메뉴 건너뛰기




Volumn 11, Issue 5, 2004, Pages 443-449

Transition states for protein folding have native topologies despite high structural variability

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN SH3; UNCLASSIFIED DRUG;

EID: 2342451295     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb765     Document Type: Article
Times cited : (85)

References (50)
  • 1
    • 0032842870 scopus 로고    scopus 로고
    • The fundamentals of protein folding: Bringing together theory and experiment
    • Dobson, C.M. & Karplus, M. The fundamentals of protein folding: Bringing together theory and experiment. Curr. Opin. Struct. Biol. 9, 92-101 (1999).
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 92-101
    • Dobson, C.M.1    Karplus, M.2
  • 2
    • 0037221599 scopus 로고    scopus 로고
    • Is there a unifying mechanism for protein folding?
    • Daggett, V. & Fersht, A.R. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28, 18-25 (2003).
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 18-25
    • Daggett, V.1    Fersht, A.R.2
  • 3
    • 0037311666 scopus 로고    scopus 로고
    • Protein folding: Bringing theory and experiment closer together
    • Vendruscolo, M. & Paci, E. Protein folding: Bringing theory and experiment closer together. Curr. Opin. Struct. Biol. 13, 82-87 (2003).
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 82-87
    • Vendruscolo, M.1    Paci, E.2
  • 4
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson, S.E. How do small single-domain proteins fold? Fold. Des. 3, R81-R91 (1998).
    • (1998) Fold. Des. , vol.3
    • Jackson, S.E.1
  • 6
    • 0024358426 scopus 로고
    • Mapping the transition state and pathway of protein folding by protein engineering
    • Matouschek, A., Kellis, J.T., Serrano, L. & Fersht, A.R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340, 122-126 (1989).
    • (1989) Nature , vol.340 , pp. 122-126
    • Matouschek, A.1    Kellis, J.T.2    Serrano, L.3    Fersht, A.R.4
  • 7
    • 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. & Karplus, M. Three key residues form a critical contact network in a protein folding transition state. Nature 409, 641-645 (2001).
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 8
    • 0036435907 scopus 로고    scopus 로고
    • Determination of a transition state at atomic resolution from protein engineering data
    • Paci, E., Vendruscolo, M., Dobson, C.M. & Karplus, M. Determination of a transition state at atomic resolution from protein engineering data. J. Mol. Biol. 324, 151-163 (2002).
    • (2002) J. Mol. Biol. , vol.324 , pp. 151-163
    • Paci, E.1    Vendruscolo, M.2    Dobson, C.M.3    Karplus, M.4
  • 9
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez, J.C., Pisabarro, M.T. & Serrano, L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Biol. 5, 721-729 (1998).
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 10
    • 0032734515 scopus 로고    scopus 로고
    • Experiment and theory highlight role of native state topology in SH3 folding
    • Riddle, D.S. et al. Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 6, 1016-1024 (1999).
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 1016-1024
    • Riddle, D.S.1
  • 11
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH 3 domains is conformationally restricted and evolutionarily conserved
    • Martinez, J.C. & Serrano, L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat. Struct. Biol. 6, 1010-1016 (1999).
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 1010-1016
    • Martinez, J.C.1    Serrano, L.2
  • 12
    • 0036172116 scopus 로고    scopus 로고
    • Hydrophobic core packing in the SH3 domain folding transition state
    • Northey, J.G., Nardo, A.D. & Davidson, A.R. Hydrophobic core packing in the SH3 domain folding transition state. Nat. Struct. Biol. 9, 126-130 (2002).
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 126-130
    • Northey, J.G.1    Nardo, A.D.2    Davidson, A.R.3
  • 13
    • 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, J.G., Maxwell, K.L. & Davidson, A.R. 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).
    • (2002) J. Mol. Biol. , vol.320 , pp. 389-402
    • Northey, J.G.1    Maxwell, K.L.2    Davidson, A.R.3
  • 14
    • 0034486070 scopus 로고    scopus 로고
    • The identification of conserved interactions within the SH3 domain by alignment of sequences and structures
    • Larson, S.M. & Davidson, A.R. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci. 9, 2170-2180 (2000).
    • (2000) Protein Sci. , vol.9 , pp. 2170-2180
    • Larson, S.M.1    Davidson, A.R.2
  • 15
    • 0036266942 scopus 로고    scopus 로고
    • Conformational strain in the hydrophobic core and its implications for protein folding and design
    • Ventura, S. et al. Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat. Struct. Biol. 9, 485-493 (2002).
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 485-493
    • Ventura, S.1
  • 16
    • 0028037217 scopus 로고
    • Single versus parallel pathways of protein folding and fractional structure in the transition state
    • Fersht, A.R., Itzhaki, L.S., elMasry, N.F., Matthews, J.M. & Otzen, D.E. Single versus parallel pathways of protein folding and fractional structure in the transition state. Proc. Natl. Acad. Sci. USA 91, 10426-10429 (1994).
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 10426-10429
    • Fersht, A.R.1    Itzhaki, L.S.2    ElMasry, N.F.3    Matthews, J.M.4    Otzen, D.E.5
  • 17
    • 0037159944 scopus 로고    scopus 로고
    • Determination of the structures of distinct transition state ensembles for a β-sheet peptide with parallel folding pathways
    • Davis, R., Dobson, C.M. & Vendruscolo, M. Determination of the structures of distinct transition state ensembles for a β-sheet peptide with parallel folding pathways. J. Chem. Phys. 117, 9510-9517 (2002).
    • (2002) J. Chem. Phys. , vol.117 , pp. 9510-9517
    • Davis, R.1    Dobson, C.M.2    Vendruscolo, M.3
  • 18
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for protein dynamics and thermodynamics
    • Lazaridis, T. & Karplus, M. Effective energy function for protein dynamics and thermodynamics. Proteins 35, 133-152 (1999).
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 19
    • 0041843690 scopus 로고    scopus 로고
    • Calculation of mutational free energy changes in transition states for protein folding
    • Lindorff-Larsen, K., Paci, E., Serrano, L., Dobson, C.M. & Vendruscolo, M. Calculation of mutational free energy changes in transition states for protein folding. Biophys. J. 85, 1207-1214 (2003).
    • (2003) Biophys. J. , vol.85 , pp. 1207-1214
    • Lindorff-Larsen, K.1    Paci, E.2    Serrano, L.3    Dobson, C.M.4    Vendruscolo, M.5
  • 20
    • 0036367763 scopus 로고    scopus 로고
    • Reweighted atomic densities to represent ensembles of NMR structures
    • Schwieters, C.D. & Clore, G.M. Reweighted atomic densities to represent ensembles of NMR structures. J. Biomol. NMR 23, 221-225 (2002).
    • (2002) J. Biomol. NMR , vol.23 , pp. 221-225
    • Schwieters, C.D.1    Clore, G.M.2
  • 21
    • 0037076334 scopus 로고    scopus 로고
    • Molecular dynamics simulations of protein folding from the transition state
    • Gsponer, J. & Caflisch, A. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. USA 99, 6719-6724 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6719-6724
    • Gsponer, J.1    Caflisch, A.2
  • 22
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 (1995).
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 23
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm, L. & Sander, C. Mapping the protein universe. Science 273, 595-602 (1996).
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 24
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner, S.E., Koehl, P. & Levitt, M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res. 28, 254-256 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 27
    • 0037215268 scopus 로고    scopus 로고
    • The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
    • Makarov, D.E. & Plaxco, K.W. The topomer search model: A simple, quantitative theory of two-state protein folding kinetics. Protein Sci. 12, 17-26 (2003).
    • (2003) Protein Sci. , vol.12 , pp. 17-26
    • Makarov, D.E.1    Plaxco, K.W.2
  • 28
    • 0030057477 scopus 로고    scopus 로고
    • Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues
    • Khorasanizadeh, S., Peters, I.D. & Roder, H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat. Struct. Biol. 3, 193-205 (1996).
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 193-205
    • Khorasanizadeh, S.1    Peters, I.D.2    Roder, H.3
  • 29
    • 0034680824 scopus 로고    scopus 로고
    • Progressive stabilization of intermediate and transition states in protein folding reactions by introducing surface hydrophobic residues
    • Poso, D., Sessions, R.B., Lorch, M. & Clarke, A.R. Progressive stabilization of intermediate and transition states in protein folding reactions by introducing surface hydrophobic residues. J. Biol. Chem. 276, 35723-35726 (2000).
    • (2000) J. Biol. Chem. , vol.276 , pp. 35723-35726
    • Poso, D.1    Sessions, R.B.2    Lorch, M.3    Clarke, A.R.4
  • 30
    • 0037117477 scopus 로고    scopus 로고
    • Unspecific hydrophobic stabilization of folding transition states
    • Viguera, A.R., Vega, C. & Serrano, L. Unspecific hydrophobic stabilization of folding transition states. Proc. Natl. Acad. Sci. USA 99, 5349-5354 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5349-5354
    • Viguera, A.R.1    Vega, C.2    Serrano, L.3
  • 31
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • Cheung, M.S., Garcia, A.E. & Onuchic, J.N. Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA 99, 685-690 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garcia, A.E.2    Onuchic, J.N.3
  • 32
    • 0037058992 scopus 로고    scopus 로고
    • Probing the folding free energy landscape of the src-SH 3 protein domain
    • Shea, J.-E., Onuchic, J.N. & Brooks 3rd., C.L. Probing the folding free energy landscape of the src-SH3 protein domain. Proc. Natl. Acad. Sci. USA 99, 16064-16068 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16064-16068
    • Shea, J.-E.1    Onuchic, J.N.2    Brooks III, C.L.3
  • 33
    • 0037974485 scopus 로고    scopus 로고
    • Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain
    • Guo, Z., Brooks 3rd., C.L. & Boczko, E.M. Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. Biophys. J. 85, 61-69 (2003).
    • (2003) Biophys. J. , vol.85 , pp. 61-69
    • Guo, Z.1    Brooks III, C.L.2    Boczko, E.M.3
  • 34
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of total static accessibility
    • Lee, B. & Richards, F.M. The interpretation of protein structures: estimation of total static accessibility. J. Mol. Biol. 55, 379-400 (1971).
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 35
    • 0001843048 scopus 로고
    • Search for a realistic view of hydrophobic effects
    • Müller, N. Search for a realistic view of hydrophobic effects. Acc. Chem. Res. 23, 23-28 (1990).
    • (1990) Acc. Chem. Res. , vol.23 , pp. 23-28
    • Müller, N.1
  • 36
    • 0033080081 scopus 로고    scopus 로고
    • Is protein folding hierarchic? II. Folding intermediates and transition states
    • Baldwin, R.L. & Rose, G.D. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24, 77-83 (1999).
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 77-83
    • Baldwin, R.L.1    Rose, G.D.2
  • 37
    • 0036174712 scopus 로고    scopus 로고
    • Continuum secondary structure captures protein flexibility
    • Andersen, C.A.F., Palmer, A.G., Brunak, S. & Rost, B. Continuum secondary structure captures protein flexibility. Structure 10, 175-184 (2002).
    • (2002) Structure , vol.10 , pp. 175-184
    • Andersen, C.A.F.1    Palmer, A.G.2    Brunak, S.3    Rost, B.4
  • 38
    • 0343059020 scopus 로고    scopus 로고
    • Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain
    • Viguera, A.R., Jimenez, M.A., Rico, M. & Serrano, L. Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain. J. Mol. Biol. 255, 507-521 (1996).
    • (1996) J. Mol. Biol. , vol.255 , pp. 507-521
    • Viguera, A.R.1    Jimenez, M.A.2    Rico, M.3    Serrano, L.4
  • 39
    • 0037340910 scopus 로고    scopus 로고
    • Folding of a highly conserved diverging turn motif from the SH3 domain
    • Gnanakaran, S. & Garcia, A.E. Folding of a highly conserved diverging turn motif from the SH3 domain. Biophys. J. 84, 1548-1562 (2003).
    • (2003) Biophys. J. , vol.84 , pp. 1548-1562
    • Gnanakaran, S.1    Garcia, A.E.2
  • 40
    • 0032538302 scopus 로고    scopus 로고
    • Prediction and structural characterization of an independently folding substructure in the src SH3 domain
    • Yi, Q., Bystroff, C., Rajagopal, P., Klevit, R.E. & Baker, D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J. Mol. Biol. 283, 293-300 (1998).
    • (1998) J. Mol. Biol. , vol.283 , pp. 293-300
    • Yi, Q.1    Bystroff, C.2    Rajagopal, P.3    Klevit, R.E.4    Baker, D.5
  • 41
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small world' networks
    • Watts, D.J. & Strogatz, S.H. Collective dynamics of 'small world' networks. Nature 393, 440-442 (1998).
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 42
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding
    • Vendruscolo, M., Dokholyan, N.V., Paci, E. & Karplus, M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E65, 061910 (2002).
    • (2002) Phys. Rev. E , vol.65 , pp. 061910
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 44
    • 0037491167 scopus 로고    scopus 로고
    • β-hairpins, α-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β-hairpin of SH3 domain
    • Ikeda, K., Galzitskaya, O.V., Nakamura, H. & Higo, J. β-Hairpins, α-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β-hairpin of SH3 domain. J. Comp. Chem. 24, 310-318 (2003).
    • (2003) J. Comp. Chem. , vol.24 , pp. 310-318
    • Ikeda, K.1    Galzitskaya, O.V.2    Nakamura, H.3    Higo, J.4
  • 45
    • 0034721944 scopus 로고    scopus 로고
    • Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
    • Larson, S.M., Di Nardo, A.A. & Davidson, A.R. Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303, 433-446 (2000).
    • (2000) J. Mol. Biol. , vol.303 , pp. 433-446
    • Larson, S.M.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 46
    • 0037453348 scopus 로고    scopus 로고
    • A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core
    • Cobos, E.S. et al. A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core. J. Mol. Biol. 328, 221-122 (2003).
    • (2003) J. Mol. Biol. , vol.328 , pp. 221-122
    • Cobos, E.S.1
  • 47
    • 0037379184 scopus 로고    scopus 로고
    • Structural and kinetic characterization of the simplified SH3 domain FP1
    • Yi, Q., Rajagopal, P., Klevit, R.E. & Baker, D. Structural and kinetic characterization of the simplified SH3 domain FP1. Protein Sci. 12, 776-783 (2003).
    • (2003) Protein Sci. , vol.12 , pp. 776-783
    • Yi, Q.1    Rajagopal, P.2    Klevit, R.E.3    Baker, D.4
  • 48
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization and dynamics calculations
    • Brooks, B.R. et al. CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J. Comp. Chem. 4, 187-217 (1983).
    • (1983) J. Comp. Chem. , vol.4 , pp. 187-217
    • Brooks, B.R.1
  • 49
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular dynamics system
    • Neria, E., Fischer, S. & Karplus, M. Simulation of activation free energies in molecular dynamics system. J. Chem. Phys. 105, 1902-1921 (1996).
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 50
    • 0033824470 scopus 로고    scopus 로고
    • DaliLite workbench for protein structure comparison
    • Holm, L. & Park, J. DaliLite workbench for protein structure comparison. Bioinformatics 16, 566-567 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.