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Volumn 50, Issue 6, 2011, Pages 1029-1041

Manifestations of native topology in the denatured state ensemble of rhodopseudomonas palustris cytochrome c′

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; MOLECULAR DYNAMICS; PORPHYRINS; TOPOLOGY;

EID: 79851496655     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101551h     Document Type: Article
Times cited : (17)

References (85)
  • 1
    • 67349223613 scopus 로고    scopus 로고
    • Non-native electrostatic interactions in the denatured state ensemble: Effects on protein stability and folding
    • Creamer, T. P. Nova Science Publishers, Hauppauge, NY
    • Cho, J.-H., Saito, S., and Raleigh, D. P. (2008) Non-native electrostatic interactions in the denatured state ensemble: effects on protein stability and folding, in Unfolded Proteins: From Denatured to Intrinsically Disordered (Creamer, T. P., Ed.) pp 51 - 69, Nova Science Publishers, Hauppauge, NY.
    • (2008) Unfolded Proteins: From Denatured to Intrinsically Disordered , pp. 51-69
    • Cho, J.-H.1    Saito, S.2    Raleigh, D.P.3
  • 2
    • 64349099192 scopus 로고    scopus 로고
    • Thermodynamic approaches to understanding protein denatured states
    • (Creamer, T. P., Ed.) Nova Science Publishers, Hauppage, NY.
    • Bowler, B. E. (2008) Thermodynamic approaches to understanding protein denatured states, in Unfolded Proteins: From Denatured to Intrinsically Disordered (Creamer, T. P., Ed.) pp 23 - 50, Nova Science Publishers, Hauppage, NY.
    • (2008) Unfolded Proteins: From Denatured to Intrinsically Disordered , pp. 23-50
    • Bowler, B.E.1
  • 3
    • 23744502246 scopus 로고    scopus 로고
    • Is there or isn’t there? the case for (and against) residual structure in chemically denatured proteins
    • McCarney, E. R., Kohn, J. E., and Plaxco, K. W. (2005) Is there or isn’t there? The case for (and against) residual structure in chemically denatured proteins Crit. Rev. Biochem. Mol. Biol. 40, 181-189
    • (2005) Crit. Rev. Biochem. Mol. Biol. , vol.40 , pp. 181
    • McCarney, E.R.1    Kohn, J.E.2    Plaxco, K.W.3
  • 4
    • 33846498387 scopus 로고    scopus 로고
    • Thermodynamics of protein denatured states
    • DOI 10.1039/b611895j
    • Bowler, B. E. (2007) Thermodynamics of protein denatured states Mol. BioSyst. 3, 88-99 (Pubitemid 46155471)
    • (2007) Molecular BioSystems , vol.3 , Issue.2 , pp. 88-99
    • Bowler, B.E.1
  • 5
    • 84888644486 scopus 로고    scopus 로고
    • Conformational properties of unfolded proteins
    • (Buchner, J. and Kiefhaber, T., Eds.), Wiley-VCH, Weinheim, Germany.
    • Fleming, P. J. and Rose, G. D. (2005) Conformational properties of unfolded proteins, in Protein Folding Handbook, Part I (Buchner, J. and Kiefhaber, T., Eds.) pp 710 - 736, Wiley-VCH, Weinheim, Germany.
    • (2005) Protein Folding Handbook, Part i , pp. 710-736
    • Fleming, P.J.1    Rose, G.D.2
  • 7
    • 0029961647 scopus 로고    scopus 로고
    • Structural analysis of non-native states of proteins by NMR methods
    • DOI 10.1016/S0959-440X(96)80091-1
    • Shortle, D. (1996) Structural analysis of non-native states of proteins by NMR methods Curr. Opin. Struct. Biol. 6, 24-30 (Pubitemid 26073941)
    • (1996) Current Opinion in Structural Biology , vol.6 , Issue.1 , pp. 24-30
    • Shortle, D.R.1
  • 8
    • 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., and Winkler, J. R. (2002) Structural features of cytochrome c †folding intermediates revealed by fluorescence energy-transfer kinetics Proc. Natl. Acad. Sci. U.S.A. 99, 14778-14782
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 14778
    • Lee, J.C.1    Engman, K.C.2    Tezcan, F.A.3    Gray, H.B.4    Winkler, J.R.5
  • 9
    • 33846041173 scopus 로고    scopus 로고
    • Site-specific collapse dynamics guide the formation of the cytochrome c †four-helix bundle
    • Kimura, T., Lee, J. C., Gray, H. B., and Winkler, J. R. (2007) Site-specific collapse dynamics guide the formation of the cytochrome c †four-helix bundle Proc. Natl. Acad. Sci. U.S.A. 104, 117-122
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 117
    • Kimura, T.1    Lee, J.C.2    Gray, H.B.3    Winkler, J.R.4
  • 10
    • 51549105097 scopus 로고    scopus 로고
    • The low-pH unfolded state of the C-terminal domain of the ribosomal protein L9 contains significant secondary structure in the absence of denaturant but is no more compact than the low-pH urea unfolded state
    • Shan, B., Bhattacharya, S., Eliezer, D., and Raleigh, D. P. (2008) The low-pH unfolded state of the C-terminal domain of the ribosomal protein L9 contains significant secondary structure in the absence of denaturant but is no more compact than the low-pH urea unfolded state Biochemistry 47, 9565-9573
    • (2008) Biochemistry , vol.47 , pp. 9565
    • Shan, B.1    Bhattacharya, S.2    Eliezer, D.3    Raleigh, D.P.4
  • 11
    • 33846913510 scopus 로고    scopus 로고
    • Atomic-level characterization of disordered protein ensembles
    • Mittag, T. and Forman-Kay, J. D. (2007) Atomic-level characterization of disordered protein ensembles Curr. Opin. Struct. Biol. 17, 3-14
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 3
    • Mittag, T.1    Forman-Kay, J.D.2
  • 12
    • 33646171099 scopus 로고    scopus 로고
    • Characterization of intramolecular distances and site-specific dynamics in chemically unfolded barstar: Evidence for denaturant-dependent non-random structure
    • Saxena, A. M., Udgoankar, J. B., and Krishnamoorthy, G. (2006) Characterization of intramolecular distances and site-specific dynamics in chemically unfolded barstar: evidence for denaturant-dependent non-random structure J. Mol. Biol. 359, 174-189
    • (2006) J. Mol. Biol. , vol.359 , pp. 174
    • Saxena, A.M.1    Udgoankar, J.B.2    Krishnamoorthy, G.3
  • 14
    • 67650684936 scopus 로고    scopus 로고
    • Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints
    • Marsh, J. A. and Forman-Kay, J. D. (2009) Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints J. Mol. Biol. 391, 359-374
    • (2009) J. Mol. Biol. , vol.391 , pp. 359
    • Marsh, J.A.1    Forman-Kay, J.D.2
  • 15
    • 49449094012 scopus 로고    scopus 로고
    • Zinc porphyrin: A fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer
    • Ensign, A. A., Jo, I., Yildirim, I., Krauss, T. D., and Bren, K. L. (2008) Zinc porphyrin: a fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer Proc. Natl. Acad. Sci. U.S.A. 105, 10779-10784
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 10779
    • Ensign, A.A.1    Jo, I.2    Yildirim, I.3    Krauss, T.D.4    Bren, K.L.5
  • 16
    • 10044269982 scopus 로고    scopus 로고
    • Many faces of the unfolded state: Conformational heterogeneity in denatured yeast cytochrome c
    • Pletneva, E. V., Gray, H. B., and Winkler, J. R. (2005) Many faces of the unfolded state: conformational heterogeneity in denatured yeast cytochrome c J. Mol. Biol. 345, 855-867
    • (2005) J. Mol. Biol. , vol.345 , pp. 855
    • Pletneva, E.V.1    Gray, H.B.2    Winkler, J.R.3
  • 17
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill, K. A. and Chan, H. S. (1997) From Levinthal to pathways to funnels Nat. Struct. Biol. 4, 10-19
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10
    • Dill, K.A.1    Chan, H.S.2
  • 19
    • 0036401140 scopus 로고    scopus 로고
    • Toward a taxonomy of the denatured state: Small angle X-ray scattering studies of unfolded proteins
    • Millett, I. S., Doniach, S., and Plaxco, K. W. (2002) Toward a taxonomy of the denatured state: small angle X-ray scattering studies of unfolded proteins Adv. Protein Chem. 62, 241-262
    • (2002) Adv. Protein Chem. , vol.62 , pp. 241
    • Millett, I.S.1    Doniach, S.2    Plaxco, K.W.3
  • 20
    • 0014364651 scopus 로고
    • Protein denaturation
    • Tanford, C. (1968) Protein denaturation Adv. Protein Chem. 23, 121-282
    • (1968) Adv. Protein Chem. , vol.23 , pp. 121-282
    • Tanford, C.1
  • 21
    • 0034759469 scopus 로고    scopus 로고
    • A semiflexible polymer model applied to loop formation in DNA hairpins
    • Kuznetsov, S. V., Shen, Y., Benight, A. S., and Ansari, A. (2001) A semiflexible polymer model applied to loop formation in DNA hairpins Biophys. J. 81, 2864-2875
    • (2001) Biophys. J. , vol.81 , pp. 2864
    • Kuznetsov, S.V.1    Shen, Y.2    Benight, A.S.3    Ansari, A.4
  • 22
    • 0035979801 scopus 로고    scopus 로고
    • Denatured state thermodynamics: Residual structure, chain stiffness and scaling factors
    • Hammack, B. N., Smith, C. R., and Bowler, B. E. (2001) Denatured state thermodynamics: residual structure, chain stiffness and scaling factors J. Mol. Biol. 311, 1091-1104
    • (2001) J. Mol. Biol. , vol.311 , pp. 1091
    • Hammack, B.N.1    Smith, C.R.2    Bowler, B.E.3
  • 23
    • 2342544028 scopus 로고    scopus 로고
    • Conformational properties of the iso-1-cytochrome c denatured state: Dependence on guanidine hydrochloride concentration
    • Wandschneider, E. and Bowler, B. E. (2004) Conformational properties of the iso-1-cytochrome c denatured state: dependence on guanidine hydrochloride concentration J. Mol. Biol. 339, 185-197
    • (2004) J. Mol. Biol. , vol.339 , pp. 185
    • Wandschneider, E.1    Bowler, B.E.2
  • 25
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson, H. and Stockmayer, W. H. (1950) Intramolecular reaction in polycondensations. I. The theory of linear systems J. Chem. Phys. 18, 1600-1606
    • (1950) J. Chem. Phys. , vol.18 , pp. 1600
    • Jacobson, H.1    Stockmayer, W.H.2
  • 26
    • 0001193711 scopus 로고
    • The effects of internal constraints on the configurations of chain molecules
    • Chan, H. S. and Dill, K. A. (1990) The effects of internal constraints on the configurations of chain molecules J. Chem. Phys. 92, 3118-3135
    • (1990) J. Chem. Phys. , vol.92 , pp. 3118
    • Chan, H.S.1    Dill, K.A.2
  • 28
    • 0000232764 scopus 로고
    • Distribution functions in the interior of polymer chains
    • Redner, S. (1980) Distribution functions in the interior of polymer chains J. Phys. A: Math. Gen. 13, 3525-3541
    • (1980) J. Phys. A: Math. Gen. , vol.13 , pp. 3525-3541
    • Redner, S.1
  • 29
    • 50049104164 scopus 로고    scopus 로고
    • Rate of loop formation in peptides: A simulation study
    • Feige, M. J. and Paci, E. (2008) Rate of loop formation in peptides: a simulation study J. Mol. Biol. 382, 556-565
    • (2008) J. Mol. Biol. , vol.382 , pp. 556
    • Feige, M.J.1    Paci, E.2
  • 30
    • 24944542708 scopus 로고    scopus 로고
    • Statistical coil model of the unfolded state: Resolving the reconciliation problem
    • Jha, A. K., Colubri, A., Freed, K. F., and Sosnick, T. R. (2005) Statistical coil model of the unfolded state: resolving the reconciliation problem Proc. Natl. Acad. Sci. U.S.A. 102, 13099-13104
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 13099
    • Jha, A.K.1    Colubri, A.2    Freed, K.F.3    Sosnick, T.R.4
  • 31
    • 23944453852 scopus 로고    scopus 로고
    • Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins
    • Tran, H. T., Wang, X., and Pappu, R. V. (2005) Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins Biochemistry 44, 11369-11380
    • (2005) Biochemistry , vol.44 , pp. 11369
    • Tran, H.T.1    Wang, X.2    Pappu, R.V.3
  • 32
    • 4344704080 scopus 로고    scopus 로고
    • Reassessing random-coil statistics in unfolded proteins
    • Fitzkee, N. C. and Rose, G. D. (2004) Reassessing random-coil statistics in unfolded proteins Proc. Natl. Acad. Sci. U.S.A. 101, 12497-12502
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 12497
    • Fitzkee, N.C.1    Rose, G.D.2
  • 33
    • 70149111242 scopus 로고    scopus 로고
    • Thermodynamics of loop formation in the denatured state of Rhodopseudomonas palustris cytochrome c â€: Scaling exponents and the reconciliation problem
    • Rao, K. S., Tzul, F. O., Christian, A. K., Gordon, T. N., and Bowler, B. E. (2009) Thermodynamics of loop formation in the denatured state of Rhodopseudomonas palustris cytochrome c â€: scaling exponents and the reconciliation problem J. Mol. Biol. 392, 1315-1325
    • (2009) J. Mol. Biol. , vol.392 , pp. 1315
    • Rao, K.S.1    Tzul, F.O.2    Christian, A.K.3    Gordon, T.N.4    Bowler, B.E.5
  • 35
    • 26244436812 scopus 로고    scopus 로고
    • Kinetics of loop formation and breakage in the denatured state of iso-1-cytochrome c
    • Kurchan, E., Roder, H., and Bowler, B. E. (2005) Kinetics of loop formation and breakage in the denatured state of iso-1-cytochrome c J. Mol. Biol. 353, 730-743
    • (2005) J. Mol. Biol. , vol.353 , pp. 730
    • Kurchan, E.1    Roder, H.2    Bowler, B.E.3
  • 36
    • 67349120000 scopus 로고    scopus 로고
    • Importance of contact persistence in denatured state loop formation: Kinetic insights into sequence effects on nucleation early in folding
    • Tzul, F. O. and Bowler, B. E. (2009) Importance of contact persistence in denatured state loop formation: kinetic insights into sequence effects on nucleation early in folding J. Mol. Biol. 390, 124-134
    • (2009) J. Mol. Biol. , vol.390 , pp. 124
    • Tzul, F.O.1    Bowler, B.E.2
  • 38
    • 0037413451 scopus 로고    scopus 로고
    • Cloning, heterologous expression, and characterization of recombinant class II cytochromes c from Rhodopseudomonas palustris
    • McGuirl, M. A., Lee, J. C., Lyubovitsky, J. G., Thanyakoop, C., Richards, J. H., Gray, H. B., and Winkler, J. R. (2003) Cloning, heterologous expression, and characterization of recombinant class II cytochromes c from Rhodopseudomonas palustris Biochim. Biophys. Acta 1619, 23-28
    • (2003) Biochim. Biophys. Acta , vol.1619 , pp. 23
    • McGuirl, M.A.1    Lee, J.C.2    Lyubovitsky, J.G.3    Thanyakoop, C.4    Richards, J.H.5    Gray, H.B.6    Winkler, J.R.7
  • 39
    • 0034743349 scopus 로고    scopus 로고
    • Cytochrome c †folding triggered by electron transfer: Fast and slow formation of four-helix bundles
    • Lee, J. C., Gray, H. B., and Winkler, J. R. (2001) Cytochrome c †folding triggered by electron transfer: fast and slow formation of four-helix bundles Proc. Natl. Acad. Sci. U.S.A. 98, 7760-7764
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 7760
    • Lee, J.C.1    Gray, H.B.2    Winkler, J.R.3
  • 40
    • 0017845014 scopus 로고
    • Test reactions for a stopped-flow apparatus. Reduction of 2,6-dicholorophenolindophenol and potassium ferricyanide by l -ascorbic acid
    • Tonomura, B., Nakatani, H., Ohnishi, M., Yamaguchi-Ito, J., and Hiromi, K. (1978) Test reactions for a stopped-flow apparatus. Reduction of 2,6-dicholorophenolindophenol and potassium ferricyanide by l -ascorbic acid Anal. Biochem. 84, 370-383
    • (1978) Anal. Biochem. , vol.84 , pp. 370
    • Tonomura, B.1    Nakatani, H.2    Ohnishi, M.3    Yamaguchi-Ito, J.4    Hiromi, K.5
  • 41
    • 44649116524 scopus 로고    scopus 로고
    • Dynameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
    • Beck, D. A. C., Jonsson, A. L., Schaeffer, R. D., Scott, K. A., Day, R., Toofanny, R. D., Alonso, D. O. V., and Daggett, V. (2008) Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations Protein Eng. Des. Sel. 21, 353-368
    • (2008) Protein Eng. Des. Sel. , vol.21 , pp. 353
    • Beck, D.A.C.1    Jonsson, A.L.2    Schaeffer, R.D.3    Scott, K.A.4    Day, R.5    Toofanny, R.D.6    Alonso, D.O.V.7    Daggett, V.8
  • 43
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt, M., Hirshberg, M., Sharon, R., and Daggett, V. (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Comput. Phys. Commun. 91, 215-231
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 215
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 44
    • 3342918929 scopus 로고    scopus 로고
    • Methods for molecular dynamics simulations of protein folding/unfolding in solution
    • Beck, D. A. C. and Daggett, V. (2004) Methods for molecular dynamics simulations of protein folding/unfolding in solution Methods 34, 112-120
    • (2004) Methods , vol.34 , pp. 112
    • Beck, D.A.C.1    Daggett, V.2
  • 45
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • Beck, D. A. C., Armen, R. S., and Daggett, V. (2005) Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides Biochemistry 44, 609-616
    • (2005) Biochemistry , vol.44 , pp. 609
    • Beck, D.A.C.1    Armen, R.S.2    Daggett, V.3
  • 46
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • Day, R., Bennion, B. J., Ham, S., and Daggett, V. (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding J. Mol. Biol. 322, 189-203
    • (2002) J. Mol. Biol. , vol.322 , pp. 189
    • Day, R.1    Bennion, B.J.2    Ham, S.3    Daggett, V.4
  • 48
    • 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
    • Levitt, M., Hirshberg, M., Sharon, R., Laidig, K., and Daggett, V. (1997) Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution J. Phys. Chem. B 101, 5051-5056
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5051
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laidig, K.4    Daggett, V.5
  • 50
    • 26444534036 scopus 로고    scopus 로고
    • Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases
    • Armen, R. S., Bernard, B. M., Day, R., Alonso, D. O. V., and Daggett, V. (2005) Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases Proc. Natl. Acad. Sci. U.S.A. 102, 12433-12438
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 12433
    • Armen, R.S.1    Bernard, B.M.2    Day, R.3    Alonso, D.O.V.4    Daggett, V.5
  • 51
    • 0031584267 scopus 로고    scopus 로고
    • A histidine variant of yeast iso-1-cytochrome c that strongly affects the energetics of the denatured state
    • Godbole, S. and Bowler, B. E. (1997) A histidine variant of yeast iso-1-cytochrome c that strongly affects the energetics of the denatured state J. Mol. Biol. 268, 816-821
    • (1997) J. Mol. Biol. , vol.268 , pp. 816
    • Godbole, S.1    Bowler, B.E.2
  • 52
    • 1942521649 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of non-native interactions in protein folding: A single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state
    • Cho, J.-H., Sato, S., and Raleigh, D. P. (2004) Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state J. Mol. Biol. 338, 827-837
    • (2004) J. Mol. Biol. , vol.338 , pp. 827
    • Cho, J.-H.1    Sato, S.2    Raleigh, D.P.3
  • 53
    • 0033551039 scopus 로고    scopus 로고
    • a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions
    • a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions Biochemistry 38, 4896-4903
    • (1999) Biochemistry , vol.38 , pp. 4896
    • Kuhlman, B.1    Luisi, D.L.2    Young, P.3    Raleigh, D.P.4
  • 54
    • 0028569153 scopus 로고
    • Protein denaturation with guanidine hydrochloride or urea provides a different estimate of stability depending on the contributions of electrostatic interactions
    • Monera, O. D., Kay, C. M., and Hodges, R. S. (1994) Protein denaturation with guanidine hydrochloride or urea provides a different estimate of stability depending on the contributions of electrostatic interactions Protein Sci. 3, 1984-1991
    • (1994) Protein Sci. , vol.3 , pp. 1984
    • Monera, O.D.1    Kay, C.M.2    Hodges, R.S.3
  • 55
    • 0037465522 scopus 로고    scopus 로고
    • Effect of pH on the iso-1-cytochrome c denatured state: Changing constraints due to heme ligation
    • Smith, C. R., Wandschneider, E., and Bowler, B. E. (2003) Effect of pH on the iso-1-cytochrome c denatured state: changing constraints due to heme ligation Biochemistry 42, 2174-2184
    • (2003) Biochemistry , vol.42 , pp. 2174
    • Smith, C.R.1    Wandschneider, E.2    Bowler, B.E.3
  • 56
    • 77954942428 scopus 로고    scopus 로고
    • Denatured states of low complexity polypeptide sequences differ dramatically from those of foldable sequences
    • Tzul, F. O. and Bowler, B. E. (2010) Denatured states of low complexity polypeptide sequences differ dramatically from those of foldable sequences Proc. Natl. Acad. Sci. U.S.A. 107, 11364-11369
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 11364
    • Tzul, F.O.1    Bowler, B.E.2
  • 58
    • 9644310200 scopus 로고    scopus 로고
    • Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains
    • MoÌ̂glich, A., Krieger, F., and Kiefhaber, T. (2005) Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains J. Mol. Biol. 345, 153-162
    • (2005) J. Mol. Biol. , vol.345 , pp. 153
    • Moì̂glich, A.1    Krieger, F.2    Kiefhaber, T.3
  • 59
    • 0032853084 scopus 로고    scopus 로고
    • Diffusional barrier crossing in a two-state protein folding reaction
    • Jacob, M., Geeves, M., Holtermann, G., and Schmid, F. X. (1999) Diffusional barrier crossing in a two-state protein folding reaction Nat. Struct. Mol. Biol. 6, 923-926
    • (1999) Nat. Struct. Mol. Biol. , vol.6 , pp. 923
    • Jacob, M.1    Geeves, M.2    Holtermann, G.3    Schmid, F.X.4
  • 60
    • 1642379707 scopus 로고    scopus 로고
    • A limiting speed for protein folding at low solvent viscosity
    • Qiu, L. and Hagen, S. J. (2004) A limiting speed for protein folding at low solvent viscosity J. Am. Chem. Soc. 126, 3398-3399
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 3398
    • Qiu, L.1    Hagen, S.J.2
  • 61
    • 33748472551 scopus 로고    scopus 로고
    • Internal friction in the ultrafast folding of the tryptophan cage
    • Qiu, L. and Hagen, S. J. (2005) Internal friction in the ultrafast folding of the tryptophan cage Chem. Phys. 312, 327-333
    • (2005) Chem. Phys. , vol.312 , pp. 327
    • Qiu, L.1    Hagen, S.J.2
  • 62
    • 0032506017 scopus 로고    scopus 로고
    • Limited internal friction in the rate-limited step of a two-state protein folding reaction
    • Plaxco, K. W. and Baker, D. (1998) Limited internal friction in the rate-limited step of a two-state protein folding reaction Proc. Natl. Acad. Sci. U.S.A. 95, 13591-13596
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 13591
    • Plaxco, K.W.1    Baker, D.2
  • 63
    • 24144469761 scopus 로고    scopus 로고
    • Diffusional limits to the speed limit of protein folding: Fact or friction?
    • Hagen, S. J., Qui, L., and Pabit, S. A. (2005) Diffusional limits to the speed limit of protein folding: fact or friction? J. Phys.: Condens. Matter 17, S1503-S1514
    • (2005) J. Phys.: Condens. Matter , vol.17 , pp. 1503
    • Hagen, S.J.1    Qui, L.2    Pabit, S.A.3
  • 64
    • 34447624167 scopus 로고    scopus 로고
    • Sequence composition effects on denatured state loop formation in iso-1-cytochrome c variants: Polyalanine versus polyglycine inserts
    • Tzul, F. O., Kurchan, E., and Bowler, B. E. (2007) Sequence composition effects on denatured state loop formation in iso-1-cytochrome c variants: polyalanine versus polyglycine inserts J. Mol. Biol. 371, 577-584
    • (2007) J. Mol. Biol. , vol.371 , pp. 577
    • Tzul, F.O.1    Kurchan, E.2    Bowler, B.E.3
  • 65
    • 0028834210 scopus 로고
    • Elucidating the folding problem of α-helical peptides using empirical parameters III: Temperature and pH dependence
    • MunÌoz, V. and Serrano, L. (1994) Elucidating the folding problem of α-helical peptides using empirical parameters III: temperature and pH dependence J. Mol. Biol. 245, 297-308
    • (1994) J. Mol. Biol. , vol.245 , pp. 297
    • Munìoz, V.1    Serrano, L.2
  • 66
    • 0017802519 scopus 로고
    • Solvent denaturation
    • DOI 10.1002/bip.1978.360170515
    • Schellman, J. A. (1978) Solvent denaturation Biopolymers 17, 1305-1322 (Pubitemid 8326933)
    • (1978) Biopolymers , vol.17 , Issue.5 , pp. 1305-1322
    • Schellman, J.A.1
  • 67
    • 0028820703 scopus 로고
    • Denaturant m values and heat capacity changes: Relation to changes in accessible surface area of protein unfolding
    • Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Denaturant m values and heat capacity changes: relation to changes in accessible surface area of protein unfolding Protein Sci. 4, 2138-2148
    • (1995) Protein Sci. , vol.4 , pp. 2138
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 68
    • 0035836687 scopus 로고    scopus 로고
    • Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution
    • Kazmirski, S. L., Wong, K.-B., Freund, S. M. V., Tan, Y.-J., Fersht, A. R., and Daggett, V. (2001) Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution Proc. Natl. Acad. Sci. U.S.A. 98, 4349-4354
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 4349
    • Kazmirski, S.L.1    Wong, K.-B.2    Freund, S.M.V.3    Tan, Y.-J.4    Fersht, A.R.5    Daggett, V.6
  • 69
    • 26444608613 scopus 로고    scopus 로고
    • Ensemble versus single-molecule protein unfolding
    • Day, R. and Daggett, V. (2005) Ensemble versus single-molecule protein unfolding Proc. Natl. Acad. Sci. U.S.A. 102, 13445-13450
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 13445
    • Day, R.1    Daggett, V.2
  • 70
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • Mayor, U., Johnson, C. M., Daggett, V., and Fersht, A. R. (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl. Acad. Sci. U.S.A. 97, 13518-13522
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 13518
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 72
    • 3843135179 scopus 로고    scopus 로고
    • Diffusing and colliding: The atomic level folding/unfolding pathway of a small helical protein
    • DeMarco, M. L., Alonso, D. O. V., and Daggett, V. (2004) Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein J. Mol. Biol. 341, 1109-1124
    • (2004) J. Mol. Biol. , vol.341 , pp. 1109
    • Demarco, M.L.1    Alonso, D.O.V.2    Daggett, V.3
  • 73
    • 0029964867 scopus 로고    scopus 로고
    • Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding
    • Hagen, S. J., Hofrichter, J., Szabo, A., and Eaton, W. A. (1996) Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding Proc. Natl. Acad. Sci. U.S.A. 93, 11615-11617
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 11615
    • Hagen, S.J.1    Hofrichter, J.2    Szabo, A.3    Eaton, W.A.4
  • 74
    • 0031095826 scopus 로고    scopus 로고
    • Rate of intrachain diffusion of unfolded cytochrome c
    • Hagen, S. J., Hofrichter, J., and Eaton, W. A. (1997) Rate of intrachain diffusion of unfolded cytochrome c J. Phys. Chem. B 101, 2352-2365
    • (1997) J. Phys. Chem. B , vol.101 , pp. 2352
    • Hagen, S.J.1    Hofrichter, J.2    Eaton, W.A.3
  • 76
    • 0041825363 scopus 로고    scopus 로고
    • Folding kinetics of two-state proteins: Effect of circularization, permutation, and crosslinks
    • Weikl, T. R. and Dill, K. A. (2003) Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks J. Mol. Biol. 332, 953-963
    • (2003) J. Mol. Biol. , vol.332 , pp. 953
    • Weikl, T.R.1    Dill, K.A.2
  • 77
    • 0038630483 scopus 로고    scopus 로고
    • Folding rates and low-entropy-loss routes of two-state proteins
    • Weikl, T. R. and Dill, K. A. (2003) Folding rates and low-entropy-loss routes of two-state proteins J. Mol. Biol. 329, 585-598
    • (2003) J. Mol. Biol. , vol.329 , pp. 585
    • Weikl, T.R.1    Dill, K.A.2
  • 78
    • 58149396567 scopus 로고    scopus 로고
    • Early closure of a long loop in the refolding of adenylate kinase: A possible key role of non-local interactions in the initial folding steps
    • Orevi, T., Ishay, E. B., Pirchi, M., Jacob, M. H., Amir, D., and Haas, E. (2009) Early closure of a long loop in the refolding of adenylate kinase: a possible key role of non-local interactions in the initial folding steps J. Mol. Biol. 385, 1230-1242
    • (2009) J. Mol. Biol. , vol.385 , pp. 1230
    • Orevi, T.1    Ishay, E.B.2    Pirchi, M.3    Jacob, M.H.4    Amir, D.5    Haas, E.6
  • 80
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R. (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot J. Mol. Biol. 179, 125-142
    • (1984) J. Mol. Biol. , vol.179 , pp. 125
    • Eisenberg, D.1    Schwarz, E.2    Komaromy, M.3    Wall, R.4
  • 81
    • 0030900199 scopus 로고    scopus 로고
    • NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
    • Zhang, O. and Forman-Kay, J. D. (1997) NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions Biochemistry 36, 3959-3970
    • (1997) Biochemistry , vol.36 , pp. 3959
    • Zhang, O.1    Forman-Kay, J.D.2
  • 82
    • 62649138787 scopus 로고    scopus 로고
    • Experimental characterization of the denatured state ensemble of proteins
    • Cho, J.-H. and Raleigh, D. P. (2009) Experimental characterization of the denatured state ensemble of proteins Methods Mol. Biol. (Totowa, NJ) 490, 339-351
    • (2009) Methods Mol. Biol. (Totowa, NJ) , vol.490 , pp. 339
    • Cho, J.-H.1    Raleigh, D.P.2
  • 83
    • 34848916114 scopus 로고    scopus 로고
    • Anatomy of energetic changes accompanying urea-induced protein denaturation
    • Auton, M., Holthauzen, L. M. F., and Bolen, D. W. (2007) Anatomy of energetic changes accompanying urea-induced protein denaturation Proc. Natl. Acad. Sci. U.S.A. 104, 15317-15322
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 15317
    • Auton, M.1    Holthauzen, L.M.F.2    Bolen, D.W.3
  • 84
    • 46449109015 scopus 로고    scopus 로고
    • Structure and energetics of the hydrogen-bonded backbone in protein folding
    • Bolen, D. W. and Rose, G. D. (2008) Structure and energetics of the hydrogen-bonded backbone in protein folding Annu. Rev. Biochem. 77, 339-362
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 339
    • Bolen, D.W.1    Rose, G.D.2


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