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Volumn 342, Issue 1, 2004, Pages 261-273

Switching two-state to three-state kinetics in the helical protein Im9 via the optimisation of stabilising non-native interactions by design

Author keywords

folding; immunity protein; intermediate; non native; rational design

Indexed keywords

BINDING PROTEIN; PROTEIN IM7; PROTEIN IM9; UNCLASSIFIED DRUG;

EID: 4143061715     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.06.076     Document Type: Article
Times cited : (64)

References (42)
  • 1
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • S.E. Jackson How do small single-domain proteins fold? Fold. Des. 3 1998 R81 R91
    • (1998) Fold. Des. , vol.3
    • Jackson, S.E.1
  • 2
    • 0028856785 scopus 로고
    • Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
    • A.R. Fersht Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications Proc. Natl Acad. Sci. USA 92 1995 10869 10873
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 3
    • 0032867418 scopus 로고    scopus 로고
    • Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing
    • S.H. Park, M.C. Shastry, and H. Roder Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing Nature Struct. Biol. 6 1999 943 947
    • (1999) Nature Struct. Biol. , vol.6 , pp. 943-947
    • Park, S.H.1    Shastry2    Roder, H.M.C.3
  • 5
    • 0033548553 scopus 로고    scopus 로고
    • Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9
    • N. Ferguson, A.P. Capaldi, R. James, C. Kleanthous, and S.E. Radford Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9 J. Mol. Biol. 286 1999 1597 1608
    • (1999) J. Mol. Biol. , vol.286 , pp. 1597-1608
    • Ferguson, N.1    Capaldi, A.P.2    James, R.3    Kleanthous4    Radford, S.E.C.5
  • 6
    • 0035965128 scopus 로고    scopus 로고
    • Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9
    • S.A. Gorski, A.P. Capaldi, C. Kleanthous, and S.E. Radford Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9 J. Mol. Biol. 312 2001 849 863
    • (2001) J. Mol. Biol. , vol.312 , pp. 849-863
    • Gorski, S.A.1    Capaldi, A.P.2    Kleanthous3    Radford, S.E.C.4
  • 7
    • 0037162450 scopus 로고    scopus 로고
    • Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing
    • K. Teilum, K. Maki, B.B. Kragelund, F.M. Poulsen, and H. Roder Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing Proc. Natl Acad. Sci. USA 99 2002 9807 9812
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 9807-9812
    • Teilum, K.1    Maki, K.2    Kragelund, B.B.3    Poulsen4    Roder, H.F.M.5
  • 8
    • 0037456298 scopus 로고    scopus 로고
    • The complete folding pathway of a protein from nanoseconds to microseconds
    • U. Mayor, N.R. Guydosh, C.M. Johnson, J.G. Grossmann, S. Sato, and G.S. Jas The complete folding pathway of a protein from nanoseconds to microseconds Nature 421 2003 863 867
    • (2003) Nature , vol.421 , pp. 863-867
    • Mayor, U.1    Guydosh, N.R.2    Johnson, C.M.3    Grossmann, J.G.4    Sato5    Jas, G.S.S.6
  • 9
    • 0029868589 scopus 로고    scopus 로고
    • Nonlinear free energy relationships in Arc Repressor unfolding imply the existence of unstable, native-like folding intermediates
    • T. Jonsson, C.D. Waldburger, and R.T. Sauer Nonlinear free energy relationships in Arc Repressor unfolding imply the existence of unstable, native-like folding intermediates Biochemistry 35 1996 4795 4802
    • (1996) Biochemistry , vol.35 , pp. 4795-4802
    • Jonsson, T.1    Waldburger2    Sauer, R.T.C.D.3
  • 10
    • 0037225280 scopus 로고    scopus 로고
    • Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding
    • I.E. Sanchez, and T. Kiefhaber Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding J. Mol. Biol. 325 2003 367 376
    • (2003) J. Mol. Biol. , vol.325 , pp. 367-376
    • Sanchez1    Kiefhaber, T.I.E.2
  • 11
    • 0030057477 scopus 로고    scopus 로고
    • Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues
    • S. Khorasanizadeh, I.D. Peters, and H. Roder Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues Nature Struct. Biol. 3 1996 193 205
    • (1996) Nature Struct. Biol. , vol.3 , pp. 193-205
    • Khorasanizadeh, S.1    Peters2    Roder, H.I.D.3
  • 13
    • 0036183221 scopus 로고    scopus 로고
    • Im7 folding mechanism: Misfolding on a path to the native state
    • A.P. Capaldi, C. Kleanthous, and S.E. Radford Im7 folding mechanism: misfolding on a path to the native state Nature Struct. Biol. 9 2002 209 216
    • (2002) Nature Struct. Biol. , vol.9 , pp. 209-216
    • Capaldi, A.P.1    Kleanthous2    Radford, S.E.C.3
  • 14
    • 0037423705 scopus 로고    scopus 로고
    • Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: Similarities and differences in the folding of homologous proteins
    • C.T. Friel, A.P. Capaldi, and S.E. Radford Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins J. Mol. Biol. 326 2003 293 305
    • (2003) J. Mol. Biol. , vol.326 , pp. 293-305
    • Friel, C.T.1    Capaldi2    Radford, S.E.A.P.3
  • 15
    • 0031127043 scopus 로고    scopus 로고
    • Development of multiple sequence approximation within the Agadir model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms
    • V. Munoz, and L. Serrano Development of multiple sequence approximation within the Agadir model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms Biopolymers 41 1997 495 509
    • (1997) Biopolymers , vol.41 , pp. 495-509
    • Munoz1    Serrano, L.V.2
  • 17
    • 36549094651 scopus 로고
    • Intrachain loops in polymers: Effects of excluded volume
    • H.S. Chan, and K.A. Dill Intrachain loops in polymers: effects of excluded volume J. Chem. Phys. 90 1989 492 509
    • (1989) J. Chem. Phys. , vol.90 , pp. 492-509
    • Chan1    Dill, K.A.H.S.2
  • 18
    • 0032516433 scopus 로고    scopus 로고
    • Toward understanding tryptophan fluorescence in proteins
    • Y. Chen, and M.D. Barkley Toward understanding tryptophan fluorescence in proteins Biochemistry 37 1998 9976 9982
    • (1998) Biochemistry , vol.37 , pp. 9976-9982
    • Chen1    Barkley, M.D.Y.2
  • 19
    • 0032127769 scopus 로고    scopus 로고
    • A structural comparison of the colicin immunity proteins Im7 and Im9 gives new insights into the molecular determinants of immunity-protein specificity
    • C.A. Dennis, H. Videler, R.A. Paupit, R. Wallis, R. James, G.R. Moore, and C. Kleanthous A structural comparison of the colicin immunity proteins Im7 and Im9 gives new insights into the molecular determinants of immunity-protein specificity Biochem. J. 333 1998 183 191
    • (1998) Biochem. J. , vol.333 , pp. 183-191
    • Dennis, C.A.1    Videler, H.2    Paupit, R.A.3    Wallis, R.4    James, R.5    Moore6    Kleanthous, C.G.R.7
  • 20
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • S. Nauli, B. Kuhlman, and D. Baker Computer-based redesign of a protein folding pathway Nature Struct. Biol. 8 2001 602 605
    • (2001) Nature Struct. Biol. , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman2    Baker, D.B.3
  • 21
    • 0036300662 scopus 로고    scopus 로고
    • Accurate computer-based design of a new backbone conformation in the second turn of Protein L
    • B. Kuhlman, J.W. O'Neill, D.E. Kim, K.Y.L. Zhang, and D. Baker Accurate computer-based design of a new backbone conformation in the second turn of Protein L J. Mol. Biol. 315 2002 471 477
    • (2002) J. Mol. Biol. , vol.315 , pp. 471-477
    • Kuhlman, B.1    O'Neill, J.W.2    Kim, D.E.3    Zhang4    Baker, D.K.Y.L.5
  • 22
    • 0036829967 scopus 로고    scopus 로고
    • Complete change of the protein folding transition state upon circular permutation
    • M. Lindberg, J. Tangrot, and M. Oliveberg Complete change of the protein folding transition state upon circular permutation Nature Struct. Biol. 9 2002 818 822
    • (2002) Nature Struct. Biol. , vol.9 , pp. 818-822
    • Lindberg, M.1    Tangrot2    Oliveberg, M.J.3
  • 23
    • 0029760326 scopus 로고    scopus 로고
    • Different folding transition states may result in the same native structure
    • A.R. Viguera, L. Serrano, and M. Wilmanns Different folding transition states may result in the same native structure Nature Struct. Biol. 3 1996 874 880
    • (1996) Nature Struct. Biol. , vol.3 , pp. 874-880
    • Viguera, A.R.1    Serrano2    Wilmanns, M.L.3
  • 24
    • 0032718386 scopus 로고    scopus 로고
    • Salt-induced detour through compact regions of the protein folding landscape
    • D.E. Otzen, and M. Oliveberg Salt-induced detour through compact regions of the protein folding landscape Proc. Natl Acad. Sci. USA 96 1999 11746 11751
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11746-11751
    • Otzen1    Oliveberg, M.D.E.2
  • 25
    • 0347627528 scopus 로고    scopus 로고
    • Destabilization of the Escherichia coli RNase H kinetic intermediate: Switching between a two-state and three-state folding mechanism
    • G.M. Spudich, E.J. Miller, and S. Marqusee Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism J. Mol. Biol. 335 2004 609 618
    • (2004) J. Mol. Biol. , vol.335 , pp. 609-618
    • Spudich, G.M.1    Miller2    Marqusee, S.E.J.3
  • 26
    • 0034283147 scopus 로고    scopus 로고
    • Specificity in protein-protein interactions: The structural basis for dual recognition in endonuclease colicin-community protein complexes
    • U.C. Kuhlmann, A.J. Pommer, G.R. Moore, R. James, and C. Kleanthous Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-community protein complexes J. Mol. Biol. 301 2000 1163 1178
    • (2000) J. Mol. Biol. , vol.301 , pp. 1163-1178
    • Kuhlmann, U.C.1    Pommer, A.J.2    Moore, G.R.3    James4    Kleanthous, C.R.5
  • 27
    • 0035193250 scopus 로고    scopus 로고
    • Diffusion-collision model study of misfolding in a four helix bundle protein
    • C. Beck, X. Siemens, and D.L. Weaver Diffusion-collision model study of misfolding in a four helix bundle protein Biophys. J. 81 2001 3105 3115
    • (2001) Biophys. J. , vol.81 , pp. 3105-3115
    • Beck, C.1    Siemens2    Weaver, D.L.X.3
  • 28
    • 1042279571 scopus 로고    scopus 로고
    • Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints
    • E. Paci, C.T. Friel, K. Lindorff-Larsen, S.E. Radford, M. Karplus, and M. Vendruscolo Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints Proteins: Struct. Func. Genet. 54 2004 513 525
    • (2004) Proteins: Struct. Func. Genet. , vol.54 , pp. 513-525
    • Paci, E.1    Friel, C.T.2    Lindorff-Larsen, K.3    Radford, S.E.4    Karplus5    Vendruscolo, M.M.6
  • 29
    • 0031588693 scopus 로고    scopus 로고
    • Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities
    • E. Lopez-Hernandez, P. Cronet, L. Serrano, and V. Munoz Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities J. Mol. Biol. 266 1997 610 620
    • (1997) J. Mol. Biol. , vol.266 , pp. 610-620
    • Lopez-Hernandez, E.1    Cronet, P.2    Serrano3    Munoz, V.L.4
  • 31
    • 0036074173 scopus 로고    scopus 로고
    • Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
    • S.B. Ozkan, K.A. Dill, and I. Bahar Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model Protein Sci. 11 2002 1958 1970
    • (2002) Protein Sci. , vol.11 , pp. 1958-1970
    • Ozkan, S.B.1    Dill2    Bahar, I.K.A.3
  • 32
    • 0033535951 scopus 로고    scopus 로고
    • Intermediates can accelerate protein folding
    • C. Wagner, and T. Kiefhaber Intermediates can accelerate protein folding Proc. Natl Acad. Sci. USA 96 1999 6716 6721
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 6716-6721
    • Wagner1    Kiefhaber, T.C.2
  • 34
    • 0030623698 scopus 로고    scopus 로고
    • Favourable native-like helical local interactions can accelerate protein folding
    • A.R. Viguera, V. Villegas, F.X. Aviles, and L. Serrano Favourable native-like helical local interactions can accelerate protein folding Fold. Des. 2 1997 23 33
    • (1997) Fold. Des. , vol.2 , pp. 23-33
    • Viguera, A.R.1    Villegas, V.2    Aviles3    Serrano, L.F.X.4
  • 35
    • 0032555115 scopus 로고    scopus 로고
    • Synergy between simulation and experiment in describing the energy landscape of protein folding
    • A.G. Ladurner, L.S. Itzhaki, V. Daggett, and A.R. Fersht Synergy between simulation and experiment in describing the energy landscape of protein folding Proc. Natl Acad. Sci. USA 95 1998 8473 8478
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 8473-8478
    • Ladurner, A.G.1    Itzhaki, L.S.2    Daggett3    Fersht, A.R.V.4
  • 36
    • 0030627747 scopus 로고    scopus 로고
    • Speeding up protein folding: Mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude
    • M. Munson, K.S. Anderson, and L. Regan Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude Fold. Des. 2 1997 77 87
    • (1997) Fold. Des. , vol.2 , pp. 77-87
    • Munson, M.1    Anderson2    Regan, L.K.S.3
  • 37
    • 0242383943 scopus 로고    scopus 로고
    • Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions
    • J. Karanicolas, and C.L. Brooks III Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions J. Mol. Biol. 334 2003 309 325
    • (2003) J. Mol. Biol. , vol.334 , pp. 309-325
    • Brooks III, C.L.1    Karanicolas, J.2
  • 39
    • 0023697408 scopus 로고
    • Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants
    • M.M. Santoro, and D.W. Bolen Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants Biochemistry 27 1988 8063 8068
    • (1988) Biochemistry , vol.27 , pp. 8063-8068
    • Santoro1    Bolen, D.W.M.M.2
  • 41
    • 0026244229 scopus 로고
    • Molscript-a program to produce both detailed and schematic plots of protein structures
    • P.J. Kraulis Molscript-a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 42
    • 0030815133 scopus 로고    scopus 로고
    • Raster 3D: Photorealistic molecular graphics
    • E.A. Merrit, and D.J. Bacon Raster 3D: Photorealistic molecular graphics Methods Enzymol. 277 1997 505 524
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merrit1    Bacon, D.J.E.A.2


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