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Volumn 7, Issue 9, 2012, Pages

Illuminating the Off-Pathway Nature of the Molten Globule Folding Intermediate of an α-β Parallel Protein

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA BETA PARALLEL PROTEIN; APOFLAVODOXIN; BACTERIAL PROTEIN; CYSTEINE; DYE; UNCLASSIFIED DRUG;

EID: 84866649525     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045746     Document Type: Article
Times cited : (10)

References (56)
  • 1
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: a synthesis
    • Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG, (1995) Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21: 167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 2
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill KA, Chan HS, (1997) From Levinthal to pathways to funnels. Nat Struct Biol 4: 10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 3
    • 0009586942 scopus 로고    scopus 로고
    • Understanding protein folding via free-energy surfaces from theory and experiment
    • Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M, (2000) Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci 25: 331-339.
    • (2000) Trends Biochem Sci , vol.25 , pp. 331-339
    • Dinner, A.R.1    Sali, A.2    Smith, L.J.3    Dobson, C.M.4    Karplus, M.5
  • 4
    • 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, (2001) Three key residues form a critical contact network in a protein folding transition state. Nature 409: 641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 5
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • Fersht AR, Daggett V, (2002) Protein folding and unfolding at atomic resolution. Cell 108: 573-582.
    • (2002) Cell , vol.108 , pp. 573-582
    • Fersht, A.R.1    Daggett, V.2
  • 6
    • 36749078792 scopus 로고    scopus 로고
    • Folding versus aggregation: polypeptide conformations on competing pathways
    • Jahn TR, Radford SE, (2008) Folding versus aggregation: polypeptide conformations on competing pathways. Arch Biochem Biophys 469: 100-117.
    • (2008) Arch Biochem Biophys , vol.469 , pp. 100-117
    • Jahn, T.R.1    Radford, S.E.2
  • 7
    • 0021114569 scopus 로고
    • Molten-globule state': a compact form of globular proteins with mobile side-chains
    • Ohgushi M, Wada A, (1983) 'Molten-globule state': a compact form of globular proteins with mobile side-chains. FEBS Lett 164: 21-24.
    • (1983) FEBS Lett , vol.164 , pp. 21-24
    • Ohgushi, M.1    Wada, A.2
  • 10
    • 0034581327 scopus 로고    scopus 로고
    • Role of the molten globule state in protein folding
    • Arai M, Kuwajima K, (2000) Role of the molten globule state in protein folding. Adv Protein Chem 53: 209-282.
    • (2000) Adv Protein Chem , vol.53 , pp. 209-282
    • Arai, M.1    Kuwajima, K.2
  • 11
    • 0035909813 scopus 로고    scopus 로고
    • Apoflavodoxin folding mechanism: an alpha/beta protein with an essentially off-pathway intermediate
    • Fernandez-Recio J, Genzor CG, Sancho J, (2001) Apoflavodoxin folding mechanism: an alpha/beta protein with an essentially off-pathway intermediate. Biochemistry 40: 15234-15245.
    • (2001) Biochemistry , vol.40 , pp. 15234-15245
    • Fernandez-Recio, J.1    Genzor, C.G.2    Sancho, J.3
  • 12
    • 0038070096 scopus 로고    scopus 로고
    • Trehalose favors a cutinase compact intermediate off-folding pathway
    • Melo EP, Chen L, Cabral JM, Fojan P, Petersen SB, et al. (2003) Trehalose favors a cutinase compact intermediate off-folding pathway. Biochemistry 42: 7611-7617.
    • (2003) Biochemistry , vol.42 , pp. 7611-7617
    • Melo, E.P.1    Chen, L.2    Cabral, J.M.3    Fojan, P.4    Petersen, S.B.5
  • 13
    • 4043074820 scopus 로고    scopus 로고
    • Formation of on- and off-pathway intermediates in the folding kinetics of Azotobacter vinelandii apoflavodoxin
    • Bollen YJ, Sanchéz IE, van Mierlo CP, (2004) Formation of on- and off-pathway intermediates in the folding kinetics of Azotobacter vinelandii apoflavodoxin. Biochemistry 43: 10475-10489.
    • (2004) Biochemistry , vol.43 , pp. 10475-10489
    • Bollen, Y.J.1    Sanchéz, I.E.2    van Mierlo, C.P.3
  • 14
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid, and human disease
    • Chiti F, Dobson CM, (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75: 333-366.
    • (2006) Annu Rev Biochem , vol.75 , pp. 333-366
    • Chiti, F.1    Dobson, C.M.2
  • 15
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson CM, (2003) Protein folding and misfolding. Nature 426: 884-890.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 18
    • 0026633175 scopus 로고
    • Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor
    • Amir D, Krausz S, Haas E, (1992) Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor. Proteins 13: 162-173.
    • (1992) Proteins , vol.13 , pp. 162-173
    • Amir, D.1    Krausz, S.2    Haas, E.3
  • 19
    • 18744389451 scopus 로고    scopus 로고
    • The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements
    • Haas E, (2005) The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. Chemphyschem: a European journal of chemical physics and physical chemistry 6: 858-870.
    • (2005) Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry , vol.6 , pp. 858-870
    • Haas, E.1
  • 20
    • 84981779372 scopus 로고
    • Zwischenmolekulare energiewanderung und fluoreszenz
    • Förster T, (1948) Zwischenmolekulare energiewanderung und fluoreszenz. Ann Phys-Berlin 2: 55-75.
    • (1948) Ann Phys-Berlin , vol.2 , pp. 55-75
    • Förster, T.1
  • 22
    • 0000323018 scopus 로고
    • General properties of flavodoxins
    • In: Müller F, editor, Boca Raton, Florida: CRC press
    • Mayhew SG, Tollin G (1992) General properties of flavodoxins. In: Müller F, editor. Chemistry and biochemistry of flavoenzymes. Boca Raton, Florida: CRC press. 389-426.
    • (1992) Chemistry and biochemistry of flavoenzymes , pp. 389-426
    • Mayhew, S.G.1    Tollin, G.2
  • 23
    • 33645217096 scopus 로고    scopus 로고
    • The folding energy landscape of apoflavodoxin is rugged: Hydrogen exchange reveals nonproductive misfolded intermediates
    • Bollen YJ, Kamphuis MB, van Mierlo CP, (2006) The folding energy landscape of apoflavodoxin is rugged: Hydrogen exchange reveals nonproductive misfolded intermediates. Proc Natl Acad Sci U S A 103: 4095-4100.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 4095-4100
    • Bollen, Y.J.1    Kamphuis, M.B.2    van Mierlo, C.P.3
  • 24
    • 14844322304 scopus 로고    scopus 로고
    • Last in, first out: The role of cofactor binding in flavodoxin folding
    • Bollen YJ, Nabuurs SM, van Berkel WJ, van Mierlo CP, (2005) Last in, first out: The role of cofactor binding in flavodoxin folding. J Biol Chem 280: 7836-7844.
    • (2005) J Biol Chem , vol.280 , pp. 7836-7844
    • Bollen, Y.J.1    Nabuurs, S.M.2    van Berkel, W.J.3    van Mierlo, C.P.4
  • 25
    • 0032566696 scopus 로고    scopus 로고
    • Structural characterisation of apoflavodoxin shows that the location of the stable nucleus differs among proteins with a flavodoxin-like topology
    • Steensma E, van Mierlo CP, (1998) Structural characterisation of apoflavodoxin shows that the location of the stable nucleus differs among proteins with a flavodoxin-like topology. J Mol Biol 282: 653-666.
    • (1998) J Mol Biol , vol.282 , pp. 653-666
    • Steensma, E.1    van Mierlo, C.P.2
  • 26
    • 0031952923 scopus 로고    scopus 로고
    • Apparent local stability of the secondary structure of Azotobacter vinelandii holoflavodoxin II as probed by hydrogen exchange: implications for redox potential regulation and flavodoxin folding
    • Steensma E, Nijman MJ, Bollen YJ, de Jager PA, van den Berg WA, et al. (1998) Apparent local stability of the secondary structure of Azotobacter vinelandii holoflavodoxin II as probed by hydrogen exchange: implications for redox potential regulation and flavodoxin folding. Protein Sci 7: 306-317.
    • (1998) Protein Sci , vol.7 , pp. 306-317
    • Steensma, E.1    Nijman, M.J.2    Bollen, Y.J.3    de Jager, P.A.4    van den Berg, W.A.5
  • 27
    • 17144415198 scopus 로고    scopus 로고
    • Protein topology affects the appearance of intermediates during the folding of proteins with a flavodoxin-like fold
    • Bollen YJ, van Mierlo CP, (2005) Protein topology affects the appearance of intermediates during the folding of proteins with a flavodoxin-like fold. Biophys Chem 114: 181-189.
    • (2005) Biophys Chem , vol.114 , pp. 181-189
    • Bollen, Y.J.1    van Mierlo, C.P.2
  • 28
    • 50049084050 scopus 로고    scopus 로고
    • Kinetic traps in the folding of beta alpha-repeat proteins: CheY initially misfolds before accessing the native conformation
    • Kathuria SV, Day IJ, Wallace LA, Matthews CR, (2008) Kinetic traps in the folding of beta alpha-repeat proteins: CheY initially misfolds before accessing the native conformation. J Mol Biol 382: 467-484.
    • (2008) J Mol Biol , vol.382 , pp. 467-484
    • Kathuria, S.V.1    Day, I.J.2    Wallace, L.A.3    Matthews, C.R.4
  • 29
    • 33846795794 scopus 로고    scopus 로고
    • Aggregation as the basis for complex behaviour of cutinase in different denaturants
    • Otzen DE, Giehm L, Baptista RP, Kristensen SR, Melo EP, et al. (2007) Aggregation as the basis for complex behaviour of cutinase in different denaturants. Biochim Biophys Acta 1774: 323-333.
    • (2007) Biochim Biophys Acta , vol.1774 , pp. 323-333
    • Otzen, D.E.1    Giehm, L.2    Baptista, R.P.3    Kristensen, S.R.4    Melo, E.P.5
  • 30
    • 47049127092 scopus 로고    scopus 로고
    • The influence of proline isomerization and off-pathway intermediates on the folding mechanism of eukaryotic UMP/CMP Kinase
    • Lorenz T, Reinstein J, (2008) The influence of proline isomerization and off-pathway intermediates on the folding mechanism of eukaryotic UMP/CMP Kinase. J Mol Biol 381: 443-455.
    • (2008) J Mol Biol , vol.381 , pp. 443-455
    • Lorenz, T.1    Reinstein, J.2
  • 31
    • 0031792027 scopus 로고    scopus 로고
    • The equilibrium unfolding of Azotobacter vinelandii apoflavodoxin II occurs via a relatively stable folding intermediate
    • van Mierlo CP, van Dongen WM, Vergeldt F, van Berkel WJ, Steensma E, (1998) The equilibrium unfolding of Azotobacter vinelandii apoflavodoxin II occurs via a relatively stable folding intermediate. Protein Sci 7: 2331-2344.
    • (1998) Protein Sci , vol.7 , pp. 2331-2344
    • van Mierlo, C.P.1    van Dongen, W.M.2    Vergeldt, F.3    van Berkel, W.J.4    Steensma, E.5
  • 32
    • 0033980811 scopus 로고    scopus 로고
    • Apoflavodoxin (un)folding followed at the residue level by NMR
    • van Mierlo CP, van den Oever JM, Steensma E, (2000) Apoflavodoxin (un)folding followed at the residue level by NMR. Protein Sci 9: 145-157.
    • (2000) Protein Sci , vol.9 , pp. 145-157
    • van Mierlo, C.P.1    van den Oever, J.M.2    Steensma, E.3
  • 33
    • 55549084888 scopus 로고    scopus 로고
    • Macromolecular crowding compacts unfolded apoflavodoxin and causes severe aggregation of the off-pathway intermediate during apoflavodoxin folding
    • Engel R, Westphal AH, Huberts DH, Nabuurs SM, Lindhoud S, et al. (2008) Macromolecular crowding compacts unfolded apoflavodoxin and causes severe aggregation of the off-pathway intermediate during apoflavodoxin folding. J Biol Chem 283: 27383-27394.
    • (2008) J Biol Chem , vol.283 , pp. 27383-27394
    • Engel, R.1    Westphal, A.H.2    Huberts, D.H.3    Nabuurs, S.M.4    Lindhoud, S.5
  • 34
    • 58049200780 scopus 로고    scopus 로고
    • Extensive formation of off-pathway species during folding of an alpha-beta parallel protein is due to docking of (non)native structure elements in unfolded molecules
    • Nabuurs SM, Westphal AH, van Mierlo CP, (2008) Extensive formation of off-pathway species during folding of an alpha-beta parallel protein is due to docking of (non)native structure elements in unfolded molecules. J Am Chem Soc 130: 16914-16920.
    • (2008) J Am Chem Soc , vol.130 , pp. 16914-16920
    • Nabuurs, S.M.1    Westphal, A.H.2    van Mierlo, C.P.3
  • 35
    • 67749133718 scopus 로고    scopus 로고
    • Non-cooperative formation of the off-pathway molten globule during folding of the α-β parallel protein apoflavodoxin
    • Nabuurs SM, Westphal AH, van Mierlo CP, (2009) Non-cooperative formation of the off-pathway molten globule during folding of the α-β parallel protein apoflavodoxin. J Am Chem Soc 131: 2739-2746.
    • (2009) J Am Chem Soc , vol.131 , pp. 2739-2746
    • Nabuurs, S.M.1    Westphal, A.H.2    van Mierlo, C.P.3
  • 36
    • 77950490437 scopus 로고    scopus 로고
    • Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of α-β parallel protein flavodoxin
    • Nabuurs SM, van Mierlo CP, (2010) Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of α-β parallel protein flavodoxin. J Biol Chem 285: 4165-4172.
    • (2010) J Biol Chem , vol.285 , pp. 4165-4172
    • Nabuurs, S.M.1    van Mierlo, C.P.2
  • 37
    • 77952099348 scopus 로고    scopus 로고
    • Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement
    • Nabuurs SM, de Kort BJ, Westphal AH, van Mierlo CP, (2009) Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement. Eur Biophys J 39: 689-698.
    • (2009) Eur Biophys J , vol.39 , pp. 689-698
    • Nabuurs, S.M.1    de Kort, B.J.2    Westphal, A.H.3    van Mierlo, C.P.4
  • 38
    • 67650546929 scopus 로고    scopus 로고
    • Topological switching between an α-β parallel protein and a remarkably helical molten globule
    • Nabuurs SM, Westphal AH, Aan den Toorn M, Lindhoud S, van Mierlo CP, (2009) Topological switching between an α-β parallel protein and a remarkably helical molten globule. J Am Chem Soc 131: 8290-8295.
    • (2009) J Am Chem Soc , vol.131 , pp. 8290-8295
    • Nabuurs, S.M.1    Westphal, A.H.2    Aan den Toorn, M.3    Lindhoud, S.4    van Mierlo, C.P.5
  • 39
    • 0036737063 scopus 로고    scopus 로고
    • A general strategy for site-specific double labeling of globular proteins for kinetic FRET studies
    • Ratner V, Kahana E, Eichler M, Haas E, (2002) A general strategy for site-specific double labeling of globular proteins for kinetic FRET studies. Bioconjugate chemistry 13: 1163-1170.
    • (2002) Bioconjugate Chemistry , vol.13 , pp. 1163-1170
    • Ratner, V.1    Kahana, E.2    Eichler, M.3    Haas, E.4
  • 42
    • 51649117375 scopus 로고    scopus 로고
    • Tryptophan-tryptophan energy migration as a tool to follow apoflavodoxin folding
    • Visser NV, Westphal AH, van Hoek A, van Mierlo CP, Visser AJ, et al. (2008) Tryptophan-tryptophan energy migration as a tool to follow apoflavodoxin folding. Biophys J 95: 2462-2469.
    • (2008) Biophys J , vol.95 , pp. 2462-2469
    • Visser, N.V.1    Westphal, A.H.2    van Hoek, A.3    van Mierlo, C.P.4    Visser, A.J.5
  • 43
    • 0027958069 scopus 로고
    • The use of fluorescence methods to monitor unfolding transitions in proteins
    • Eftink MR, (1994) The use of fluorescence methods to monitor unfolding transitions in proteins. Biophys J 66: 482-501.
    • (1994) Biophys J , vol.66 , pp. 482-501
    • Eftink, M.R.1
  • 44
    • 40049106475 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer analysis of the folding pathway of Engrailed Homeodomain
    • Huang F, Settanni G, Fersht AR, (2008) Fluorescence resonance energy transfer analysis of the folding pathway of Engrailed Homeodomain. Protein engineering, design & selection: PEDS 21: 131-146.
    • (2008) Protein Engineering, Design & Selection: PEDS , vol.21 , pp. 131-146
    • Huang, F.1    Settanni, G.2    Fersht, A.R.3
  • 45
    • 79955448604 scopus 로고    scopus 로고
    • A general approach for detecting folding intermediates from steady-state and time-resolved fluorescence of single-tryptophan-containing proteins
    • Laptenok SP, Visser NV, Engel R, Westphal AH, van Hoek A, et al. (2011) A general approach for detecting folding intermediates from steady-state and time-resolved fluorescence of single-tryptophan-containing proteins. Biochemistry 50: 3441-3450.
    • (2011) Biochemistry , vol.50 , pp. 3441-3450
    • Laptenok, S.P.1    Visser, N.V.2    Engel, R.3    Westphal, A.H.4    van Hoek, A.5
  • 46
    • 78049441725 scopus 로고    scopus 로고
    • Distance mapping in proteins using fluorescence spectroscopy: the tryptophan-induced quenching (TrIQ) method
    • Mansoor SE, Dewitt MA, Farrens DL, (2010) Distance mapping in proteins using fluorescence spectroscopy: the tryptophan-induced quenching (TrIQ) method. Biochemistry 49: 9722-9731.
    • (2010) Biochemistry , vol.49 , pp. 9722-9731
    • Mansoor, S.E.1    Dewitt, M.A.2    Farrens, D.L.3
  • 48
    • 0037162160 scopus 로고    scopus 로고
    • Refractive index dependence of the Förster resonance excitation transfer rate
    • Knox RS, van Amerongen H, (2002) Refractive index dependence of the Förster resonance excitation transfer rate. Journal of Physical Chemistry B 106: 5289-5293.
    • (2002) Journal of Physical Chemistry B , vol.106 , pp. 5289-5293
    • Knox, R.S.1    van Amerongen, H.2
  • 49
    • 0037061949 scopus 로고    scopus 로고
    • Effect of the solvent refractive index on the excited-state lifetime of a single tryptophan residue in a protein
    • Toptygin D, Savtchenko RS, Meadow ND, Roseman S, Brand L, (2002) Effect of the solvent refractive index on the excited-state lifetime of a single tryptophan residue in a protein. Journal of Physical Chemistry B 106: 3724-3734.
    • (2002) Journal of Physical Chemistry B , vol.106 , pp. 3724-3734
    • Toptygin, D.1    Savtchenko, R.S.2    Meadow, N.D.3    Roseman, S.4    Brand, L.5
  • 50
    • 2542516405 scopus 로고    scopus 로고
    • The density and refractive index of adsorbing protein layers
    • Vörös J, (2004) The density and refractive index of adsorbing protein layers. Biophysical journal 87: 553-561.
    • (2004) Biophysical Journal , vol.87 , pp. 553-561
    • Vörös, J.1
  • 51
    • 0001545374 scopus 로고
    • Theory of Fluorescence Depolarization in Macromolecules and Membranes
    • Szabo A, (1984) Theory of Fluorescence Depolarization in Macromolecules and Membranes. Journal of Chemical Physics 81: 150-167.
    • (1984) Journal of Chemical Physics , vol.81 , pp. 150-167
    • Szabo, A.1
  • 52
    • 0038167027 scopus 로고    scopus 로고
    • Site-directed mutagenesis using a single mutagenic oligonucleotide and DpnI digestion of template DNA
    • Shenoy AR, Visweswariah SS, (2003) Site-directed mutagenesis using a single mutagenic oligonucleotide and DpnI digestion of template DNA. Analytical Biochemistry 319: 735-336.
    • (2003) Analytical Biochemistry , vol.319 , pp. 336-735
    • Shenoy, A.R.1    Visweswariah, S.S.2
  • 54
    • 18644377743 scopus 로고    scopus 로고
    • Effects of refractive index and viscosity on fluorescence and anisotropy decays of enhanced cyan and yellow fluorescent proteins
    • Borst JW, Hink MA, van Hoek A, Visser AJ, (2005) Effects of refractive index and viscosity on fluorescence and anisotropy decays of enhanced cyan and yellow fluorescent proteins. Journal of fluorescence 15: 153-160.
    • (2005) Journal of Fluorescence , vol.15 , pp. 153-160
    • Borst, J.W.1    Hink, M.A.2    van Hoek, A.3    Visser, A.J.4
  • 55
    • 16644402505 scopus 로고    scopus 로고
    • Evidence for a novel mechanism of time-resolved flavin fluorescence depolarization in glutathione reductase
    • van den Berg PA, van Hoek A, Visser AJ, (2004) Evidence for a novel mechanism of time-resolved flavin fluorescence depolarization in glutathione reductase. Biophysical journal 87: 2577-2586.
    • (2004) Biophysical Journal , vol.87 , pp. 2577-2586
    • van den Berg, P.A.1    van Hoek, A.2    Visser, A.J.3
  • 56
    • 24344449928 scopus 로고    scopus 로고
    • A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential
    • Alagaratnam S, van Pouderoyen G, Pijning T, Dijkstra BW, Cavazzini D, et al. (2005) A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential. Protein Sci 14: 2284-2295.
    • (2005) Protein Sci , vol.14 , pp. 2284-2295
    • Alagaratnam, S.1    van Pouderoyen, G.2    Pijning, T.3    Dijkstra, B.W.4    Cavazzini, D.5


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