메뉴 건너뛰기




Volumn 339, Issue 1, 2004, Pages 185-197

Conformational properties of the iso-1-cytochrome c denatured state: Dependence on guanidine hydrochloride concentration

Author keywords

cytochrome c; denatured states; guanidine hydrochloride; protein folding; random coil

Indexed keywords

AMINO ACID; GUANIDINE; HEME; HISTIDINE; ISOCYTOCHROME C1; ISOPROTEIN; MONOMER; UNCLASSIFIED DRUG;

EID: 2342544028     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(04)00331-6     Document Type: Article
Times cited : (27)

References (60)
  • 2
    • 0033871781 scopus 로고    scopus 로고
    • Protein folding intermediates and pathways studied by hydrogen exchange
    • Englander S.W. Protein folding intermediates and pathways studied by hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29:2000;213-238
    • (2000) Annu. Rev. Biophys. Biomol. Struct. , vol.29 , pp. 213-238
    • Englander, S.W.1
  • 3
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill K.A. Polymer principles and protein folding. Protein Sci. 8:1999;1166-1180
    • (1999) Protein Sci. , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 5
    • 0037221599 scopus 로고    scopus 로고
    • Is there a unifying mechanism for protein folding?
    • Daggett V., Fersht A.R. 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
    • 0026672305 scopus 로고
    • NMR determination of residual structure in a urea-denatured protein the 434-repressor
    • Neri D., Billeter M., Wider G., Wüthrich K. NMR determination of residual structure in a urea-denatured protein the 434-repressor. Science. 257:1992;1559-1563
    • (1992) Science , vol.257 , pp. 1559-1563
    • Neri, D.1    Billeter, M.2    Wider, G.3    Wüthrich, K.4
  • 8
    • 0029961647 scopus 로고    scopus 로고
    • Structural analysis of non-native states of proteins by NMR methods
    • Shortle D. Structural analysis of non-native states of proteins by NMR methods. Curr. Opin. Struct. Biol. 6:1996;24-30
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 24-30
    • Shortle, D.1
  • 10
    • 0030900199 scopus 로고    scopus 로고
    • NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
    • Zhang O., Forman-Kay J. NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. Biochemistry. 36:1997;3959-3970
    • (1997) Biochemistry , vol.36 , pp. 3959-3970
    • Zhang, O.1    Forman-Kay, J.2
  • 11
    • 0033546123 scopus 로고    scopus 로고
    • NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions
    • Mok Y.-K., Kay C.M., Kay L.E., Forman-Kay J. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions. J. Mol. Biol. 289:1999;619-638
    • (1999) J. Mol. Biol. , vol.289 , pp. 619-638
    • Mok, Y.-K.1    Kay, C.M.2    Kay, L.E.3    Forman-Kay, J.4
  • 13
    • 0027394283 scopus 로고
    • Denatured states of proteins and their roles in folding and stability
    • Shortle D. Denatured states of proteins and their roles in folding and stability. Curr. Opin. Struct. Biol. 3:1993;66-74
    • (1993) Curr. Opin. Struct. Biol. , vol.3 , pp. 66-74
    • Shortle, D.1
  • 14
    • 0034628913 scopus 로고    scopus 로고
    • Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
    • Wong K.B., Clarke J., Bond C.J., Neira J.L., Freund S.M.V., Fersht A.R., Daggett V. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J. Mol. Biol. 296:2000;1257-1282
    • (2000) J. Mol. Biol. , vol.296 , pp. 1257-1282
    • Wong, K.B.1    Clarke, J.2    Bond, C.J.3    Neira, J.L.4    Freund, S.M.V.5    Fersht, A.R.6    Daggett, V.7
  • 15
    • 0034691198 scopus 로고    scopus 로고
    • Measuring the rate of intramolecular contact formation in polypeptides
    • Lapidus L.J., Eaton W.A., Hofrichter J. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl Acad. Sci. USA. 97:2000;7220-7225
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 7220-7225
    • Lapidus, L.J.1    Eaton, W.A.2    Hofrichter, J.3
  • 16
    • 0542397796 scopus 로고    scopus 로고
    • Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins
    • Eaton W.A., Munoz V., Thompson P.A., Henry E.R., Hofrichter J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Accts Chem. Res. 31:1998;745-753
    • (1998) Accts Chem. Res. , vol.31 , pp. 745-753
    • Eaton, W.A.1    Munoz, V.2    Thompson, P.A.3    Henry, E.R.4    Hofrichter, J.5
  • 17
    • 0036304892 scopus 로고    scopus 로고
    • Measuring dynamic flexibility of the coil state of a helix-forming peptide
    • Lapidus L.J., Eaton W.A., Hofrichter J. Measuring dynamic flexibility of the coil state of a helix-forming peptide. J. Mol. Biol. 319:2002;19-25
    • (2002) J. Mol. Biol. , vol.319 , pp. 19-25
    • Lapidus, L.J.1    Eaton, W.A.2    Hofrichter, J.3
  • 19
    • 0043237588 scopus 로고    scopus 로고
    • Dynamics of unfolded polypeptide chains as models for the earliest steps in protein folding
    • Krieger F., Fierz B., Bieri O., Drewello M., Kiefhaber T. Dynamics of unfolded polypeptide chains as models for the earliest steps in protein folding. J. Mol. Biol. 332:2003;265-274
    • (2003) J. Mol. Biol. , vol.332 , pp. 265-274
    • Krieger, F.1    Fierz, B.2    Bieri, O.3    Drewello, M.4    Kiefhaber, T.5
  • 20
    • 0035979801 scopus 로고    scopus 로고
    • Denatured state thermodynamics: Residual structure, chain stiffness and scaling factors
    • Hammack B.N., Smith C.R., Bowler B.E. Denatured state thermodynamics: residual structure, chain stiffness and scaling factors. J. Mol. Biol. 311:2001;1091-1104
    • (2001) J. Mol. Biol. , vol.311 , pp. 1091-1104
    • Hammack, B.N.1    Smith, C.R.2    Bowler, B.E.3
  • 21
    • 0001193711 scopus 로고
    • The effects of internal constraints on conformations of chain molecules
    • Chan H.S., Dill K.A. The effects of internal constraints on conformations of chain molecules. J. Chem. Phys. 92:1990;3118-3135
    • (1990) J. Chem. Phys. , vol.92 , pp. 3118-3135
    • Chan, H.S.1    Dill, K.A.2
  • 22
    • 0000232764 scopus 로고
    • Distribution functions in the interior of polymer chains
    • Redner S. Distribution functions in the interior of polymer chains. J. Phys. A. 13:1980;3525-3541
    • (1980) J. Phys. a , vol.13 , pp. 3525-3541
    • Redner, S.1
  • 23
    • 0014364651 scopus 로고
    • Protein denaturation
    • Tanford C. Protein denaturation. Advan. Protein Chem. 23:1968;121-282
    • (1968) Advan. Protein Chem. , vol.23 , pp. 121-282
    • Tanford, C.1
  • 25
    • 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
  • 26
    • 0028220311 scopus 로고
    • The role of a conserved internal water molecule and its associated hydrogen bond network in cytochrome c
    • Berghuis A.M., Guillemette J.G., McLendon G., Sherman F., Smith M., Brayer G.D. The role of a conserved internal water molecule and its associated hydrogen bond network in cytochrome c. J. Mol. Biol. 236:1994;786-799
    • (1994) J. Mol. Biol. , vol.236 , pp. 786-799
    • Berghuis, A.M.1    Guillemette, J.G.2    McLendon, G.3    Sherman, F.4    Smith, M.5    Brayer, G.D.6
  • 27
    • 0343170500 scopus 로고
    • Dramatic thermostabilization of yeast iso-1-cytochrome c by an asparagine→isoleucine replacement at position 57
    • Das G., Hickey D.R., McLendon D., McLendon G., Sherman F. Dramatic thermostabilization of yeast iso-1-cytochrome c by an asparagine→isoleucine replacement at position 57. Proc. Natl Acad. Sci. USA. 86:1989;496-499
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 496-499
    • Das, G.1    Hickey, D.R.2    McLendon, D.3    McLendon, G.4    Sherman, F.5
  • 29
    • 0042820062 scopus 로고    scopus 로고
    • Evaluation of cooperative interactions between substructures of iso-1-cytochrome c using double mutant cycles
    • Wandschneider E., Hammack B.N., Bowler B.E. Evaluation of cooperative interactions between substructures of iso-1-cytochrome c using double mutant cycles. Biochemistry. 42:2003;10659-10666
    • (2003) Biochemistry , vol.42 , pp. 10659-10666
    • Wandschneider, E.1    Hammack, B.N.2    Bowler, B.E.3
  • 30
    • 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., Bowler B.E. Effect of pH on the iso-1-cytochrome c denatured state: changing constraints due to heme ligation. Biochemistry. 42:2003;2174-2184
    • (2003) Biochemistry , vol.42 , pp. 2174-2184
    • Smith, C.R.1    Wandschneider, E.2    Bowler, B.E.3
  • 31
    • 0037031261 scopus 로고    scopus 로고
    • Effects of topology and excluded volume on protein denatured state conformational properties
    • Smith C.R., Mateljevic N., Bowler B.E. Effects of topology and excluded volume on protein denatured state conformational properties. Biochemistry. 41:2002;10173-10181
    • (2002) Biochemistry , vol.41 , pp. 10173-10181
    • Smith, C.R.1    Mateljevic, N.2    Bowler, B.E.3
  • 32
    • 0034619421 scopus 로고    scopus 로고
    • PH dependence of formation of a partially unfolded state of a Lys 73→His variant of iso-1-cytochrome c: Implications for the alkaline conformational transition of cytochrome c
    • Nelson C.J., Bowler B.E. pH dependence of formation of a partially unfolded state of a Lys 73→His variant of iso-1-cytochrome c: implications for the alkaline conformational transition of cytochrome c. Biochemistry. 44:2000;13584-13594
    • (2000) Biochemistry , vol.44 , pp. 13584-13594
    • Nelson, C.J.1    Bowler, B.E.2
  • 33
    • 0014203499 scopus 로고
    • Acid-base titrations in concentrated guanidine hydrochloride. Dissociation constants of the guanidinium ion and of some amino acids
    • Nozaki Y., Tanford C. Acid-base titrations in concentrated guanidine hydrochloride. Dissociation constants of the guanidinium ion and of some amino acids. J. Am. Chem. Soc. 89:1967;736-742
    • (1967) J. Am. Chem. Soc. , vol.89 , pp. 736-742
    • Nozaki, Y.1    Tanford, C.2
  • 34
    • 0028941444 scopus 로고
    • Theoretical predictions of folding pathways by using the proximity rule with applications to bovine pancreatic trypsin inhibitor
    • Camacho C.J., Thirumalai D. Theoretical predictions of folding pathways by using the proximity rule with applications to bovine pancreatic trypsin inhibitor. Proc. Natl Acad. Sci. USA. 92:1995;1277-1281
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 1277-1281
    • Camacho, C.J.1    Thirumalai, D.2
  • 35
    • 0016885151 scopus 로고
    • Moments and distribution functions for polypeptide chains. Poly-L-alanine
    • Conrad J.C., Flory P.J. Moments and distribution functions for polypeptide chains. Poly-L-alanine. Macromolecules. 9:1976;41-47
    • (1976) Macromolecules , vol.9 , pp. 41-47
    • Conrad, J.C.1    Flory, P.J.2
  • 36
    • 0037424614 scopus 로고    scopus 로고
    • Computational simulation of the statistical properties of unfolded proteins
    • Goldenberg D.P. Computational simulation of the statistical properties of unfolded proteins. J. Mol. Biol. 326:2003;1615-1633
    • (2003) J. Mol. Biol. , vol.326 , pp. 1615-1633
    • Goldenberg, D.P.1
  • 37
    • 0000484499 scopus 로고
    • Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides
    • Fauchère J.-L., Pliška V. Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. 18:1983;369-375
    • (1983) Eur. J. Med. Chem. , vol.18 , pp. 369-375
    • Fauchère, J.-L.1    Pliška, V.2
  • 39
    • 0024324626 scopus 로고
    • Urea dependence of thiol-disulfide equilibria in thioredoxin: Confirmation of the linkage relationship and a sensitive assay for structure
    • Lin T.Y., Kim P.S. Urea dependence of thiol-disulfide equilibria in thioredoxin: confirmation of the linkage relationship and a sensitive assay for structure. Biochemistry. 28:1989;5282-5287
    • (1989) Biochemistry , vol.28 , pp. 5282-5287
    • Lin, T.Y.1    Kim, P.S.2
  • 40
    • 0015919686 scopus 로고
    • On the role of heme in the formation of the structure of cytochrome c
    • Fisher W.R., Taniuchi H., Anfinsen C.B. On the role of heme in the formation of the structure of cytochrome c. J. Biol. Chem. 248:1973;3188-3195
    • (1973) J. Biol. Chem. , vol.248 , pp. 3188-3195
    • Fisher, W.R.1    Taniuchi, H.2    Anfinsen, C.B.3
  • 41
    • 0016380496 scopus 로고
    • The Trp-59 fluorescence of ferricytochrome c as a sensitive measure of the over-all protein conformation
    • Tsong T.Y. The Trp-59 fluorescence of ferricytochrome c as a sensitive measure of the over-all protein conformation. J. Biol. Chem. 249:1974;1988-1990
    • (1974) J. Biol. Chem. , vol.249 , pp. 1988-1990
    • Tsong, T.Y.1
  • 42
    • 2342523668 scopus 로고    scopus 로고
    • Estimation of the compaction of the denatured state by a protein variant involved in a reverse hydrophobic effect
    • Zhang M.-M., Ford C.D., Bowler B.E. Estimation of the compaction of the denatured state by a protein variant involved in a reverse hydrophobic effect. Protein J. 23:2004;119-126
    • (2004) Protein J. , vol.23 , pp. 119-126
    • Zhang, M.-M.1    Ford, C.D.2    Bowler, B.E.3
  • 43
    • 0032497321 scopus 로고    scopus 로고
    • Protein denaturation: A small angle X-ray scattering study of the ensemble of unfolded states of cytochrome c
    • Segel D.J., Fink A.L., Hodgson K.O., Doniach S. Protein denaturation: a small angle X-ray scattering study of the ensemble of unfolded states of cytochrome c. Biochemistry. 37:1998;12443-12451
    • (1998) Biochemistry , vol.37 , pp. 12443-12451
    • Segel, D.J.1    Fink, A.L.2    Hodgson, K.O.3    Doniach, S.4
  • 44
    • 0034635341 scopus 로고    scopus 로고
    • Measuring denatured state energetics: Deviations from random coil behavior and implications for the folding of iso-1-cytochrome c
    • Godbole S., Hammack B.N., Bowler B.E. Measuring denatured state energetics: deviations from random coil behavior and implications for the folding of iso-1-cytochrome c. J. Mol. Biol. 296:2000;217-228
    • (2000) J. Mol. Biol. , vol.296 , pp. 217-228
    • Godbole, S.1    Hammack, B.N.2    Bowler, B.E.3
  • 45
    • 0031866483 scopus 로고    scopus 로고
    • Amide protection in an early folding intermediate of cytochrome c
    • Sauder J.M., Roder H. Amide protection in an early folding intermediate of cytochrome c. Fold. Des. 3:1998;293-301
    • (1998) Fold. Des. , vol.3 , pp. 293-301
    • Sauder, J.M.1    Roder, H.2
  • 46
    • 0032972986 scopus 로고    scopus 로고
    • Is protein folding hierarchic? I. Local structure and peptide folding
    • Baldwin R.L., Rose G.D. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24:1999;26-33
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 26-33
    • Baldwin, R.L.1    Rose, G.D.2
  • 48
    • 0038630483 scopus 로고    scopus 로고
    • Folding rates and low-entropy-loss routes of two state proteins
    • Weikl T.R., Dill K.A. Folding rates and low-entropy-loss routes of two state proteins. J. Mol. Biol. 329:2003;585-598
    • (2003) J. Mol. Biol. , vol.329 , pp. 585-598
    • Weikl, T.R.1    Dill, K.A.2
  • 49
    • 0041825363 scopus 로고    scopus 로고
    • Folding kinetics of two-state proteins: Effect of circularization, permutation and crosslinks
    • Weikl T.R., Dill K.A. Folding kinetics of two-state proteins: effect of circularization, permutation and crosslinks. J. Mol. Biol. 332:2003;953-963
    • (2003) J. Mol. Biol. , vol.332 , pp. 953-963
    • Weikl, T.R.1    Dill, K.A.2
  • 50
    • 0042631521 scopus 로고    scopus 로고
    • Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences
    • Kaya H., Chan H.S. Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins: Struct. Funct. Genet. 52:2003;524-533
    • (2003) Proteins: Struct. Funct. Genet. , vol.52 , pp. 524-533
    • Kaya, H.1    Chan, H.S.2
  • 51
    • 1542319916 scopus 로고    scopus 로고
    • Cooperativity principles in protein folding
    • Chan H.S., Shimizu S., Kaya H. Cooperativity principles in protein folding. Methods Enzymol. 380:2004;350-379
    • (2004) Methods Enzymol. , vol.380 , pp. 350-379
    • Chan, H.S.1    Shimizu, S.2    Kaya, H.3
  • 52
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 227:1998;985-994
    • (1998) J. Mol. Biol. , vol.227 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 53
    • 0036295960 scopus 로고    scopus 로고
    • Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
    • Klimov D.K., Thirumalai D. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J. Mol. Biol. 315:2002;721-737
    • (2002) J. Mol. Biol. , vol.315 , pp. 721-737
    • Klimov, D.K.1    Thirumalai, D.2
  • 54
    • 0026601458 scopus 로고
    • Site directed mutagenesis of virtually any plasmid by eliminating a unique site
    • Deng W.P.D., Nickoloff J.A. Site directed mutagenesis of virtually any plasmid by eliminating a unique site. Anal. Biochem. 200:1992;81-88
    • (1992) Anal. Biochem. , vol.200 , pp. 81-88
    • Deng, W.P.D.1    Nickoloff, J.A.2
  • 55
    • 0027464611 scopus 로고
    • Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: Implications for the denatured state
    • Bowler B.E., May K., Zaragoza T., York P., Dong A., Caughey W.S. Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: implications for the denatured state. Biochemistry. 32:1993;183-190
    • (1993) Biochemistry , vol.32 , pp. 183-190
    • Bowler, B.E.1    May, K.2    Zaragoza, T.3    York, P.4    Dong, A.5    Caughey, W.S.6
  • 56
    • 0002038533 scopus 로고    scopus 로고
    • Site-directed replacement of the invariant lysine 73 of Saccharamyces cerevisiae iso-1-cytochrome c with all ribosomally encoded amino acids
    • Herrmann L., Flatt P., Bowler B.E. Site-directed replacement of the invariant lysine 73 of Saccharamyces cerevisiae iso-1-cytochrome c with all ribosomally encoded amino acids. Inorg. Chim. Acta. 242:1996;97-103
    • (1996) Inorg. Chim. Acta , vol.242 , pp. 97-103
    • Herrmann, L.1    Flatt, P.2    Bowler, B.E.3
  • 57
    • 0028287068 scopus 로고
    • Characterization of the guanidine hydrochloride denatured state of iso-1-cytochrome c by infrared spectroscopy
    • Bowler B.E., Dong A., Caughey W.S. Characterization of the guanidine hydrochloride denatured state of iso-1-cytochrome c by infrared spectroscopy. Biochemistry. 33:1994;2402-2408
    • (1994) Biochemistry , vol.33 , pp. 2402-2408
    • Bowler, B.E.1    Dong, A.2    Caughey, W.S.3
  • 58
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • Pace C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 113:1986;266-280
    • (1986) Methods Enzymol. , vol.113 , pp. 266-280
    • Pace, C.N.1
  • 59
    • 0032488914 scopus 로고    scopus 로고
    • Cytochrome c folding traps are not due solely to histidine-heme ligation: Direct demonstration of a role for N-terminal amino group-heme ligation
    • Hammack B.N., Godbole S., Bowler B.E. Cytochrome c folding traps are not due solely to histidine-heme ligation: direct demonstration of a role for N-terminal amino group-heme ligation. J. Mol. Biol. 275:1998;715-724
    • (1998) J. Mol. Biol. , vol.275 , pp. 715-724
    • Hammack, B.N.1    Godbole, S.2    Bowler, B.E.3
  • 60
    • 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., Bowler B.E. A histidine variant of yeast iso-1-cytochrome c that strongly affects the energetics of the denatured state. J. Mol. Biol. 268:1997;816-821
    • (1997) J. Mol. Biol. , vol.268 , pp. 816-821
    • Godbole, S.1    Bowler, B.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.