메뉴 건너뛰기




Volumn 350, Issue 4, 2005, Pages 757-775

Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding

Author keywords

Folding intermediate; Folding mechanism; Molecular dynamics; Phi value analysis; Protein folding

Indexed keywords

MUTANT PROTEIN; PROTEIN C MYB;

EID: 20544462511     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.05.005     Document Type: Article
Times cited : (67)

References (40)
  • 2
    • 0030478947 scopus 로고    scopus 로고
    • A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy
    • K. Furukawa, M. Oda, and H. Nakamura A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy Proc. Natl Acad. Sci. USA 93 1996 13583 13588
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 13583-13588
    • Furukawa, K.1    Oda, M.2    Nakamura, H.3
  • 3
    • 0028327236 scopus 로고
    • Protein folding dynamics: The diffusion-collision model and experimental data
    • M. Karplus, and D.L. Weaver Protein folding dynamics: the diffusion-collision model and experimental data Protein Sci. 3 1994 650 668
    • (1994) Protein Sci. , vol.3 , pp. 650-668
    • Karplus, M.1    Weaver, D.L.2
  • 4
    • 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
    • L.S. Itzhaki, D.E. Otzen, and A.R. Fersht 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 1995 260 288
    • (1995) J. Mol. Biol. , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 5
    • 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
  • 6
    • 0037221599 scopus 로고    scopus 로고
    • Is there a unifying mechanism for protein folding?
    • V. Daggett, and A.R. Fersht Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28 2003 18 25
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 18-25
    • Daggett, V.1    Fersht, A.R.2
  • 7
    • 3843135179 scopus 로고    scopus 로고
    • Diffusing and colliding: The atomic level folding/unfolding pathway of a small helical protein
    • M.L. DeMarco, and V. Daggett Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein J. Mol. Biol. 2004 1109 1124
    • (2004) J. Mol. Biol. , pp. 1109-1124
    • Demarco, M.L.1    Daggett, V.2
  • 8
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition
    • S.E. Jackson, and A.R. Fersht Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition Biochemistry 30 1991 10428 10435
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 9
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • A. Li, and V. Daggett Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations J. Mol. Biol. 257 1996 412 429
    • (1996) J. Mol. Biol. , vol.257 , pp. 412-429
    • Li, A.1    Daggett, V.2
  • 10
    • 0025698613 scopus 로고
    • Transient folding intermediates characterized by protein engineering
    • A. Matouschek, J.T. Kellis, L. Serrano, M. Bycroft, and A.R. Fersht Transient folding intermediates characterized by protein engineering Nature 346 1990 440 445
    • (1990) Nature , vol.346 , pp. 440-445
    • Matouschek, A.1    Kellis, J.T.2    Serrano, L.3    Bycroft, M.4    Fersht, A.R.5
  • 12
    • 0031127043 scopus 로고    scopus 로고
    • Development of the 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 the 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
    • Munoz, V.1    Serrano, L.2
  • 13
    • 0028834210 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence
    • V. Munoz, and L. Serrano Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence J. Mol. Biol. 245 1995 297 308
    • (1995) J. Mol. Biol. , vol.245 , pp. 297-308
    • Munoz, V.1    Serrano, L.2
  • 14
    • 0024999332 scopus 로고
    • Improved detection of helix-turn-helix DNA-binding motifs in protein sequences
    • I.B. Dodd, and J.B. Eagan Improved detection of helix-turn-helix DNA-binding motifs in protein sequences Nucl. Acids Res. 18 1990 5019 5026
    • (1990) Nucl. Acids Res. , vol.18 , pp. 5019-5026
    • Dodd, I.B.1    Eagan, J.B.2
  • 15
    • 0036280655 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the protein unfolding/folding reaction
    • V. Daggett Molecular dynamics simulations of the protein unfolding/folding reaction Accts Chem. Res. 35 2002 422 429
    • (2002) Accts Chem. Res. , vol.35 , pp. 422-429
    • Daggett, V.1
  • 16
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • R. Day, B. Bennion, S. Ham, and V. Daggett Increasing temperature accelerates protein unfolding without changing the pathway of unfolding J. Mol. Biol. 322 2002 189 203
    • (2002) J. Mol. Biol. , vol.322 , pp. 189-203
    • Day, R.1    Bennion, B.2    Ham, S.3    Daggett, V.4
  • 17
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
    • A. Li, and V. Daggett Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2 Proc. Natl Acad. Sci. USA 91 1994 10430 10434
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 10430-10434
    • Li, A.1    Daggett, V.2
  • 18
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • A.R. Fersht, and V. Daggett Protein folding and unfolding at atomic resolution Cell 108 2002 573 582
    • (2002) Cell , vol.108 , pp. 573-582
    • Fersht, A.R.1    Daggett, V.2
  • 19
    • 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    Capaldi, A.P.2    Radford, S.E.3
  • 21
    • 0032812796 scopus 로고    scopus 로고
    • Mapping the interactions present in the transition state for the folding/unfolding of FKBP12
    • K.F. Fulton, E.R.G. Main, V. Daggett, and S.E. Jackson Mapping the interactions present in the transition state for the folding/unfolding of FKBP12 J. Mol. Biol. 291 1999 445 461
    • (1999) J. Mol. Biol. , vol.291 , pp. 445-461
    • Fulton, K.F.1    Main, E.R.G.2    Daggett, V.3    Jackson, S.E.4
  • 22
    • 0037686252 scopus 로고    scopus 로고
    • The present view of the mechanism of protein folding
    • V. Daggett, and A.R. Fersht The present view of the mechanism of protein folding Nature Rev. Mol. Cell Biol. 4 2003 497 502
    • (2003) Nature Rev. Mol. Cell Biol. , vol.4 , pp. 497-502
    • Daggett, V.1    Fersht, A.R.2
  • 23
    • 2342655032 scopus 로고    scopus 로고
    • Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation
    • P. Jemth, S. Gianni, R. Day, B. Li, C.M. Johnson, V. Daggett, and A.R. Fersht Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation Proc. Natl Acad. Sci. USA 101 2004 6450 6455
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6450-6455
    • Jemth, P.1    Gianni, S.2    Day, R.3    Li, B.4    Johnson, C.M.5    Daggett, V.6    Fersht, A.R.7
  • 24
    • 0032579189 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate
    • A. Li, and V. Daggett Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate J. Mol. Biol. 275 1998 677 694
    • (1998) J. Mol. Biol. , vol.275 , pp. 677-694
    • Li, A.1    Daggett, V.2
  • 25
    • 0032484148 scopus 로고    scopus 로고
    • Non-native interactions in protein folding intermediates: Molecular dynamics simulations of hen lysozyme
    • S.L. Kazmirski, and V. Daggett Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme J. Mol. Biol. 284 1998 793 806
    • (1998) J. Mol. Biol. , vol.284 , pp. 793-806
    • Kazmirski, S.L.1    Daggett, V.2
  • 26
    • 0034491563 scopus 로고    scopus 로고
    • Spring mechanics of α-helical polypeptide
    • A. Idiris, M.T. Alam, and A. Ikai Spring mechanics of α-helical polypeptide Protein Eng. 13 2000 763 770
    • (2000) Protein Eng. , vol.13 , pp. 763-770
    • Idiris, A.1    Alam, M.T.2    Ikai, A.3
  • 27
    • 0025420076 scopus 로고
    • Measuring and increasing protein stability
    • C.N. Pace Measuring and increasing protein stability Trends Biotechnol. 8 1990 93 98
    • (1990) Trends Biotechnol. , vol.8 , pp. 93-98
    • Pace, C.N.1
  • 28
    • 0142185492 scopus 로고    scopus 로고
    • The denatured state of Engrailed homeodomain under denaturing and native conditions
    • U. Mayor, J.G. Grossmann, N.W. Foster, S.M. Freund, and A.R. Fersht The denatured state of Engrailed homeodomain under denaturing and native conditions J. Mol. Biol. 333 2003 977 991
    • (2003) J. Mol. Biol. , vol.333 , pp. 977-991
    • Mayor, U.1    Grossmann, J.G.2    Foster, N.W.3    Freund, S.M.4    Fersht, A.R.5
  • 29
    • 0027163998 scopus 로고
    • The sixth Datta Lecture. Protein folding and stability: The pathway of folding of barnase
    • A.R. Fersht The sixth Datta Lecture. Protein folding and stability: the pathway of folding of barnase FEBS Letters 325 1993 5 16
    • (1993) FEBS Letters , vol.325 , pp. 5-16
    • Fersht, A.R.1
  • 30
    • 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    Sato, S.5    Jas, G.S.6
  • 31
    • 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    Kleanthous, C.3    Radford, S.E.4
  • 32
    • 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    Peters, I.D.2    Roder, H.3
  • 33
    • 0038286126 scopus 로고    scopus 로고
    • Hydrogen-exchange stability analysis of Bergerac-Src homology 3 variants allows the characterization of a folding intermediate in equilibrium
    • A.R. Viguera, and L. Serrano Hydrogen-exchange stability analysis of Bergerac-Src homology 3 variants allows the characterization of a folding intermediate in equilibrium Proc. Natl Acad. Sci. USA 100 2003 5730 5735
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 5730-5735
    • Viguera, A.R.1    Serrano, L.2
  • 34
    • 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    Miller, E.J.2    Marqusee, S.3
  • 36
    • 0029633167 scopus 로고
    • Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution
    • M. Levitt, M. Hirshberg, R. Sharon, and V. Daggett Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution Comput. Phys. Commun. 91 1995 215 231
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 37
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • M. Levitt, M. Hirshberg, R. Sharon, K.E. Laidig, and V. Daggett Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution J. Phys. Chem. 101 1997 5051 5061
    • (1997) J. Phys. Chem. , vol.101 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laidig, K.E.4    Daggett, V.5
  • 38
    • 0009979659 scopus 로고
    • Precise representation of volume properties of water at one atmosphere
    • G.S. Kell Precise representation of volume properties of water at one atmosphere J. Chem. Eng. Data 12 1967 66 69
    • (1967) J. Chem. Eng. Data , vol.12 , pp. 66-69
    • Kell, G.S.1
  • 39
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • U. Mayor, C.M. Johnson, V. Daggett, and A.R. Fersht Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl Acad. Sci. USA 97 2000 13518 13522
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 40
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.