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Volumn 44, Issue 16, 2005, Pages 6269-6275

Urea promotes polyproline II helix formation: Implications for protein denatured states

Author keywords

[No Author keywords available]

Indexed keywords

BONE; CONFORMATIONS; POLYMERS; POLYPEPTIDES; PROTEINS; SPECTROSCOPIC ANALYSIS;

EID: 17644422781     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050124u     Document Type: Article
Times cited : (97)

References (51)
  • 2
    • 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
  • 4
    • 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. 12497-12502
    • Fitzkee, N.C.1    Rose, G.D.2
  • 5
    • 0028790273 scopus 로고
    • Comparison between the φ distribution of the amino acids in the protein database and NMR data indicates that amino acids have various φ propensities in the random coil conformation
    • Serrano, L. (1995) Comparison between the φ distribution of the amino acids in the protein database and NMR data indicates that amino acids have various φ propensities in the random coil conformation, J. Mol. Biol. 254, 322-333.
    • (1995) J. Mol. Biol. , vol.254 , pp. 322-333
    • Serrano, L.1
  • 6
    • 0029978353 scopus 로고    scopus 로고
    • Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations
    • Smith, L. J., Bolin, K. A., Schwalbe, H., MacArthur, M. W., Thornton, J. M., and Dobson, C. M. (1996) Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations, J. Mol. Biol. 255, 494-506.
    • (1996) J. Mol. Biol. , vol.255 , pp. 494-506
    • Smith, L.J.1    Bolin, K.A.2    Schwalbe, H.3    MacArthur, M.W.4    Thornton, J.M.5    Dobson, C.M.6
  • 7
    • 0029147823 scopus 로고
    • Intrinsic propensities of amino acids, derived from the coil regions of known structures
    • Swindells, M. B., MacArthur, M. W., and Thornton, J. M. (1995) Intrinsic propensities of amino acids, derived from the coil regions of known structures, Nat. Struct. Biol. 2, 596-603.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 596-603
    • Swindells, M.B.1    MacArthur, M.W.2    Thornton, J.M.3
  • 8
    • 0014227144 scopus 로고
    • New chain conformations of poly(glutamic acid) and polylysine
    • Tiffany, M. L., and Krimm, S. (1968) New chain conformations of poly(glutamic acid) and polylysine, Biopolymers 6, 1379-1382.
    • (1968) Biopolymers , vol.6 , pp. 1379-1382
    • Tiffany, M.L.1    Krimm, S.2
  • 9
    • 0015888586 scopus 로고
    • Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride
    • Tiffany, M. L., and Krimm, S. (1973) Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride, Biopolymers 12, 575-587.
    • (1973) Biopolymers , vol.12 , pp. 575-587
    • Tiffany, M.L.1    Krimm, S.2
  • 10
    • 0036400325 scopus 로고    scopus 로고
    • Is polyproline II a major backbone conformation in unfolded proteins?
    • Shi, Z., Woody, R. W., and Kallenbach, N. R. (2002) Is polyproline II a major backbone conformation in unfolded proteins? Adv. Protein Chem. 62, 163-240.
    • (2002) Adv. Protein Chem. , vol.62 , pp. 163-240
    • Shi, Z.1    Woody, R.W.2    Kallenbach, N.R.3
  • 12
    • 0037372297 scopus 로고    scopus 로고
    • The effect of the polyproline II (PPII) conformation on the denatured state entropy
    • Ferreon, J. C., and Hilser, V. J. (2003) The effect of the polyproline II (PPII) conformation on the denatured state entropy, Protein Sci. 12, 447-457.
    • (2003) Protein Sci. , vol.12 , pp. 447-457
    • Ferreon, J.C.1    Hilser, V.J.2
  • 13
    • 0036129072 scopus 로고    scopus 로고
    • Polyproline II helical structure in protein unfolded states: Lysine peptides revisited
    • Rucker, A. L., and Creamer, T. P. (2002) Polyproline II helical structure in protein unfolded states: Lysine peptides revisited, Protein Sci. 11, 980-985.
    • (2002) Protein Sci. , vol.11 , pp. 980-985
    • Rucker, A.L.1    Creamer, T.P.2
  • 14
    • 2442522724 scopus 로고    scopus 로고
    • Short sequences of non-proline residues can adopt the polyproline II helical conformation
    • Chellgren, B. W., and Creamer, T. P. (2004) Short sequences of non-proline residues can adopt the polyproline II helical conformation, Biochemistry 43, 5864-5869.
    • (2004) Biochemistry , vol.43 , pp. 5864-5869
    • Chellgren, B.W.1    Creamer, T.P.2
  • 15
    • 0037021502 scopus 로고    scopus 로고
    • Tripeptides adopt stable structures in water. A combined polarized visible Roman, FTIR, and VCD spectroscopy study
    • Eker, F., Cao, X., Nafie, L., and Schweitzer-Stenner, R. (2002) Tripeptides adopt stable structures in water. A combined polarized visible Roman, FTIR, and VCD spectroscopy study, J. Am. Chem. Soc. 124, 14330-14341.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 14330-14341
    • Eker, F.1    Cao, X.2    Nafie, L.3    Schweitzer-Stenner, R.4
  • 16
    • 3042750640 scopus 로고    scopus 로고
    • Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution
    • Eker, F., Griebenow, K., Cao, X., Nafie, L. A., and Schweitzer-Stenner, R. (2004) Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution, Proc. Natl. Acad. Sci. U.S.A. 101, 10054-10059.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 10054-10059
    • Eker, F.1    Griebenow, K.2    Cao, X.3    Nafie, L.A.4    Schweitzer-Stenner, R.5
  • 17
    • 1542366657 scopus 로고    scopus 로고
    • Role of solvent in determining conformational preferences of alanine dipeptide in water
    • Drozdov, A. N., Grossfield, A., and Pappu, R. V. (2004) Role of solvent in determining conformational preferences of alanine dipeptide in water, J. Am. Chem. Soc. 126, 2574-2581.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 2574-2581
    • Drozdov, A.N.1    Grossfield, A.2    Pappu, R.V.3
  • 18
    • 0036784642 scopus 로고    scopus 로고
    • A simple model for polyproline II structure in unfolded states of alanine-based peptides
    • Pappu, R. V., and Rose, G. D. (2002) A simple model for polyproline II structure in unfolded states of alanine-based peptides, Protein Sci. 11, 2437-2455.
    • (2002) Protein Sci. , vol.11 , pp. 2437-2455
    • Pappu, R.V.1    Rose, G.D.2
  • 19
    • 0345862082 scopus 로고    scopus 로고
    • Characterization of non-α helical conformations in Ala peptides
    • Garcia, A. E. (2004) Characterization of non-α helical conformations in Ala peptides, Polymer 45, 669-676.
    • (2004) Polymer , vol.45 , pp. 669-676
    • Garcia, A.E.1
  • 20
    • 1842500993 scopus 로고    scopus 로고
    • Unfolded state of polyalanine is a segmented polyproline II helix
    • Kentsis, A., Mezei, M., Gindin, T., and Osman, R. (2004) Unfolded state of polyalanine is a segmented polyproline II helix, Proteins 55, 493-501.
    • (2004) Proteins , vol.55 , pp. 493-501
    • Kentsis, A.1    Mezei, M.2    Gindin, T.3    Osman, R.4
  • 21
    • 1842500992 scopus 로고    scopus 로고
    • Polyproline II helix is the preferred conformation for unfolded polyalanine in water
    • Mezei, M., Fleming, P. J., Srinivasan, R., and Rose, G. D. (2004) Polyproline II helix is the preferred conformation for unfolded polyalanine in water, Proteins 55, 502-507.
    • (2004) Proteins , vol.55 , pp. 502-507
    • Mezei, M.1    Fleming, P.J.2    Srinivasan, R.3    Rose, G.D.4
  • 22
    • 0036401140 scopus 로고    scopus 로고
    • Toward a taxonomy of the denatured state: Small angle scattering studies of unfolded proteins
    • Millett, I. S., Doniach, S., and Plaxco, K. W. (2002) Toward a taxonomy of the denatured state: Small angle scattering studies of unfolded proteins, Adv. Protein Chem. 62, 241-262.
    • (2002) Adv. Protein Chem. , vol.62 , pp. 241-262
    • Millett, I.S.1    Doniach, S.2    Plaxco, K.W.3
  • 23
    • 0015917504 scopus 로고
    • Derivative spectroscopy applied to tyrosyl chromophores. Studies on ribonuclease, lima bean inhibitors, insulin, and pancreatic trypsin inhibitor
    • Brandts, J. F., and Kaplan, L. J. (1973) Derivative spectroscopy applied to tyrosyl chromophores. Studies on ribonuclease, lima bean inhibitors, insulin, and pancreatic trypsin inhibitor, Biochemistry 12, 2011-2024.
    • (1973) Biochemistry , vol.12 , pp. 2011-2024
    • Brandts, J.F.1    Kaplan, L.J.2
  • 24
    • 49749199032 scopus 로고
    • Cleavage of the haem-protein link by acid methylethyl ketone
    • Teale, F. W. J. (1959) Cleavage of the haem-protein link by acid methylethyl ketone, Biochim. Biophys. Acta 35, 543.
    • (1959) Biochim. Biophys. Acta , vol.35 , pp. 543
    • Teale, F.W.J.1
  • 25
    • 1942505775 scopus 로고    scopus 로고
    • The NMR structure of a stable and compact all-β-sheet variant of intestinal fatty acid-binding protein
    • Ogbay, B., Dekoster, G. T., and Cistola, D. P. (2004) The NMR structure of a stable and compact all-β-sheet variant of intestinal fatty acid-binding protein, Protein Sci. 13, 1227-1237.
    • (2004) Protein Sci. , vol.13 , pp. 1227-1237
    • Ogbay, B.1    Dekoster, G.T.2    Cistola, D.P.3
  • 26
    • 0014378447 scopus 로고
    • Circular dichroism of poly-L-proline in an unordered conformation
    • Tiffany, M. L., and Krimm, S. (1968) Circular dichroism of poly-L-proline in an unordered conformation, Biopolymers 6, 1767-1770.
    • (1968) Biopolymers , vol.6 , pp. 1767-1770
    • Tiffany, M.L.1    Krimm, S.2
  • 28
    • 0018192876 scopus 로고
    • Synthesis and circular dichroism studies of two polypeptides H-[Gly-(Pro)3]-n-OH and H-[Gly-(Pro)4]n-OH
    • Helbecque, N., and Loucheux-Lefebvre, M. H. (1978) Synthesis and circular dichroism studies of two polypeptides H-[Gly-(Pro)3]-n-OH and H-[Gly-(Pro)4]n-OH, Int. J. Pept. Protein Res. 11, 353-362.
    • (1978) Int. J. Pept. Protein Res. , vol.11 , pp. 353-362
    • Helbecque, N.1    Loucheux-Lefebvre, M.H.2
  • 29
    • 0002251831 scopus 로고
    • Circular dichroism and conformation of unordered polypeptides
    • Woody, R. W. (1992) Circular dichroism and conformation of unordered polypeptides, Adv. Biophys. Chem. 2, 37-79.
    • (1992) Adv. Biophys. Chem. , vol.2 , pp. 37-79
    • Woody, R.W.1
  • 30
    • 0031692650 scopus 로고    scopus 로고
    • Left-handed polyproline II helix formation is (very) locally driven
    • Creamer, T. P. (1998) Left-handed polyproline II helix formation is (very) locally driven, Proteins 33, 218-226.
    • (1998) Proteins , vol.33 , pp. 218-226
    • Creamer, T.P.1
  • 32
    • 1542347945 scopus 로고    scopus 로고
    • The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy
    • Schweitzer-Stenner, R., Eker, F., Griebenow, K., Cao, X., and Nafie, L. A. (2004) The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy, J. Am. Chem. Soc. 126, 2768-2776.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 2768-2776
    • Schweitzer-Stenner, R.1    Eker, F.2    Griebenow, K.3    Cao, X.4    Nafie, L.A.5
  • 34
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • Levitt, M., and Chothia, C. (1976) Structural patterns in globular proteins, Nature 261, 552-558.
    • (1976) Nature , vol.261 , pp. 552-558
    • Levitt, M.1    Chothia, C.2
  • 35
    • 16644392534 scopus 로고    scopus 로고
    • Thermal and alkaline denaturation of bovine β-casein
    • Qi, P. X., Wickham, E. D., and Farrell, H. M., Jr. (2004) Thermal and alkaline denaturation of bovine β-casein, Protein J. 23, 389-402.
    • (2004) Protein J. , vol.23 , pp. 389-402
    • Qi, P.X.1    Wickham, E.D.2    Farrell Jr., H.M.3
  • 36
  • 37
    • 9344251691 scopus 로고    scopus 로고
    • Solvent dependence of PII conformation in model alanine peptides
    • Liu, Z., Chen, K., Ng, A., Shi, Z., Woody, R. W., and Kallenbach, N. R. (2004) Solvent dependence of PII conformation in model alanine peptides, J. Am. Chem. Soc. 126, 15141-15150.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 15141-15150
    • Liu, Z.1    Chen, K.2    Ng, A.3    Shi, Z.4    Woody, R.W.5    Kallenbach, N.R.6
  • 38
    • 0038344087 scopus 로고    scopus 로고
    • Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy
    • Eker, F., Griebenow, K., and Schweitzer-Stenner, R. (2003) Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy, J. Am. Chem. Soc. 125, 8178-8185.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 8178-8185
    • Eker, F.1    Griebenow, K.2    Schweitzer-Stenner, R.3
  • 39
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty, A., Kortemme, T., and Baldwin, R. L. (1994) Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions, Protein Sci. 3, 843-852.
    • (1994) Protein Sci. , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 40
    • 3242789489 scopus 로고    scopus 로고
    • Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings
    • Mohana-Borges, R., Goto, N. K., Kroon, G. J., Dyson, H. J., and Wright, P. E. (2004) Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings, J. Mol. Biol. 340, 1131-1142.
    • (2004) J. Mol. Biol. , vol.340 , pp. 1131-1142
    • Mohana-Borges, R.1    Goto, N.K.2    Kroon, G.J.3    Dyson, H.J.4    Wright, P.E.5
  • 41
    • 4143148674 scopus 로고    scopus 로고
    • Guanidine hydrochloride can induce amyloid fibril formation from hen egg-white lysozyme
    • Vernaglia, B. A., Huang, J., and Clark, E. D. (2004) Guanidine hydrochloride can induce amyloid fibril formation from hen egg-white lysozyme, Biomacromolecules 5, 1362-1370.
    • (2004) Biomacromolecules , vol.5 , pp. 1362-1370
    • Vernaglia, B.A.1    Huang, J.2    Clark, E.D.3
  • 42
    • 0032190351 scopus 로고    scopus 로고
    • Folding mechanism of three structurally similar β-sheet proteins
    • Burns, L. L., Dalessio, P. M., and Ropson, I. J. (1998) Folding mechanism of three structurally similar β-sheet proteins, Proteins 33, 107-118.
    • (1998) Proteins , vol.33 , pp. 107-118
    • Burns, L.L.1    Dalessio, P.M.2    Ropson, I.J.3
  • 43
    • 78651119214 scopus 로고
    • The solubility of amino acids and related compounds in aqueous urea solutions
    • Nozaki, Y., and Tanford, C. (1963) The solubility of amino acids and related compounds in aqueous urea solutions, J. Biol. Chem. 238, 4074-4081.
    • (1963) J. Biol. Chem. , vol.238 , pp. 4074-4081
    • Nozaki, Y.1    Tanford, C.2
  • 44
    • 0001664170 scopus 로고
    • The effect of compounds of the urea-guanidinium class on the activity coefficient of acetyltetraglycine ethyl ester and related compounds
    • Robinson, D. R., and Jencks, W. L. (1965) The effect of compounds of the urea-guanidinium class on the activity coefficient of acetyltetraglycine ethyl ester and related compounds, J. Am. Chem. Soc. 87, 2462-2470.
    • (1965) J. Am. Chem. Soc. , vol.87 , pp. 2462-2470
    • Robinson, D.R.1    Jencks, W.L.2
  • 45
    • 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., and Doniach, S. (1998) Protein denaturation: A small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c, Biochemistry 37, 12443-12451.
    • (1998) Biochemistry , vol.37 , pp. 12443-12451
    • Segel, D.J.1    Fink, A.L.2    Hodgson, K.O.3    Doniach, S.4
  • 46
    • 0037610743 scopus 로고    scopus 로고
    • Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of φ
    • Avbelj, F., and Baldwin, R. L. (2003) Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of φ, Proc. Natl. Acad. Sci. U.S.A. 100, 5742-5747.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 5742-5747
    • Avbelj, F.1    Baldwin, R.L.2
  • 47
    • 0347694974 scopus 로고    scopus 로고
    • On the extended β-conformation propensity of polypeptides at high temperature
    • Yang, W. Y., Larios, E., and Gruebele, M. (2003) On the extended β-conformation propensity of polypeptides at high temperature, J. Am. Chem. Soc. 125, 16220-16227.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 16220-16227
    • Yang, W.Y.1    Larios, E.2    Gruebele, M.3
  • 48
    • 0026672305 scopus 로고
    • NMR determination of residual structure in a urea-denatured protein, the 434-repressor
    • Neri, D., Billeter, M., Wider, G., and Wuthrich, K. (1992) NMR determination of residual structure in a urea-denatured protein, the 434-repressor, Science 257, 1559-1563.
    • (1992) Science , vol.257 , pp. 1559-1563
    • Neri, D.1    Billeter, M.2    Wider, G.3    Wuthrich, K.4
  • 49
    • 0027772180 scopus 로고
    • Urea-induced unfolding of the α subunit of tryptophan synthase: One-dimensional proton NMR evidence for residual structure near histidine-92 at high denaturant concentration
    • Saab-Rincon, G., Froebe, C. L., and Matthews, C. R. (1993) Urea-induced unfolding of the α subunit of tryptophan synthase: One-dimensional proton NMR evidence for residual structure near histidine-92 at high denaturant concentration, Biochemistry 32, 13981-13990.
    • (1993) Biochemistry , vol.32 , pp. 13981-13990
    • Saab-Rincon, G.1    Froebe, C.L.2    Matthews, C.R.3
  • 50
    • 0035919635 scopus 로고    scopus 로고
    • Persistence of native-like topology in a denatured protein in 8 M urea
    • Shortle, D., and Ackerman, M. S. (2001) Persistence of native-like topology in a denatured protein in 8 M urea, Science 293, 487-489.
    • (2001) Science , vol.293 , pp. 487-489
    • Shortle, D.1    Ackerman, M.S.2


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