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Volumn 47, Issue 48, 2008, Pages 12910-12922

Aromatic residues engineered into the β-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps

Author keywords

[No Author keywords available]

Indexed keywords

AGGLOMERATION; AROMATIC COMPOUNDS; FLOW INTERACTIONS; FORMING; NUCLEATION; PORT TERMINALS; POWDERS; PROTEINS;

EID: 57049128788     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801330r     Document Type: Article
Times cited : (18)

References (50)
  • 1
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson, S. E. (1998) How do small single-domain proteins fold? Folding Des. 3, R81-R91.
    • (1998) Folding Des , vol.3
    • Jackson, S.E.1
  • 2
    • 33846577660 scopus 로고    scopus 로고
    • NMR analysis of the conformational properties of the trapped on-pathway folding intermediate of the bacterial immunity protein Im7
    • Whittaker, S. B. M., Spence, G. R., Grossmann, J. G., Radford, S. E., and Moore, G. R. (2007) NMR analysis of the conformational properties of the trapped on-pathway folding intermediate of the bacterial immunity protein Im7. J. Mol. Biol. 366, 1001-1015.
    • (2007) J. Mol. Biol , vol.366 , pp. 1001-1015
    • Whittaker, S.B.M.1    Spence, G.R.2    Grossmann, J.G.3    Radford, S.E.4    Moore, G.R.5
  • 3
    • 33644940724 scopus 로고    scopus 로고
    • Structural characterization of an equilibrium unfolding intermediate in cytochrome c
    • Latypov, R. F., Cheng, H., Roder, N. A., Zhang, J., and Roder, H. (2006) Structural characterization of an equilibrium unfolding intermediate in cytochrome c. J. Mol. Biol. 357, 1009-1025.
    • (2006) J. Mol. Biol , vol.357 , pp. 1009-1025
    • Latypov, R.F.1    Cheng, H.2    Roder, N.A.3    Zhang, J.4    Roder, H.5
  • 4
    • 0037225280 scopus 로고    scopus 로고
    • Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding
    • Sanchez, I. E., and Kiefhaber, T. (2003) Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325, 367-376.
    • (2003) J. Mol. Biol , vol.325 , pp. 367-376
    • Sanchez, I.E.1    Kiefhaber, T.2
  • 5
    • 33947327195 scopus 로고    scopus 로고
    • Kinetics of Staphylococcal Nuclease Studied by Tryptophan Engineering and Rapid Mixing Methods
    • Maki, K., Cheng, H., Dolgikh, D. A., and Roder, H. (2007) Kinetics of Staphylococcal Nuclease Studied by Tryptophan Engineering and Rapid Mixing Methods. J. Mol. Biol. 368, 244-255.
    • (2007) J. Mol. Biol , vol.368 , pp. 244-255
    • Maki, K.1    Cheng, H.2    Dolgikh, D.A.3    Roder, H.4
  • 7
    • 57049146345 scopus 로고    scopus 로고
    • Roder, H., Maki, K., Latypov, R. F., Cheng, H., Ramachandra Shastry, M. C. (2005) Early events in protein folding explored by rapid mixing methods In Protein Folding Handbook (Kiefhaber, T., Buchner, J., Eds.) Part I, Wiley-VCH, Weinheim, Germany.
    • Roder, H., Maki, K., Latypov, R. F., Cheng, H., Ramachandra Shastry, M. C. (2005) Early events in protein folding explored by rapid mixing methods In Protein Folding Handbook (Kiefhaber, T., Buchner, J., Eds.) Part I, Wiley-VCH, Weinheim, Germany.
  • 8
    • 0032919144 scopus 로고    scopus 로고
    • Acceleration of the folding of acylphosphatase by stabilization of local secondary structure
    • Chiti, F., Taddei, N., Webster, P., Hamada, D., Fiaschi, T., Ramponi, G., and Dobson, C. M. (1999) Acceleration of the folding of acylphosphatase by stabilization of local secondary structure. Nat. Struct. Biol. 6, 380-387.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 380-387
    • Chiti, F.1    Taddei, N.2    Webster, P.3    Hamada, D.4    Fiaschi, T.5    Ramponi, G.6    Dobson, C.M.7
  • 11
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and refolding rates of single domain proteins
    • Plaxco, K. W., Simons, K. T., and Baker, D. (1998) Contact order, transition state placement and 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
  • 12
    • 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
  • 14
    • 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, 359-371.
    • (2002) J. Mol. Biol , vol.324 , pp. 359-371
    • Krantz, B.A.1    Mayne, L.2    Rumbley, J.3    Englander, S.W.4    Sosnick, T.R.5
  • 15
    • 0028856785 scopus 로고
    • Optimisation of rates of protein folding: The nucleation-condensation mechanism and its implications
    • Fersht, A. R. (1995) Optimisation of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. U.S.A. 92, 10869-10873.
    • (1995) Proc. Natl. Acad. Sci. U.S.A , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 16
    • 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
  • 18
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson, C. M. (2003) Protein folding and misfolding. Nature 426, 884-890.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 19
    • 0344944630 scopus 로고    scopus 로고
    • Protein aggregation and aggregation troxicity: New insights into protein folding, misfolding diseases and biological evolution
    • Stefani, M., and Dobson, C. M. (2003) Protein aggregation and aggregation troxicity: new insights into protein folding, misfolding diseases and biological evolution. J. Mol. Med. 81, 678-699.
    • (2003) J. Mol. Med , vol.81 , pp. 678-699
    • Stefani, M.1    Dobson, C.M.2
  • 20
    • 28644437048 scopus 로고    scopus 로고
    • The importance of sequence evolution in the aggregation and evolution of proteins
    • Wright, C. F., Teichmann, S. A., Clarke, J., and Dobson, C. M. (2005) The importance of sequence evolution in the aggregation and evolution of proteins. Nature 438, 878-881.
    • (2005) Nature , vol.438 , pp. 878-881
    • Wright, C.F.1    Teichmann, S.A.2    Clarke, J.3    Dobson, C.M.4
  • 21
    • 1842635571 scopus 로고    scopus 로고
    • Characterisation of the folding energy landscape of computer generated proteins suggests high folding free energy barriers and co-operativity may be consequences of natural selection
    • Scalley-Kim, M., and Baker, D. (2004) Characterisation of the folding energy landscape of computer generated proteins suggests high folding free energy barriers and co-operativity 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
  • 22
    • 0034718524 scopus 로고    scopus 로고
    • Distinguishing between two-state and three-state models for ubiquitin folding
    • Krantz, B. A., and Sosnick, T. R. (2000) Distinguishing between two-state and three-state models for ubiquitin folding. Biochemistry 39, 11696-11701.
    • (2000) Biochemistry , vol.39 , pp. 11696-11701
    • Krantz, B.A.1    Sosnick, T.R.2
  • 23
    • 2942617191 scopus 로고    scopus 로고
    • Is an intermediate state populated on the folding pathway of ubiquitin?
    • Went, H. M., Benitez-Cardoza, C. G., and Jackson, S. E. (2004) Is an intermediate state populated on the folding pathway of ubiquitin? FEBS Lett. 567, 333-338.
    • (2004) FEBS Lett , vol.567 , pp. 333-338
    • Went, H.M.1    Benitez-Cardoza, C.G.2    Jackson, S.E.3
  • 24
    • 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., and Roder, H. (1996) 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) Nat. Struct. Biol , vol.3 , pp. 193-205
    • Khorasanizadeh, S.1    Peters, I.D.2    Roder, H.3
  • 25
    • 0030322627 scopus 로고    scopus 로고
    • Structure of very early protein folding intermediates: New insights through a variant of hydrogen exchange labelling
    • Gladwin, B. F., and Evans, P. A. (1996) Structure of very early protein folding intermediates: new insights through a variant of hydrogen exchange labelling. Folding Des. 1, 407-417.
    • (1996) Folding Des , vol.1 , pp. 407-417
    • Gladwin, B.F.1    Evans, P.A.2
  • 26
    • 33745965316 scopus 로고    scopus 로고
    • Population of on-pathway intermediates in the folding of ubiquitin
    • Crespo, M. D., Simpson, E. R., and Searle, M. S. (2006) Population of on-pathway intermediates in the folding of ubiquitin. J. Mol. Biol. 360, 1053-1066.
    • (2006) J. Mol. Biol , vol.360 , pp. 1053-1066
    • Crespo, M.D.1    Simpson, E.R.2    Searle, M.S.3
  • 27
    • 35648993490 scopus 로고    scopus 로고
    • Multiple tryptophan probes reveal that ubiquitin folds via a late misfolded intermediate
    • Vallee-Belisle, A., and Michnick, S. W. (2007) Multiple tryptophan probes reveal that ubiquitin folds via a late misfolded intermediate. J. Mol. Biol. 374, 791-805.
    • (2007) J. Mol. Biol , vol.374 , pp. 791-805
    • Vallee-Belisle, A.1    Michnick, S.W.2
  • 28
    • 48649105144 scopus 로고    scopus 로고
    • Helix mutations stabilise a late productive intermediate on the folding pathway of ubiquitin
    • Rea, A. M., Simpson, E. R., Crespo, M. D., and Searle, M. S. (2008) Helix mutations stabilise a late productive intermediate on the folding pathway of ubiquitin. Biochemistry 47, 8225-8236.
    • (2008) Biochemistry , vol.47 , pp. 8225-8236
    • Rea, A.M.1    Simpson, E.R.2    Crespo, M.D.3    Searle, M.S.4
  • 29
    • 0345708444 scopus 로고    scopus 로고
    • Stability and folding kinetics of a ubiquitin mutant with a strong propensity for nonnative beta-hairpin conformation in the unfolded state
    • Platt, G. W., Simpson, S. A., Layfield, R., and Searle, M. S. (2003) Stability and folding kinetics of a ubiquitin mutant with a strong propensity for nonnative beta-hairpin conformation in the unfolded state. Biochemistry 42, 13762-13771.
    • (2003) Biochemistry , vol.42 , pp. 13762-13771
    • Platt, G.W.1    Simpson, S.A.2    Layfield, R.3    Searle, M.S.4
  • 30
    • 33645537630 scopus 로고    scopus 로고
    • Ubiquitin folds through a highly polarised transition state
    • Went, H. M., and Jackson, S. E. (2004) Ubiquitin folds through a highly polarised transition state. Protein Eng. 18, 239-246.
    • (2004) Protein Eng , vol.18 , pp. 239-246
    • Went, H.M.1    Jackson, S.E.2
  • 31
    • 33645537945 scopus 로고    scopus 로고
    • Engineering diverse changes in β-turn propensities in the N-terminal β-hairpin of ubiquitin reveals significant effects on stability and kinetics but a robust folding transition state
    • Simpson, E. R., Meldrum, J. K., and Searle, M. S. (2006) Engineering diverse changes in β-turn propensities in the N-terminal β-hairpin of ubiquitin reveals significant effects on stability and kinetics but a robust folding transition state. Biochemistry 45, 4220-4230.
    • (2006) Biochemistry , vol.45 , pp. 4220-4230
    • Simpson, E.R.1    Meldrum, J.K.2    Searle, M.S.3
  • 32
    • 0034633950 scopus 로고    scopus 로고
    • Co-operative assembly of a native-like ubiquitin structure through peptide fragment complexation: Energetics of peptide association and folding
    • Jourdan, M., and Searle, M. S. (2000) Co-operative assembly of a native-like ubiquitin structure through peptide fragment complexation: Energetics of peptide association and folding. Biochemistry 39, 12355-12364.
    • (2000) Biochemistry , vol.39 , pp. 12355-12364
    • Jourdan, M.1    Searle, M.S.2
  • 33
    • 23744501900 scopus 로고    scopus 로고
    • Engineering enhanced protein suability through β-turn optimisation: Insights for the design of stable peptide β-hairpin systems
    • Simpson, E. R., Meldrum, J. K., Bofill, R., Crespo, M. D., Holmes, E., and Searle, M. S. (2005) Engineering enhanced protein suability through β-turn optimisation: insights for the design of stable peptide β-hairpin systems. Angew. Chem., Int. Ed. 44, 4939-4944.
    • (2005) Angew. Chem., Int. Ed , vol.44 , pp. 4939-4944
    • Simpson, E.R.1    Meldrum, J.K.2    Bofill, R.3    Crespo, M.D.4    Holmes, E.5    Searle, M.S.6
  • 34
    • 0033536659 scopus 로고    scopus 로고
    • Dissecting the stability of a β-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the β-turn and β-strand contributions to folding
    • Griffiths-Jones, S. R., Maynard, A. J., and Searle, M. S. (1999) Dissecting the stability of a β-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the β-turn and β-strand contributions to folding. J. Mol. Biol. 292, 1051-1069.
    • (1999) J. Mol. Biol , vol.292 , pp. 1051-1069
    • Griffiths-Jones, S.R.1    Maynard, A.J.2    Searle, M.S.3
  • 35
    • 33846708445 scopus 로고    scopus 로고
    • The highly co-operative folding of small naturally occurring proteins is likely the result of natural selection
    • Watters, A. L., Deka, P., Corrent, C., Callender, D., Varani, G., Sosnick, T., and Baker, D. (2007) The highly co-operative folding of small naturally occurring proteins is likely the result of natural selection. Cell 128, 613-624.
    • (2007) Cell , vol.128 , pp. 613-624
    • Watters, A.L.1    Deka, P.2    Corrent, C.3    Callender, D.4    Varani, G.5    Sosnick, T.6    Baker, D.7
  • 37
    • 25144507750 scopus 로고    scopus 로고
    • Engineering stabilising interactions into a conformationally flexible region of the folding transition state of ubiquitin
    • Bofill, R., and Searle, M. S. (2005) Engineering stabilising interactions into a conformationally flexible region of the folding transition state of ubiquitin. J. Mol. Biol. 353, 373-384.
    • (2005) J. Mol. Biol , vol.353 , pp. 373-384
    • Bofill, R.1    Searle, M.S.2
  • 38
    • 57049134644 scopus 로고    scopus 로고
    • Bachmann, A., Kiefhaber, T. (2005) Kinetic mechanisms in protein folding In Protein Folding Handbook (Kiefhaber, T., Buchner, J.) Part I, Wiley-VCH, Weinheim, Germany.
    • Bachmann, A., Kiefhaber, T. (2005) Kinetic mechanisms in protein folding In Protein Folding Handbook (Kiefhaber, T., Buchner, J.) Part I, Wiley-VCH, Weinheim, Germany.
  • 40
    • 17344384932 scopus 로고    scopus 로고
    • Fast folding of the two-domain semliki forest virus capsid protein explains co-translational proteolytic activity
    • Sanchez, I. E., Morillas, M., Zobeley, E., Kiefhaber, T., and Glockshuber, R. (2004) Fast folding of the two-domain semliki forest virus capsid protein explains co-translational proteolytic activity. J. Mol. Biol. 338, 159-167.
    • (2004) J. Mol. Biol , vol.338 , pp. 159-167
    • Sanchez, I.E.1    Morillas, M.2    Zobeley, E.3    Kiefhaber, T.4    Glockshuber, R.5
  • 42
    • 0033592403 scopus 로고    scopus 로고
    • A salt-induced kinetic intermediate is on a new parallel pathway of lysozyme folding
    • Bieri, O., Wildegger, G., Bachmann, A., Wagner, C., and Kiefhaber, T. (1999) A salt-induced kinetic intermediate is on a new parallel pathway of lysozyme folding. Biochemistry 38, 12460-12470.
    • (1999) Biochemistry , vol.38 , pp. 12460-12470
    • Bieri, O.1    Wildegger, G.2    Bachmann, A.3    Wagner, C.4    Kiefhaber, T.5
  • 43
    • 33847306593 scopus 로고    scopus 로고
    • A unified mechanism for protein folding: Predetermined pathways with optional errors
    • Krishna, M. M. G., and Englander, S. W. (2007) A unified mechanism for protein folding: predetermined pathways with optional errors. Protein Sci. 16, 449-464.
    • (2007) Protein Sci , vol.16 , pp. 449-464
    • Krishna, M.M.G.1    Englander, S.W.2
  • 44
    • 0023644679 scopus 로고
    • Structure of Ubiquitin Refined at 1.8 A Resolution
    • Vijaykumar, S., Bugg, C. E., and Cook, W. J. (1987) Structure of Ubiquitin Refined at 1.8 A Resolution. J. Mol. Biol. 194, 531-544.
    • (1987) J. Mol. Biol , vol.194 , pp. 531-544
    • Vijaykumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 45
    • 0035964177 scopus 로고    scopus 로고
    • Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity
    • Bolon, D. N., and Mayo, S. L. (2001) Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity. Biochemistry 40, 10047-10053.
    • (2001) Biochemistry , vol.40 , pp. 10047-10053
    • Bolon, D.N.1    Mayo, S.L.2
  • 46
    • 4143070403 scopus 로고    scopus 로고
    • Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding
    • Searle, M. S., and Ciani, B. (2004) Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding. Curr. Opin. Struct. Biol. 14, 458-464.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 458-464
    • Searle, M.S.1    Ciani, B.2
  • 47
    • 0037022563 scopus 로고    scopus 로고
    • Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation
    • Richardson, J. S., and Richardson, D. C. (2002) Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl. Acad. Sci. U.S.A. 99, 2754-2759.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 2754-2759
    • Richardson, J.S.1    Richardson, D.C.2
  • 48
    • 12844284527 scopus 로고    scopus 로고
    • The N-terminal to C-terminal motif in protein folding and function
    • Krishna, M. M. G., and Englander, S. W. (2005) The N-terminal to C-terminal motif in protein folding and function. Proc. Natl. Acad. Sci. U.S.A. 102, 1053-1058.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 1053-1058
    • Krishna, M.M.G.1    Englander, S.W.2
  • 49
    • 0036183221 scopus 로고    scopus 로고
    • Im7 folding mechanism: Misfolding on a path to the native state
    • Capaldi, A. P., Kleanthous, C., and Radford, S. E. (2002) Im7 folding mechanism: misfolding on a path to the native state. Nat. Struct. Biol. 9, 209-216.
    • (2002) Nat. Struct. Biol , vol.9 , pp. 209-216
    • Capaldi, A.P.1    Kleanthous, C.2    Radford, S.E.3
  • 50
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structure
    • Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structure. J. Mol. Graph. 14, 51-55.
    • (1996) J. Mol. Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3


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