메뉴 건너뛰기




Volumn 54, Issue 3, 2004, Pages 513-525

Comparison of the Transition State Ensembles for Folding of Im7 and Im9 Determined Using All-Atom Molecular Dynamics Simulations with π Value Restraints

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; COLICIN IMMUNITY PROTEINS; PROTEIN IM7; PROTEIN IM9; UNCLASSIFIED DRUG;

EID: 1042279571     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10595     Document Type: Article
Times cited : (41)

References (44)
  • 1
    • 0032707954 scopus 로고    scopus 로고
    • Finding the right fold
    • Goldenberg DP. Finding the right fold. Nat Struct Biol 1999;6:987-990.
    • (1999) Nat Struct Biol , vol.6 , pp. 987-990
    • Goldenberg, D.P.1
  • 3
    • 0034984382 scopus 로고    scopus 로고
    • Mapping the folding pathway of an immunoglobulin domain: Structural detail from φ-value analysis and movement of the transition state
    • Fowler SB, Clarke J. Mapping the folding pathway of an immunoglobulin domain: Structural detail from φ-value analysis and movement of the transition state. Structure 2001;9:355-366.
    • (2001) Structure , vol.9 , pp. 355-366
    • Fowler, S.B.1    Clarke, J.2
  • 4
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
    • Martñez JC, Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol 1999;6:1010-1016.
    • (1999) Nat Struct Biol , vol.6 , pp. 1010-1016
    • Martñez, J.C.1    Serrano, L.2
  • 6
    • 0036172116 scopus 로고    scopus 로고
    • Hydrophobic core packing in the SH3 domain folding transition state
    • Northey JG, DiNardo AA, Davidson AR. Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Biol 2002;9:126-130.
    • (2002) Nat Struct Biol , vol.9 , pp. 126-130
    • Northey, J.G.1    DiNardo, A.A.2    Davidson, A.R.3
  • 7
    • 0034671177 scopus 로고    scopus 로고
    • The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
    • Guerois R, Serrano L. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J Mol Biol 2000;304:967-982.
    • (2000) J Mol Biol , vol.304 , pp. 967-982
    • Guerois, R.1    Serrano, L.2
  • 8
    • 0033548553 scopus 로고    scopus 로고
    • Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9
    • Ferguson N, Capaldi AP, James R, Kleanthous C, Radford SE. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J Mol Biol 1999;286:1597-1608.
    • (1999) J Mol Biol , vol.286 , pp. 1597-1608
    • Ferguson, N.1    Capaldi, A.P.2    James, R.3    Kleanthous, C.4    Radford, S.E.5
  • 9
    • 0035965128 scopus 로고    scopus 로고
    • Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9
    • Gorski SA, Capaldi AP, Kleanthous C, Radford SE. Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9. J Mol Biol 2001;312:849-863.
    • (2001) J Mol Biol , vol.312 , pp. 849-863
    • Gorski, S.A.1    Capaldi, A.P.2    Kleanthous, C.3    Radford, S.E.4
  • 10
    • 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
    • Dennis CA, Videler H, Pauptit RA, Wallis R, James R, Moore GR, Kleanthous C. A structural comparison of the colicin immunity proteins Im7 and Im9 gives new insights into the molecular determinants of immunity-protein specificity. Biochem J 1998;333:183-191.
    • (1998) Biochem J , vol.333 , pp. 183-191
    • Dennis, C.A.1    Videler, H.2    Pauptit, R.A.3    Wallis, R.4    James, R.5    Moore, G.R.6    Kleanthous, C.7
  • 11
    • 0029783011 scopus 로고    scopus 로고
    • Three-dimensional solution structure and 13C nuclear magnetic resonance assignments of the colicin E9 immunity protein Im9
    • Osborne MJ, Breeze AL, Lian LY, Reilly A, James R, Kleanthous C, Moore GR. Three-dimensional solution structure and 13C nuclear magnetic resonance assignments of the colicin E9 immunity protein Im9. Biochemistry 1996;35:9505-9512.
    • (1996) Biochemistry , vol.35 , pp. 9505-9512
    • Osborne, M.J.1    Breeze, A.L.2    Lian, L.Y.3    Reilly, A.4    James, R.5    Kleanthous, C.6    Moore, G.R.7
  • 12
    • 0035860455 scopus 로고    scopus 로고
    • A microscopic basis for the global appearance of energy landscapes
    • Wales DJ. A microscopic basis for the global appearance of energy landscapes. Science 2001;293:2067-2070.
    • (2001) Science , vol.293 , pp. 2067-2070
    • Wales, D.J.1
  • 14
    • 0036435907 scopus 로고    scopus 로고
    • Determination of a transition state at atomic resolution from protein engineering data
    • Paci E, Vendruscolo M, Dobson CM, Karplus M. Determination of a transition state at atomic resolution from protein engineering data. J Mol Biol 2002;324:151-163.
    • (2002) J Mol Biol , vol.324 , pp. 151-163
    • Paci, E.1    Vendruscolo, M.2    Dobson, C.M.3    Karplus, M.4
  • 15
    • 0037457892 scopus 로고    scopus 로고
    • Self-consistent determination of the transition state for protein folding. Application to a fibronectin type III domain
    • Paci E, Clarke J, Steward A, Vendruscolo M, Karplus M. Self-consistent determination of the transition state for protein folding. Application to a fibronectin type III domain. Proc Natl Acad Sci USA 2003;100:394-399.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 394-399
    • Paci, E.1    Clarke, J.2    Steward, A.3    Vendruscolo, M.4    Karplus, M.5
  • 16
    • 0027163998 scopus 로고
    • Protein folding and stability: The pathway of folding of barnase
    • Fersht AR. Protein folding and stability: The pathway of folding of barnase. FEBS Lett 1993;325:5-16.
    • (1993) FEBS Lett , vol.325 , pp. 5-16
    • Fersht, A.R.1
  • 17
    • 0037093654 scopus 로고    scopus 로고
    • Native and non-native interactions along protein folding and unfolding pathways
    • Paci E, Vendruscolo M, Karplus M. Native and non-native interactions along protein folding and unfolding pathways. Proteins 2002;47:379-392.
    • (2002) Proteins , vol.47 , pp. 379-392
    • Paci, E.1    Vendruscolo, M.2    Karplus, M.3
  • 18
    • 0036928148 scopus 로고    scopus 로고
    • Validity of Gō models: Comparison with a solvent-shielded empirical energy decomposition
    • Paci E, Vendruscolo M, Karplus M. Validity of Gō models: Comparison with a solvent-shielded empirical energy decomposition. Biophys J 2002;83:3032-3038.
    • (2002) Biophys J , vol.83 , pp. 3032-3038
    • Paci, E.1    Vendruscolo, M.2    Karplus, M.3
  • 19
    • 0036183221 scopus 로고    scopus 로고
    • Im7 folding mechanism: Misfolding on a path to the native state
    • Capaldi AP, Kleanthous C, Radford SE. Im7 folding mechanism: misfolding on a path to the native state. Nat Struct Biol 2002;9:209-216.
    • (2002) Nat Struct Biol , vol.9 , pp. 209-216
    • Capaldi, A.P.1    Kleanthous, C.2    Radford, S.E.3
  • 20
    • 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 CM, Vendruscolo M. Calculation of mutational free energy changes in transition states for protein folding. Biophys J 2003;85:1207-1214.
    • (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
  • 21
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo M, Paci E, Dobson CM, Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature 2001;409:641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 22
    • 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
    • Friel CT, Capaldi AP, Radford SE. 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 2003;326:293-305.
    • (2003) J Mol Biol , vol.326 , pp. 293-305
    • Friel, C.T.1    Capaldi, A.P.2    Radford, S.E.3
  • 23
    • 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 CM, Vendruscolo M. Determination of the structures of distinct transition state ensembles for a Β-sheet peptide with parallel folding pathways. J Chem Phys 2002;17:9510-9517.
    • (2002) J Chem Phys , vol.17 , pp. 9510-9517
    • Davis, R.1    Dobson, C.M.2    Vendruscolo, M.3
  • 24
    • 0033592876 scopus 로고    scopus 로고
    • From snapshot to movie: Analysis of protein folding transition states taken one step further
    • Ternström T, Mayor U, Akke M, Oliveberg M. From snapshot to movie: Analysis of protein folding transition states taken one step further. Proc Natl Acad Sci 1999;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
  • 25
    • 0034635955 scopus 로고    scopus 로고
    • A statistical mechanical method to optimize energy functions for protein folding
    • Bastolla U, Vendruscolo M, Knapp EW. A statistical mechanical method to optimize energy functions for protein folding. Proc Natl Acad Sci USA 2000;97:3977-3981.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 3977-3981
    • Bastolla, U.1    Vendruscolo, M.2    Knapp, E.W.3
  • 26
    • 41349118690 scopus 로고    scopus 로고
    • A small-world view of the amino acids that play a role in protein folding
    • Vendruscolo M, Dokholyan NV, Paci E, Karplus M. A small-world view of the amino acids that play a role in protein folding. Phys Rev E 2002;65:061910.
    • (2002) Phys Rev E , vol.65 , pp. 061910
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 27
    • 0037062448 scopus 로고    scopus 로고
    • Community structure in social and biological networks
    • Girvan M and Newman MEJ. Community structure in social and biological networks. Proc Natl Acad Sci USA 2002;99:7821-7826.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7821-7826
    • Girvan, M.1    Newman, M.E.J.2
  • 28
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 29
    • 0026511656 scopus 로고
    • The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
    • Fersht AR, Matouschek A, Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 1992;224:771-782.
    • (1992) J Mol Biol , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 30
    • 0026587310 scopus 로고
    • Cooperative interactions during protein folding
    • Horovitz A, Fersht AR. Cooperative interactions during protein folding. J Mol Biol 1992;224:733-740.
    • (1992) J Mol Biol , vol.224 , pp. 733-740
    • Horovitz, A.1    Fersht, A.R.2
  • 31
    • 0032512424 scopus 로고    scopus 로고
    • Specificity in protein-protein recognition: Conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Im9 complex
    • Wallis R, Leung KY, Osborne MJ, James R, Moore GR, Kleanthous C. Specificity in protein-protein recognition: conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Im9 complex. Biochemistry 1998;37:476-485.
    • (1998) Biochemistry , vol.37 , pp. 476-485
    • Wallis, R.1    Leung, K.Y.2    Osborne, M.J.3    James, R.4    Moore, G.R.5    Kleanthous, C.6
  • 32
    • 0017251893 scopus 로고
    • Protein-folding dynamics
    • Karplus M, Weaver DL. Protein-folding dynamics. Nature 1976;260:404-406.
    • (1976) Nature , vol.260 , pp. 404-406
    • Karplus, M.1    Weaver, D.L.2
  • 33
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • Fersht AR, Daggett V. Protein folding and unfolding at atomic resolution. Cell 2002;108:573-582.
    • (2002) Cell , vol.108 , pp. 573-582
    • Fersht, A.R.1    Daggett, V.2
  • 34
    • 0033617266 scopus 로고    scopus 로고
    • From computer simulations to human disease: Emerging themes in protein folding
    • Radford SE, Dobson CM. From computer simulations to human disease: Emerging themes in protein folding. Cell 1999;97:291-298.
    • (1999) Cell , vol.97 , pp. 291-298
    • Radford, S.E.1    Dobson, C.M.2
  • 35
    • 0032842870 scopus 로고    scopus 로고
    • The fundamentals of protein folding: Bringing together theory and experiment
    • Dobson CM, Karplus M. The fundamentals of protein folding: Bringing together theory and experiment. Curr Opin Struct Biol 1999;9:92-101.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 92-101
    • Dobson, C.M.1    Karplus, M.2
  • 36
    • 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 2003;13:82-87.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 82-87
    • Vendruscolo, M.1    Paci, E.2
  • 37
    • 0034703474 scopus 로고    scopus 로고
    • Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability
    • Cota E, Hamill SJ, Fowler SB, Clarke J. Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability. J Mol Biol 2000;302:713-725.
    • (2000) J Mol Biol , vol.302 , pp. 713-725
    • Cota, E.1    Hamill, S.J.2    Fowler, S.B.3    Clarke, J.4
  • 38
    • 0014718113 scopus 로고
    • Protein denaturation. C. Theoretical models for the mechanism of denaturation
    • Tanford C. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv Protein Chem 1970;24:1-95.
    • (1970) Adv Protein Chem , vol.24 , pp. 1-95
    • Tanford, C.1
  • 39
    • 0031465967 scopus 로고    scopus 로고
    • "New View" of protein folding reconciled with the old through multiple unfolding simulations
    • Lazaridis T, Karplus M. "New View" of protein folding reconciled with the old through multiple unfolding simulations. Science 1997;278:1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 41
    • 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 1996;105:1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 42
    • 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 1999;35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 43
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometric features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometric features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 44
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R, Billeter M, Wüthrich K. MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.
    • (1996) J Mol Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.