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Volumn 337, Issue 3, 2004, Pages 699-711

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate Ensemble

Author keywords

Barstar; Conformational heterogeneity; FRET, fluorescence resonance energy transfer; MEM, maximum entropy method; Multi site FRET; N, native; Protein folding; Time resolved fluorescence; TNB, thionitrobenzoate; TRFRET, time resolved FRET; U, unfolded

Indexed keywords

BARSTAR;

EID: 1542358783     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.083     Document Type: Article
Times cited : (51)

References (54)
  • 1
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4:1997;10-19.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 3
    • 0037172946 scopus 로고    scopus 로고
    • Using deeply trapped intermediates to map the cytochrome c folding landscape
    • Tezcan F.A., et al. Using deeply trapped intermediates to map the cytochrome c folding landscape. Proc. Natl Acad. Sci. USA. 99:2002;8626-8630.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 8626-8630
    • Tezcan, F.A.1
  • 4
    • 0037069387 scopus 로고    scopus 로고
    • Structural features of cytochrome c′ folding intermediates revealed by fluorescence energy-transfer kinetics
    • Lee J.C., Engman K.C., Tezcan F.A., Gray H.B., Winkler J.R. Structural features of cytochrome c′ folding intermediates revealed by fluorescence energy-transfer kinetics. Proc. Natl Acad. Sci. USA. 99:2002;14778-14782.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 14778-14782
    • Lee, J.C.1    Engman, K.C.2    Tezcan, F.A.3    Gray, H.B.4    Winkler, J.R.5
  • 5
    • 0037162450 scopus 로고    scopus 로고
    • Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing
    • Teilum K., Maki K., Kragelund B.B., Poulsen F.M., Roder H. 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    Poulsen, F.M.4    Roder, H.5
  • 6
    • 0037452559 scopus 로고    scopus 로고
    • Surface expansion is independent of and occurs faster than core solvation during the unfolding of barstar
    • Sridevi K., Udgaonkar J.B. Surface expansion is independent of and occurs faster than core solvation during the unfolding of barstar. Biochemistry. 42:2003;1551-1563.
    • (2003) Biochemistry , vol.42 , pp. 1551-1563
    • Sridevi, K.1    Udgaonkar, J.B.2
  • 8
    • 0028295796 scopus 로고
    • Resonance energy transfer: Methods and applications
    • Wu P., Brand L. Resonance energy transfer: methods and applications. Anal. Biochem. 218:1994;1-13.
    • (1994) Anal. Biochem. , vol.218 , pp. 1-13
    • Wu, P.1    Brand, L.2
  • 9
    • 0030964626 scopus 로고
    • Design and characterization of a multisite fluorescence energy-transfer system for protein folding studies: A steady-state and time-resolved study of yeast phosphoglycerate kinase
    • Lillo M.P., Beechem J.M., Szpikowska B.K., Sherman M.A., Mas M.T. Design and characterization of a multisite fluorescence energy-transfer system for protein folding studies: a steady-state and time-resolved study of yeast phosphoglycerate kinase. Biochemistry. 36:1994;11261-11272.
    • (1994) Biochemistry , vol.36 , pp. 11261-11272
    • Lillo, M.P.1    Beechem, J.M.2    Szpikowska, B.K.3    Sherman, M.A.4    Mas, M.T.5
  • 10
    • 0023316741 scopus 로고
    • Fluorescence resonance energy transfer measurements of distances in actin and myosin. A critical evaluation
    • dos Remedios C.G., Miki M., Barden J.A. Fluorescence resonance energy transfer measurements of distances in actin and myosin. A critical evaluation. J. Muscle Res. Cell. Motil. 8:1987;97-117.
    • (1987) J. Muscle Res. Cell. Motil. , vol.8 , pp. 97-117
    • Dos Remedios, C.G.1    Miki, M.2    Barden, J.A.3
  • 11
    • 0035830438 scopus 로고    scopus 로고
    • Distributions of intra-molecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein
    • Navon A., Ittah V., Landsman P., Scheraga H.A., Haas E. Distributions of intra-molecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry. 40:2001;105-118.
    • (2001) Biochemistry , vol.40 , pp. 105-118
    • Navon, A.1    Ittah, V.2    Landsman, P.3    Scheraga, H.A.4    Haas, E.5
  • 13
    • 0036349865 scopus 로고    scopus 로고
    • Fast compaction of alpha-lactalbumin during folding studied by stopped-flow X-ray scattering
    • Arai M., Ito K., Inobe T., Nakao M., Maki K., Kamagata K., et al. Fast compaction of alpha-lactalbumin during folding studied by stopped-flow X-ray scattering. J. Mol. Biol. 321:2002;121-132.
    • (2002) J. Mol. Biol. , vol.321 , pp. 121-132
    • Arai, M.1    Ito, K.2    Inobe, T.3    Nakao, M.4    Maki, K.5    Kamagata, K.6
  • 15
    • 0031777173 scopus 로고    scopus 로고
    • Initial hydrophobic collapse is not necessary for folding RNase a
    • Noppert A., Gast K., Zirwer D., Damaschun G. Initial hydrophobic collapse is not necessary for folding RNase A. Fold. Des. 3:1998;213-221.
    • (1998) Fold. Des. , vol.3 , pp. 213-221
    • Noppert, A.1    Gast, K.2    Zirwer, D.3    Damaschun, G.4
  • 16
    • 0031707395 scopus 로고    scopus 로고
    • Compactness of the kinetic molten globule of bovine alpha-lactalbumin: A dynamic light scattering study
    • Gast K., Zirwer D., Muller-Frohne M., Damaschun G. Compactness of the kinetic molten globule of bovine alpha-lactalbumin: a dynamic light scattering study. Protein Sci. 7:1998;2004-2011.
    • (1998) Protein Sci. , vol.7 , pp. 2004-2011
    • Gast, K.1    Zirwer, D.2    Muller-Frohne, M.3    Damaschun, G.4
  • 17
    • 0028925815 scopus 로고
    • Local and global dynamics during the folding of Escherichia coli dihydrofolate reductase by time-resolved fluorescence spectroscopy
    • Jones B.E., Beechem J.M., Matthews C.R. Local and global dynamics during the folding of Escherichia coli dihydrofolate reductase by time-resolved fluorescence spectroscopy. Biochemistry. 34:1995;1867-1877.
    • (1995) Biochemistry , vol.34 , pp. 1867-1877
    • Jones, B.E.1    Beechem, J.M.2    Matthews, C.R.3
  • 18
    • 0035067076 scopus 로고    scopus 로고
    • High-sensitivity fluorescence anisotropy detection of protein-folding events: Application to alpha-lactalbumin
    • Canet D., Doering K., Dobson C.M., Dupont Y. High-sensitivity fluorescence anisotropy detection of protein-folding events: application to alpha-lactalbumin. Biophys. J. 80:2001;1996-2003.
    • (2001) Biophys. J. , vol.80 , pp. 1996-2003
    • Canet, D.1    Doering, K.2    Dobson, C.M.3    Dupont, Y.4
  • 19
    • 0033616632 scopus 로고    scopus 로고
    • Time-resolved fluorescence anisotropy study of the refolding reaction of the alpha-subunit of tryptophan synthase reveals nonmonotonic behavior of the rotational correlation time
    • Bilsel O., Yang L., Zitzewitz J.A., Beechem J.M., Matthews C.R. Time-resolved fluorescence anisotropy study of the refolding reaction of the alpha-subunit of tryptophan synthase reveals nonmonotonic behavior of the rotational correlation time. Biochemistry. 38:1999;4177-4187.
    • (1999) Biochemistry , vol.38 , pp. 4177-4187
    • Bilsel, O.1    Yang, L.2    Zitzewitz, J.A.3    Beechem, J.M.4    Matthews, C.R.5
  • 20
    • 0034665642 scopus 로고    scopus 로고
    • The slow folding reaction of barstar: The core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain
    • Sridevi K., Juneja J., Bhuyan A.K., Krishnamoorthy G., Udgaonkar J.B. The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain. J. Mol. Biol. 302:2000;479-495.
    • (2000) J. Mol. Biol. , vol.302 , pp. 479-495
    • Sridevi, K.1    Juneja, J.2    Bhuyan, A.K.3    Krishnamoorthy, G.4    Udgaonkar, J.B.5
  • 21
    • 0028672799 scopus 로고
    • Maximum entropy method of data analysis in time-resolved spectroscopy
    • Brochon J.C. Maximum entropy method of data analysis in time-resolved spectroscopy. Methods Enzymol. 240:1994;262-311.
    • (1994) Methods Enzymol. , vol.240 , pp. 262-311
    • Brochon, J.C.1
  • 22
    • 0027985340 scopus 로고
    • Similarity of fluorescence lifetime distributions for single tryptophan proteins in the random coil state
    • Swaminathan R., Krishnamoorthy G., Periasamy N. Similarity of fluorescence lifetime distributions for single tryptophan proteins in the random coil state. Biophys. J. 67:1994;2013-2023.
    • (1994) Biophys. J. , vol.67 , pp. 2013-2023
    • Swaminathan, R.1    Krishnamoorthy, G.2    Periasamy, N.3
  • 24
    • 0034625167 scopus 로고    scopus 로고
    • Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2
    • Deniz A.A., Laurence T.A., Beligere G.S., Dahan M., Martin A.B., Chemla D.S., et al. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc. Natl Acad. Sci. USA. 97:2000;5179-5184.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 5179-5184
    • Deniz, A.A.1    Laurence, T.A.2    Beligere, G.S.3    Dahan, M.4    Martin, A.B.5    Chemla, D.S.6
  • 25
    • 0037126290 scopus 로고    scopus 로고
    • Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
    • Schuler B., Lipman E.A., Eaton W.A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:2002;743-747.
    • (2002) Nature , vol.419 , pp. 743-747
    • Schuler, B.1    Lipman, E.A.2    Eaton, W.A.3
  • 27
    • 0027385015 scopus 로고
    • The refolding of cis- and trans-peptidylprolyl isomers of barstar
    • Schreiber G., Fersht A.R. The refolding of cis- and trans-peptidylprolyl isomers of barstar. Biochemistry. 32:1993;11195-11203.
    • (1993) Biochemistry , vol.32 , pp. 11195-11203
    • Schreiber, G.1    Fersht, A.R.2
  • 28
    • 0028901085 scopus 로고
    • The folding mechanism of barstar: Evidence for multiple pathways and multiple intermediates
    • Shastry M.C., Udgaonkar J.B. The folding mechanism of barstar: evidence for multiple pathways and multiple intermediates. J. Mol. Biol. 247:1995;1013-1027.
    • (1995) J. Mol. Biol. , vol.247 , pp. 1013-1027
    • Shastry, M.C.1    Udgaonkar, J.B.2
  • 29
    • 0028072360 scopus 로고
    • Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone
    • Shastry M.C., Agashe V.R., Udgaonkar J.B. Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone. Protein Sci. 3:1994;1409-1417.
    • (1994) Protein Sci. , vol.3 , pp. 1409-1417
    • Shastry, M.C.1    Agashe, V.R.2    Udgaonkar, J.B.3
  • 30
    • 0028802181 scopus 로고
    • Initial hydrophobic collapse in the folding of barstar
    • Agashe V.R., Shastry M.C., Udgaonkar J.B. Initial hydrophobic collapse in the folding of barstar. Nature. 377:1995;754-757.
    • (1995) Nature , vol.377 , pp. 754-757
    • Agashe, V.R.1    Shastry, M.C.2    Udgaonkar, J.B.3
  • 31
    • 0033551522 scopus 로고    scopus 로고
    • Observation of multistate kinetics during the slow folding and unfolding of barstar
    • Bhuyan A.K., Udgaonkar J.B. Observation of multistate kinetics during the slow folding and unfolding of barstar. Biochemistry. 38:1999;9158-9168.
    • (1999) Biochemistry , vol.38 , pp. 9158-9168
    • Bhuyan, A.K.1    Udgaonkar, J.B.2
  • 33
    • 0028947236 scopus 로고
    • Thermodynamics of denaturation of barstar: Evidence for cold denaturation and evaluation of the interaction with guanidine hydrochloride
    • Agashe V.R., Udgaonkar J.B. Thermodynamics of denaturation of barstar: evidence for cold denaturation and evaluation of the interaction with guanidine hydrochloride. Biochemistry. 34:1995;3286-3299.
    • (1995) Biochemistry , vol.34 , pp. 3286-3299
    • Agashe, V.R.1    Udgaonkar, J.B.2
  • 34
    • 0025603661 scopus 로고
    • Conformational studies of a constrained tryptophan derivative: Implications for the fluorescence quenching mechanism
    • Colucci W.J., Tilstra L., Sattler M.C., Fronczek F.R., Barkley M.D. Conformational studies of a constrained tryptophan derivative: implications for the fluorescence quenching mechanism. J. Am. Chem. Soc. 112:1990;9182-9190.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 9182-9190
    • Colucci, W.J.1    Tilstra, L.2    Sattler, M.C.3    Fronczek, F.R.4    Barkley, M.D.5
  • 35
    • 0027966019 scopus 로고
    • Three-dimensional solution structure and 13C assignments of barstar using nuclear magnetic resonance spectroscopy
    • Lubienski M.J., Bycroft M., Freund S.M., Fersht A.R. Three-dimensional solution structure and 13C assignments of barstar using nuclear magnetic resonance spectroscopy. Biochemistry. 33:1994;8866-8877.
    • (1994) Biochemistry , vol.33 , pp. 8866-8877
    • Lubienski, M.J.1    Bycroft, M.2    Freund, S.M.3    Fersht, A.R.4
  • 37
    • 0032519738 scopus 로고    scopus 로고
    • Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange
    • Bhuyan A.K., Udgaonkar J.B. Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange. Proteins: Struct. Funct. Genet. 30:1998;295-308.
    • (1998) Proteins: Struct. Funct. Genet. , vol.30 , pp. 295-308
    • Bhuyan, A.K.1    Udgaonkar, J.B.2
  • 39
    • 0009586942 scopus 로고    scopus 로고
    • Understanding protein folding via free-energy surfaces from theory and experiment
    • Dinner A.R., Sali A., Smith L.J., Dobson C.M., Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25:2000;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
  • 40
    • 0031919973 scopus 로고    scopus 로고
    • Evidence for barrier-limited protein folding kinetics on the microsecond time scale
    • Shastry M.C., Roder H. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nature Struct. Biol. 5:1998;385-392.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 385-392
    • Shastry, M.C.1    Roder, H.2
  • 41
    • 0036438892 scopus 로고    scopus 로고
    • Differential salt-induced stabilization of structure in the initial folding intermediate ensemble of barstar
    • Pradeep L., Udgaonkar J.B. Differential salt-induced stabilization of structure in the initial folding intermediate ensemble of barstar. J. Mol. Biol. 324:2002;331-347.
    • (2002) J. Mol. Biol. , vol.324 , pp. 331-347
    • Pradeep, L.1    Udgaonkar, J.B.2
  • 43
    • 0031697733 scopus 로고    scopus 로고
    • The burst phase in ribonuclease a folding and solvent dependence of the unfolded state
    • Qi P.X., Sosnick T.R., Englander S.W. The burst phase in ribonuclease A folding and solvent dependence of the unfolded state. Nature Struct. Biol. 5:1998;882-884.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 882-884
    • Qi, P.X.1    Sosnick, T.R.2    Englander, S.W.3
  • 44
    • 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., Sosnick T.R. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. 324:2002;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
  • 45
    • 0037065672 scopus 로고    scopus 로고
    • Mechanism of formation of a productive molten globule form of barstar
    • Rami B.R., Udgaonkar J.B. Mechanism of formation of a productive molten globule form of barstar. Biochemistry. 41:2002;1710-1716.
    • (2002) Biochemistry , vol.41 , pp. 1710-1716
    • Rami, B.R.1    Udgaonkar, J.B.2
  • 46
    • 0344301982 scopus 로고    scopus 로고
    • Protein folding: A perspective from theory and experiment
    • Dobson C.M., Sali A., Karplus M. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. 37:1998;868-893.
    • (1998) Angew. Chem. Int. Ed. , vol.37 , pp. 868-893
    • Dobson, C.M.1    Sali, A.2    Karplus, M.3
  • 47
    • 0029738416 scopus 로고    scopus 로고
    • Circular dichroism evidence for the presence of burst-phase intermediates on the conformational folding pathway of ribonuclease a
    • Houry W.A., Rothwarf D.M., Scheraga H.A. Circular dichroism evidence for the presence of burst-phase intermediates on the conformational folding pathway of ribonuclease A. Biochemistry. 35:1996;10125-10133.
    • (1996) Biochemistry , vol.35 , pp. 10125-10133
    • Houry, W.A.1    Rothwarf, D.M.2    Scheraga, H.A.3
  • 48
    • 0029811091 scopus 로고    scopus 로고
    • Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease a probed by hydrogen-deuterium exchange
    • Houry W.A., Scheraga H.A. Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease A probed by hydrogen-deuterium exchange. Biochemistry. 35:1996;11734-11746.
    • (1996) Biochemistry , vol.35 , pp. 11734-11746
    • Houry, W.A.1    Scheraga, H.A.2
  • 49
    • 0032499639 scopus 로고    scopus 로고
    • Characterization of collapsed states in the early stages of the refolding of hen lysozyme
    • Morgan C.J., Miranker A., Dobson C.M. Characterization of collapsed states in the early stages of the refolding of hen lysozyme. Biochemistry. 37:1998;8473-8480.
    • (1998) Biochemistry , vol.37 , pp. 8473-8480
    • Morgan, C.J.1    Miranker, A.2    Dobson, C.M.3
  • 50
    • 0036382667 scopus 로고    scopus 로고
    • The apomyoglobin folding pathway revisited: Structural heterogeneity in the kinetic burst phase intermediate
    • Nishimura C., Dyson H.J., Wright P.E. The apomyoglobin folding pathway revisited: structural heterogeneity in the kinetic burst phase intermediate. J. Mol. Biol. 322:2002;483-489.
    • (2002) J. Mol. Biol. , vol.322 , pp. 483-489
    • Nishimura, C.1    Dyson, H.J.2    Wright, P.E.3
  • 51
    • 0032516445 scopus 로고    scopus 로고
    • Proline isomerization-independent accumulation of an early intermediate and heterogeneity of the folding pathways of a mixed alpha/beta protein, Escherichia coli thioredoxin
    • Georgescu R.E., Li J.H., Goldberg M.E., Tasayco M.L., Chaffotte A.F. Proline isomerization-independent accumulation of an early intermediate and heterogeneity of the folding pathways of a mixed alpha/beta protein, Escherichia coli thioredoxin. Biochemistry. 37:1998;10286-10297.
    • (1998) Biochemistry , vol.37 , pp. 10286-10297
    • Georgescu, R.E.1    Li, J.H.2    Goldberg, M.E.3    Tasayco, M.L.4    Chaffotte, A.F.5
  • 52
    • 0032586678 scopus 로고    scopus 로고
    • Solvent-exposed tryptophans probe the dynamics at protein surfaces
    • Lakshmikanth G.S., Krishnamoorthy G. Solvent-exposed tryptophans probe the dynamics at protein surfaces. Biophys. J. 77:1999;1100-1106.
    • (1999) Biophys. J. , vol.77 , pp. 1100-1106
    • Lakshmikanth, G.S.1    Krishnamoorthy, G.2
  • 53
    • 0000431384 scopus 로고
    • Maximum entropy image reconstruction: General algorithm
    • Skilling J., Bryan R.K. Maximum entropy image reconstruction: general algorithm. Mon. Not. R. Astr. Soc. 211:1984;111-124.
    • (1984) Mon. Not. R. Astr. Soc. , vol.211 , pp. 111-124
    • Skilling, J.1    Bryan, R.K.2
  • 54
    • 0030087307 scopus 로고    scopus 로고
    • Analysis of fluorescence decay by the maximum entropy method: Influence of noise and analysis parameters on the width of the distribution of lifetimes
    • Swaminathan R., Periasamy N. Analysis of fluorescence decay by the maximum entropy method: Influence of noise and analysis parameters on the width of the distribution of lifetimes. Proc. Indian Acad. Sci. Chem. Sci. 108:1996;39-49.
    • (1996) Proc. Indian Acad. Sci. Chem. Sci. , vol.108 , pp. 39-49
    • Swaminathan, R.1    Periasamy, N.2


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