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Volumn 30, Issue , 2011, Pages 24-30

Simulation of urea-induced protein unfolding: A lesson from bovine β-lactoglobulin

Author keywords

Molecular dynamics; Nuclear magnetic resonance; Osmolyte; Protein structure

Indexed keywords

HYDROGEN BONDS; HYDROPHOBICITY; MAMMALS; METABOLISM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; UREA;

EID: 84855298578     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.06.004     Document Type: Article
Times cited : (14)

References (39)
  • 1
    • 73949154012 scopus 로고    scopus 로고
    • Molecular simulations of peptides: A useful tool for the development of new drugs and for the study of molecular recognition
    • M. Meli, G. Colombo, Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition, Methods Mol. Biol. 570 (2009) 77-153.
    • (2009) Methods Mol. Biol. , vol.570 , pp. 77-153
    • Meli, M.1    Colombo, G.2
  • 2
    • 23244452958 scopus 로고    scopus 로고
    • Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization
    • DOI 10.1529/biophysj.105.061978
    • A. Caballero-Herrera, K. Nordstrand, K.D. Berndt, L. Nilsson, Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization, Biophys. J. 89 (2005) 842-857. (Pubitemid 41098971)
    • (2005) Biophysical Journal , vol.89 , Issue.2 , pp. 842-857
    • Caballero-Herrera, A.1    Nordstrand, K.2    Berndt, K.D.3    Nilsson, L.4
  • 3
    • 45849084663 scopus 로고    scopus 로고
    • Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations
    • C. Camilloni, A.G. Rocco, I. Eberini, E. Gianazza, R.A. Broglia, G. Tiana, Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations, Biophys. J. 94 (2008) 4654-4661.
    • (2008) Biophys. J. , vol.94 , pp. 4654-4661
    • Camilloni, C.1    Rocco, A.G.2    Eberini, I.3    Gianazza, E.4    Broglia, R.A.5    Tiana, G.6
  • 4
    • 34250869055 scopus 로고    scopus 로고
    • Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism
    • DOI 10.1021/ja069232+
    • E.P. O'Brien, R.I. Dima, B. Brooks, D. Thirumalai, Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism, J. Am. Chem. Soc. 129 (2007) 7346-7353. (Pubitemid 46980813)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.23 , pp. 7346-7353
    • O'Brien, E.P.1    Dima, R.I.2    Brooks, B.3    Thirumalai, D.4
  • 5
    • 55949131241 scopus 로고    scopus 로고
    • Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
    • L. Hua, R. Zhou, D. Thirumalai, B.J. Berne, Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding, Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 16928-16933.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 16928-16933
    • Hua, L.1    Zhou, R.2    Thirumalai, D.3    Berne, B.J.4
  • 7
    • 47749106779 scopus 로고    scopus 로고
    • Atomistic mechanism of protein denaturation by urea
    • A. Das, C. Mukhopadhyay, Atomistic mechanism of protein denaturation by urea, J. Phys. Chem. B 112 (2008) 7903-7908.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 7903-7908
    • Das, A.1    Mukhopadhyay, C.2
  • 9
    • 57149110439 scopus 로고    scopus 로고
    • Polar or apolar- The role of polarity for ureainduced protein denaturation
    • M.C. Stumpe, H. Grubmuller, Polar or apolar-the role of polarity for ureainduced protein denaturation, PLoS Comput. Biol. 4 (2008) e1000221.
    • (2008) PLoS Comput. Biol. , vol.4
    • Stumpe, M.C.1    Grubmuller, H.2
  • 10
    • 67650363919 scopus 로고    scopus 로고
    • Urea impedes the hydrophobic collapse of partially unfolded proteins
    • M.C. Stumpe, H. Grubmuller, Urea impedes the hydrophobic collapse of partially unfolded proteins, Biophys. J. 96 (2009) 3744-3752.
    • (2009) Biophys. J. , vol.96 , pp. 3744-3752
    • Stumpe, M.C.1    Grubmuller, H.2
  • 11
    • 63149153986 scopus 로고    scopus 로고
    • Urea's action on hydrophobic interactions
    • R. Zangi, R.H. Zhou, B.J. Berne, Urea's action on hydrophobic interactions, J. Am. Chem. Soc. 131 (2009) 1535-1541.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 1535-1541
    • Zangi, R.1    Zhou, R.H.2    Berne, B.J.3
  • 12
    • 77749285768 scopus 로고    scopus 로고
    • Equilibrium study of protein denaturation by urea
    • D.R. Canchi, D. Paschek, A.E. Garcia, Equilibrium study of protein denaturation by urea, J. Am. Chem. Soc. 132 (2010) 2338-2344.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 2338-2344
    • Canchi, D.R.1    Paschek, D.2    Garcia, A.E.3
  • 13
    • 0029294696 scopus 로고
    • Multiple molecular recognition properties of the lipocalin protein family
    • D.R. Flower, Multiple molecular recognition properties of the lipocalin protein family, J. Mol. Recognit. 8 (1995) 185-195.
    • (1995) J. Mol. Recognit. , vol.8 , pp. 185-195
    • Flower, D.R.1
  • 14
    • 0032491188 scopus 로고    scopus 로고
    • Structural basis of the tanford transition of bovine β-lactoglobulin
    • DOI 10.1021/bi981016t
    • B.Y. Qin, M.C. Bewley, L.K. Creamer, H.M. Baker, E.N. Baker, G.B. Jameson, Structural basis of the Tanford transition of bovine beta-lactoglobulin, Biochemistry-US 37 (1998) 14014-14023. (Pubitemid 28471234)
    • (1998) Biochemistry , vol.37 , Issue.40 , pp. 14014-14023
    • Qin, B.Y.1    Bewley, M.C.2    Creamer, L.K.3    Baker, H.M.4    Baker, E.N.5    Jameson, G.B.6
  • 16
    • 0029944773 scopus 로고    scopus 로고
    • Partially folded structure of monomeric bovine β-lactoglobulin
    • DOI 10.1016/0014-5793(96)00100-7
    • H. Molinari, L. Ragona, L. Varani, G. Musco, R. Consonni, L. Zetta, H.L. Monaco, Partially folded structure of monomeric bovine beta-lactoglobulin, FEBS Lett. 381 (1996) 237-243. (Pubitemid 26080343)
    • (1996) FEBS Letters , vol.381 , Issue.3 , pp. 237-243
    • Molinari, H.1    Ragona, L.2    Varani, L.3    Musco, G.4    Consonni, R.5    Zetta, L.6    Monaco, H.L.7
  • 17
    • 0032475891 scopus 로고    scopus 로고
    • Monomeric bovine β-lactoglobulin adopts a β-barrel fold at pH 2
    • DOI 10.1016/S0014-5793(98)00936-3, PII S0014579398009363
    • F. Fogolari, L. Ragona, L. Zetta, S. Romagnoli, K.G. De Kruif, H. Molinari, Monomeric bovine beta-lactoglobulin adopts a beta-barrel fold at pH 2, FEBS Lett. 436 (1998) 149-154. (Pubitemid 28468545)
    • (1998) FEBS Letters , vol.436 , Issue.2 , pp. 149-154
    • Fogolari, F.1    Ragona, L.2    Zetta, L.3    Romagnoli, S.4    De Kruif, K.G.5    Molinari, H.6
  • 18
    • 0030635208 scopus 로고    scopus 로고
    • Identification of a conserved Hydrophobie cluster in partially folded bovine β-lactoglobulin at pH 2
    • L. Ragona, F. Pusterla, L. Zetta, H.L. Monaco, H. Molinari, Identification of a conserved hydrophobic cluster in partially folded bovine beta-lactoglobulin at pH 2, Fold. Des. 2 (1997) 281-290. (Pubitemid 127740550)
    • (1997) Folding and Design , vol.2 , Issue.5 , pp. 281-290
    • Ragona, L.1    Pusterla, F.2    Zetta, L.3    Monaco, H.L.4    Molinari, H.5
  • 19
    • 0032741871 scopus 로고    scopus 로고
    • Solution structure and dynamics of bovine β-lactoglobulin A
    • K. Kuwata, M. Hoshino, V. Forge, S. Era, C.A. Batt, Y. Goto, Solution structure and dynamics of bovine beta-lactoglobulin A, Protein Sci. 8 (1999) 2541-2545. (Pubitemid 29536426)
    • (1999) Protein Science , vol.8 , Issue.11 , pp. 2541-2545
    • Kuwata, K.1    Hoshino, M.2    Forge, V.3    Era, S.4    Batt, C.A.5    Goto, Y.6
  • 20
    • 0033135870 scopus 로고    scopus 로고
    • Equilibrium unfolding cd studies of bovine β-lactoglobulin and its 14- 52 fragment at acidic pH
    • DOI 10.1002/(SICI)1097-0282(199905)49:6<441::AID-BIP2>3.0.CO;2-A
    • L. Ragona, L. Confalonieri, L. Zetta, K.G. De Kruif, S. Mammi, E. Peggion, R. Longhi, H. Molinari, Equilibrium unfolding CD studies of bovine beta-lactoglobulin and its 14-52 fragment at acidic pH, Biopolymers 49 (1999) 441-450. (Pubitemid 29157356)
    • (1999) Biopolymers , vol.49 , Issue.6 , pp. 441-450
    • Ragona, L.1    Confalonieri, L.2    Zetta, L.3    De Kruif, K.G.4    Mammi, S.5    Peggion, E.6    Longhi, R.7    Molinari, H.8
  • 21
    • 0033527582 scopus 로고    scopus 로고
    • Unfolding and refolding of bovine β-lactoglobulin monitored by hydrogen exchange measurements
    • DOI 10.1006/jmbi.1999.3191
    • L. Ragona, F. Fogolari, S. Romagnoli, L. Zetta, J.L. Maubois, H. Molinari, Unfolding and refolding of bovine beta-lactoglobulin monitored by hydrogen exchange measurements, J. Mol. Biol. 293 (1999) 953-969. (Pubitemid 29527676)
    • (1999) Journal of Molecular Biology , vol.293 , Issue.4 , pp. 953-969
    • Ragona, L.1    Fogolari, F.2    Romagnoli, S.3    Zetta, L.4    Maubois, J.L.5    Molinari, H.6
  • 22
    • 67349093283 scopus 로고    scopus 로고
    • Structural dynamics and folding of beta-lactoglobulin probed by heteronuclear NMR
    • K. Sakurai, T. Konuma, M. Yagi, Y. Goto, Structural dynamics and folding of beta-lactoglobulin probed by heteronuclear NMR, Biochim. Biophys. Acta 1790 (2009) 527-537.
    • (2009) Biochim. Biophys. Acta , vol.1790 , pp. 527-537
    • Sakurai, K.1    Konuma, T.2    Yagi, M.3    Goto, Y.4
  • 24
    • 0035150938 scopus 로고    scopus 로고
    • Structural and kinetic characterization of early folding events in β-lactoglobulin
    • DOI 10.1038/84145
    • K. Kuwata, R. Shastry, H. Cheng, M. Hoshino, C.A. Batt, Y. Goto, H. Roder, Structural and kinetic characterization of early folding events in beta-lactoglobulin, Nat. Struct. Biol. 8 (2001) 151-155. (Pubitemid 32116068)
    • (2001) Nature Structural Biology , vol.8 , Issue.2 , pp. 151-155
    • Kuwata, K.1    Shastry, R.2    Cheng, H.3    Hoshino, M.4    Batt, C.A.5    Goto, Y.6    Roder, H.7
  • 25
    • 0034598947 scopus 로고    scopus 로고
    • Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix
    • V. Forge, M. Hoshino, K. Kuwata, M. Arai, K. Kuwajima, C.A. Batt, Y. Goto, Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix, J. Mol. Biol. 296 (2000) 1039-1051.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1039-1051
    • Forge, V.1    Hoshino, M.2    Kuwata, K.3    Arai, M.4    Kuwajima, K.5    Batt, C.A.6    Goto, Y.7
  • 26
    • 0038392577 scopus 로고    scopus 로고
    • Trehalose influence on beta-lactoglobulin stability and hydration by time resolved fluorescence
    • DOI 10.1046/j.1432-1033.2003.03621.x
    • L. D'Alfonso, M. Collini, G. Baldini, Trehalose influence on beta-lactoglobulin stability and hydration by time resolved fluorescence, Eur. J. Biochem. 270 (2003) 2497-2504. (Pubitemid 36645368)
    • (2003) European Journal of Biochemistry , vol.270 , Issue.11 , pp. 2497-2504
    • D'Alfonso, L.1    Collini, M.2    Baldini, G.3
  • 27
    • 0346668369 scopus 로고    scopus 로고
    • PH and ionic strength dependence of protein (Un)folding and ligand binding to bovine β-lactoglobulins A and B
    • DOI 10.1021/bi020493f
    • T. Beringhelli, I. Eberini, M. Galliano, A. Pedoto, M. Perduca, A. Sportiello, E. Fontana, H.L. Monaco, E. Gianazza, pH and ionic strength dependence of protein (un)folding and ligand binding to bovine beta-lactoglobulins A and B, Biochemistry-US 41 (2002) 15415-15422. (Pubitemid 36008153)
    • (2002) Biochemistry , vol.41 , Issue.51 , pp. 15415-15422
    • Beringhelli, T.1    Eberini, I.2    Galliano, M.3    Pedoto, A.4    Perduca, M.5    Sportiello, A.6    Fontana, E.7    Monaco, H.L.8    Gianazza, E.9
  • 28
    • 0034825616 scopus 로고    scopus 로고
    • 1: Structural differences between genetic variants A and B and features of the Tanford transition
    • DOI 10.1046/j.1432-1327.2001.01918.x
    • K.M. Oliveira, V.L. Valente-Mesquita, M.M. Botelho, L. Sawyer, S.T. Ferreira, I. Polikarpov, Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transition, Eur. J. Biochem. 268 (2001) 477-483. (Pubitemid 32862681)
    • (2001) European Journal of Biochemistry , vol.268 , Issue.2 , pp. 477-483
    • Oliveira, K.M.G.1    Valente-Mesquita, V.L.2    Botelho, M.M.3    Sawyer, L.4    Ferreira, S.T.5    Polikarpov, I.6
  • 29
    • 0000371745 scopus 로고
    • Do denaturants interact with aromatic-hydrocarbons in water
    • E.M. Duffy, P.J. Kowalczyk, W.L. Jorgensen, Do denaturants interact with aromatic-hydrocarbons in water, J. Am. Chem. Soc. 115 (1993) 9271-9275.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 9271-9275
    • Duffy, E.M.1    Kowalczyk, P.J.2    Jorgensen, W.L.3
  • 30
    • 32044466479 scopus 로고    scopus 로고
    • Urea parametrization for molecular dynamics simulations
    • A. Caballero-Herrera, L. Nilsson, Urea parametrization for molecular dynamics simulations, J. Mol. Struct.: Theochem 758 (2006) 139-148.
    • (2006) J. Mol. Struct.: Theochem , vol.758 , pp. 139-148
    • Caballero-Herrera, A.1    Nilsson, L.2
  • 32
    • 35748935079 scopus 로고    scopus 로고
    • Wordom: A program for efficient analysis of molecular dynamics simulations
    • DOI 10.1093/bioinformatics/btm378
    • M. Seeber, M. Cecchini, F. Rao, G. Settanni, A. Caflisch, Wordom: a program for efficient analysis of molecular dynamics simulations, Bioinformatics 23 (2007) 2625-2627. (Pubitemid 350048368)
    • (2007) Bioinformatics , vol.23 , Issue.19 , pp. 2625-2627
    • Seeber, M.1    Cecchini, M.2    Rao, F.3    Settanni, G.4    Caflisch, A.5
  • 33
    • 0033134665 scopus 로고    scopus 로고
    • Structural details of urea binding to barnase: A molecular dynamics analysis
    • DOI 10.1016/S0969-2126(99)80064-1
    • A. Caflisch, M. Karplus, Structural details of urea binding to barnase: amolecular dynamics analysis, Structure 7 (1999) 477-488. (Pubitemid 29230482)
    • (1999) Structure , vol.7 , Issue.5 , pp. 477-488
    • Caflisch, A.1    Karplus, M.2
  • 35
    • 0035816223 scopus 로고    scopus 로고
    • Native-like β-hairpin retained in the cold-denatured state of bovine β-lactoglobulin
    • DOI 10.1006/jmbi.2001.4777
    • H. Katou, M. Hoshino, H. Kamikubo, C.A. Batt, Y. Goto, Native-like beta-hairpin retained in the cold-denatured state of bovine beta-lactoglobulin, J. Mol. Biol. 310 (2001) 471-484. (Pubitemid 32664880)
    • (2001) Journal of Molecular Biology , vol.310 , Issue.2 , pp. 471-484
    • Katou, H.1    Hoshino, M.2    Kamikubo, H.3    Batt, C.A.4    Goto, Y.5
  • 36
    • 0037176830 scopus 로고    scopus 로고
    • Peptide models of folding initiation sites of bovine β- lactoglobulin: Identification of nativelike hydrophobic interactions involving G and H strands
    • DOI 10.1021/bi011615r
    • L. Ragona, M. Catalano, L. Zetta, R. Longhi, F. Fogolari, H. Molinari, Peptide models of folding initiation sites of bovine beta-lactoglobulin: identification of nativelike hydrophobic interactions involving G and H strands, Biochemistry- US 41 (2002) 2786-2796. (Pubitemid 34168948)
    • (2002) Biochemistry , vol.41 , Issue.8 , pp. 2786-2796
    • Ragona, L.1    Catalano, M.2    Zetta, L.3    Longhi, R.4    Fogolari, F.5    Molinari, H.6
  • 37
    • 0028168283 scopus 로고
    • Tryptophan-19 of beta-lactoglobulin, the only residue completely conserved in the lipocalin superfamily, is not essential for binding retinol, but relevant to stabilizing bound retinol and maintaining its structure
    • Y. Katakura, M. Totsuka, A. Ametani, S. Kaminogawa, Tryptophan-19 of beta-lactoglobulin, the only residue completely conserved in the lipocalin superfamily, is not essential for binding retinol, but relevant to stabilizing bound retinol and maintaining its structure, Biochim. Biophys. Acta 1207 (1994) 58-67.
    • (1994) Biochim. Biophys. Acta , vol.1207 , pp. 58-67
    • Katakura, Y.1    Totsuka, M.2    Ametani, A.3    Kaminogawa, S.4
  • 38
    • 77955365355 scopus 로고    scopus 로고
    • On the stability of chymotrypsin inhibitor 2 in a 10M urea solution. The role of interaction energies for urea-induced protein denaturation
    • M. Lindgren, P.O. Westlund, On the stability of chymotrypsin inhibitor 2 in a 10M urea solution. The role of interaction energies for urea-induced protein denaturation, Phys. Chem. Chem. Phys. 12 (2010) 9358-9366.
    • Phys. Chem. Chem. Phys. , vol.12 , Issue.2010 , pp. 9358-9366
    • Lindgren, M.1    Westlund, P.O.2
  • 39
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22 (1983) 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2


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