp. 510-523
  • 50
    • 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
    • _. 2003c. Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins Struct. Funct. Genet. 52: 524-533.
    • (2003) Proteins Struct. Funct. Genet. , vol.52 , pp. 524-533
  • 51
    • 10844267966 scopus 로고    scopus 로고
    • Explicit-chain model of native-state hydrogen exchange: Implications for event ordering and cooperativity in protein folding
    • _. 2005. Explicit-chain model of native-state hydrogen exchange: Implications for event ordering and cooperativity in protein folding. Proteins Struct. Funct. Bioinform. 58: 31-44.
    • (2005) Proteins Struct. Funct. Bioinform. , vol.58 , pp. 31-44
  • 52
    • 0035850732 scopus 로고    scopus 로고
    • Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
    • Koga, N. and Takada, S. 2001. Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model. J. Mol. Biol. 313: 171-180.
    • (2001) J. Mol. Biol. , vol.313 , pp. 171-180
    • Koga, N.1    Takada, S.2
  • 54
    • 0026723063 scopus 로고
    • Protein folding funnels: A kinetic approach to the sequence-structure relationship
    • Leopold, P.E., Montal, M., and Onuchic, J.N. 1992. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. 89: 8721-8725.
    • (1992) Proc. Natl. Acad. Sci. , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 56
    • 0037155403 scopus 로고    scopus 로고
    • A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results
    • Makarov, D.E. and Metiu, H. 2002. A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results. J. Chem. Phys. 116: 5205-5216.
    • (2002) J. Chem. Phys. , vol.116 , pp. 5205-5216
    • Makarov, D.E.1    Metiu, H.2
  • 57
    • 0037215268 scopus 로고    scopus 로고
    • The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
    • Makarov, D.E. 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.E.1    Plaxco, K.W.2
  • 58
    • 0037133574 scopus 로고    scopus 로고
    • How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
    • Makarov, D.E., Keller, C.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.E.1    Keller, C.A.2    Plaxco, K.W.3    Metiu, H.4
  • 59
    • 33644899039 scopus 로고
    • Simulated tempering: A new Monte Carlo scheme
    • Marinari, E. and Parisi, G. 1992. Simulated tempering: A new Monte Carlo scheme. Europhys. Lett. 19: 451-458.
    • (1992) Europhys. Lett. , vol.19 , pp. 451-458
    • Marinari, E.1    Parisi, G.2
  • 60
    • 0037375366 scopus 로고    scopus 로고
    • Prediction of folding rates and transition-state placement from native-state geometry
    • Micheletti, C. 2003. Prediction of folding rates and transition-state placement from native-state geometry. Proteins Struct. Funct. Genet. 51: 74-84.
    • (2003) Proteins Struct. Funct. Genet. , vol.51 , pp. 74-84
    • Micheletti, C.1
  • 61
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • Muñoz, 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
    • Muñoz, V.1    Eaton, W.A.2
  • 62
    • 0033602841 scopus 로고    scopus 로고
    • Contribution of a buried hydrogen bond to λ repressor folding kinetics
    • Myers, J.K. and Oas, T.G. 1999. Contribution of a buried hydrogen bond to λ repressor folding kinetics. Biochemistry 38: 6761-6768.
    • (1999) Biochemistry , vol.38 , pp. 6761-6768
    • Myers, J.K.1    Oas, T.G.2
  • 63
    • 0037452727 scopus 로고    scopus 로고
    • Packing helices in proteins by global optimization of a potential energy function
    • Nanias, M., Chinchio, M., Pillardy, J., Ripoll, D.R., and Scheraga, H.A. 2003. Packing helices in proteins by global optimization of a potential energy function. Proc. Natl. Acad. Sci. 100: 1706-1710.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 1706-1710
    • Nanias, M.1    Chinchio, M.2    Pillardy, J.3    Ripoll, D.R.4    Scheraga, H.A.5
  • 64
    • 0034681133 scopus 로고    scopus 로고
    • Landscape approaches for determining the ensemble of folding transition states: Success and failure hinges on the degree of frustration
    • Nymeyer, H., Socci, N.D., and Onuchic, J.N. 2000. Landscape approaches for determining the ensemble of folding transition states: Success and failure hinges on the degree of frustration. Proc. Natl. Acad. Sci. 97: 634-639.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 634-639
    • Nymeyer, H.1    Socci, N.D.2    Onuchic, J.N.3
  • 65
    • 6944250414 scopus 로고    scopus 로고
    • Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment
    • Ollerenshaw, J.E., Kaya, H., Chan, H.S., and Kay, L.E. 2004. Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment. Proc. Natl. Acad. Sci. 101: 14748-14753.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 14748-14753
    • Ollerenshaw, J.E.1    Kaya, H.2    Chan, H.S.3    Kay, L.E.4
  • 66
    • 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
  • 67
    • 0345304461 scopus 로고    scopus 로고
    • Origin of unusual φ-values in protein folding: Evidence against specific nucleation sites
    • Sanchez, I.E. and Kiefhaber, T. 2003. Origin of unusual φ-values in protein folding: Evidence against specific nucleation sites. J. Mol. Biol. 334: 1077-1085.
    • (2003) J. Mol. Biol. , vol.334 , pp. 1077-1085
    • Sanchez, I.E.1    Kiefhaber, T.2
  • 68
    • 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
  • 69
    • 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
    • Selvaraj, S. and Gromiha, M.M. 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
    • Selvaraj, S.1    Gromiha, M.M.2
  • 70
    • 0030750236 scopus 로고    scopus 로고
    • High-energy channeling in protein folding
    • Silow, M. and Oliveberg, M. 1997. High-energy channeling in protein folding. Biochemistry 36: 7633-7637.
    • (1997) Biochemistry , vol.36 , pp. 7633-7637
    • Silow, M.1    Oliveberg, M.2
  • 71
    • 0035191642 scopus 로고    scopus 로고
    • Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil
    • Sosnick, T.R. and Krantz, B.A. 2001. Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nat. Struct. Biol. 8: 1042-1047.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 1042-1047
    • Sosnick, T.R.1    Krantz, B.A.2
  • 72
    • 0033592876 scopus 로고    scopus 로고
    • From snapshot to movie: φ analysis of protein folding transition states taken one step further
    • Ternström, 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
    • Ternström, T.1    Mayor, U.2    Akke, M.3    Oliveberg, M.4
  • 73
    • 0028835443 scopus 로고
    • Nucleation mechanism for protein folding and theoretical predictions for hydrogen-exchange labeling experiments
    • Thirumalai, D. and Guo, Z. 1995. Nucleation mechanism for protein folding and theoretical predictions for hydrogen-exchange labeling experiments. Biopolymers 35: 137-140.
    • (1995) Biopolymers , vol.35 , pp. 137-140
    • Thirumalai, D.1    Guo, Z.2
  • 74
    • 0001103473 scopus 로고    scopus 로고
    • Kinetics of folding of proteins and RNA
    • Thirumalai, D. and Woodson, S.A. 1996. Kinetics of folding of proteins and RNA. Acc. Chem. Res. 29: 433-439.
    • (1996) Acc. Chem. Res. , vol.29 , pp. 433-439
    • Thirumalai, D.1    Woodson, S.A.2
  • 76
    • 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
  • 77
    • 0038630483 scopus 로고    scopus 로고
    • Folding rates and low-entropy-loss routes of two-state proteins
    • Weikl, T.R. 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.R.1    Dill, K.A.2
  • 78
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.