메뉴 건너뛰기




Volumn 58, Issue 2, 2005, Pages 439-449

Characterization of the denaturation of human α-lactalbumin in urea by molecular dynamics simulations

Author keywords

lactalbumin; GROMOS96; MD simulations; Molten globule; Protein folding; Urea

Indexed keywords

ALPHA LACTALBUMIN; UREA; WATER;

EID: 11344259541     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20287     Document Type: Article
Times cited : (34)

References (49)
  • 1
    • 0029124248 scopus 로고
    • Molten globule and protein folding
    • Ptitsyn OB. Molten globule and protein folding. Adv Prot Chem 1995;47:83-229.
    • (1995) Adv Prot Chem , vol.47 , pp. 83-229
    • Ptitsyn, O.B.1
  • 2
    • 0030059690 scopus 로고    scopus 로고
    • The molten globule state of α-lactalbumin
    • Kuwajima K. The molten globule state of α-lactalbumin. FASEB J 1996;10:102-109.
    • (1996) FASEB J , vol.10 , pp. 102-109
    • Kuwajima, K.1
  • 3
    • 0034581327 scopus 로고    scopus 로고
    • Role of the molten globule state in protein folding
    • Arai M, Kuwajima K. Role of the molten globule state in protein folding. Adv Protein Chem 2000;53:209-282.
    • (2000) Adv Protein Chem , vol.53 , pp. 209-282
    • Arai, M.1    Kuwajima, K.2
  • 5
    • 0001529088 scopus 로고
    • Quasielastic light scattering from human α-lactalbumin: Comparison of molecular dimensions in native and molten globule states
    • Gast K, Zirwer D, Welfle H, Bychkova V E, Ptitsyn OB. Quasielastic light scattering from human α-lactalbumin: comparison of molecular dimensions in native and molten globule states. Int J Biol Macromol 1986;8:231-236.
    • (1986) Int J Biol Macromol , vol.8 , pp. 231-236
    • Gast, K.1    Zirwer, D.2    Welfle, H.3    Bychkova, V.E.4    Ptitsyn, O.B.5
  • 7
    • 0028866620 scopus 로고
    • Different subdomains are most protected from hydrogen exchange in the molten globule and native states of human α-lactalbumin
    • Schulman BA, Redfield C, Peng ZY, Dobson CM, Kim PS. Different subdomains are most protected from hydrogen exchange in the molten globule and native states of human α-lactalbumin. J Mol Biol 1995;253:651-657.
    • (1995) J Mol Biol , vol.253 , pp. 651-657
    • Schulman, B.A.1    Redfield, C.2    Peng, Z.Y.3    Dobson, C.M.4    Kim, P.S.5
  • 8
    • 0028916267 scopus 로고
    • Local structural preferences in the α-lactalbumin molten globule
    • Peng ZY, Wu LC, Kim PS. Local structural preferences in the α-lactalbumin molten globule. Biochemistry 1995;34:3248-3252.
    • (1995) Biochemistry , vol.34 , pp. 3248-3252
    • Peng, Z.Y.1    Wu, L.C.2    Kim, P.S.3
  • 9
    • 0028952169 scopus 로고
    • Bipartite structure of the α-lactalbumin molten globule
    • Wu LC, Peng ZY, Kim PS. Bipartite structure of the α-lactalbumin molten globule. Nature Struct Biol 1995;2:281-286.
    • (1995) Nature Struct Biol , vol.2 , pp. 281-286
    • Wu, L.C.1    Peng, Z.Y.2    Kim, P.S.3
  • 12
    • 0344382167 scopus 로고
    • Characterization of unfolded and partially folded states of proteins by NMR spectroscopy
    • Nall BT, Dill KA, editors. Washington, DC: AAAS Publications
    • Dobson CM, Hanley C, Radford SE, Baum J, Evans PA. Characterization of unfolded and partially folded states of proteins by NMR spectroscopy. In: Nall BT, Dill KA, editors. Conformations and forces in protein folding. Washington, DC: AAAS Publications; 1991. p. 175-181.
    • (1991) Conformations and Forces in Protein Folding , pp. 175-181
    • Dobson, C.M.1    Hanley, C.2    Radford, S.E.3    Baum, J.4    Evans, P.A.5
  • 13
    • 0030768045 scopus 로고    scopus 로고
    • A residue-specific NMR view of the non-cooperative unfolding of a molten globule
    • Schulman B, Kim PS, Dobson CM, Redfield C. A residue-specific NMR view of the non-cooperative unfolding of a molten globule. Nature Struct Biol 1997;4:630-634.
    • (1997) Nature Struct Biol , vol.4 , pp. 630-634
    • Schulman, B.1    Kim, P.S.2    Dobson, C.M.3    Redfield, C.4
  • 14
    • 0024533979 scopus 로고
    • Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guinea pig α-lactalbumin
    • Baum J, Dobson CM, Evans PA, Hanley C. Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig α-lactalbumin. Biochemistry 1989;28:7-13.
    • (1989) Biochemistry , vol.28 , pp. 7-13
    • Baum, J.1    Dobson, C.M.2    Evans, P.A.3    Hanley, C.4
  • 15
    • 0037675760 scopus 로고    scopus 로고
    • Structural characterisation of the human alpha-lactalbumin molten globule at high temperature
    • Ramboarina S, Redfield C. Structural characterisation of the human alpha-lactalbumin molten globule at high temperature. J Mol Biol 2003;330:1177-1188.
    • (2003) J Mol Biol , vol.330 , pp. 1177-1188
    • Ramboarina, S.1    Redfield, C.2
  • 16
    • 0030939289 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea
    • Tirado-Rives J, Orozco M, Jorgensen WL. Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry 1997;36:7313-7329.
    • (1997) Biochemistry , vol.36 , pp. 7313-7329
    • Tirado-Rives, J.1    Orozco, M.2    Jorgensen, W.L.3
  • 17
    • 0033134665 scopus 로고    scopus 로고
    • Structural details of urea binding to barnase: A molecular dynamics analysis
    • Caflisch A, Karplus M. Structural details of urea binding to barnase: a molecular dynamics analysis. Struc Fold Des 1999;7:477-488.
    • (1999) Struc Fold Des , vol.7 , pp. 477-488
    • Caflisch, A.1    Karplus, M.2
  • 18
    • 0035865543 scopus 로고    scopus 로고
    • Molecular dynamics simulations of urea and thermal-induced denaturation of the S-peptide analogue
    • Zhang ZY, Zhu YJ, Shi YY. Molecular dynamics simulations of urea and thermal-induced denaturation of the S-peptide analogue. Biophys Chem 2001;89:145-162.
    • (2001) Biophys Chem , vol.89 , pp. 145-162
    • Zhang, Z.Y.1    Zhu, Y.J.2    Shi, Y.Y.3
  • 19
    • 0037343333 scopus 로고    scopus 로고
    • The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study
    • Tobi D, Elber R, Thirumalai D. The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study. Biopolymers 2003;68:359-369.
    • (2003) Biopolymers , vol.68 , pp. 359-369
    • Tobi, D.1    Elber, R.2    Thirumalai, D.3
  • 20
    • 0038370011 scopus 로고    scopus 로고
    • The molecular basis for the chemical denaturation of proteins by urea
    • Bennion BJ, Daggett V. The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci USA 2003;100:5142-5147.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 5142-5147
    • Bennion, B.J.1    Daggett, V.2
  • 21
    • 0032080534 scopus 로고    scopus 로고
    • Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect
    • Zou Q, Habermann-Rottinghaus SM, Murphy KP. Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect. Proteins 1998;31:107-115.
    • (1998) Proteins , vol.31 , pp. 107-115
    • Zou, Q.1    Habermann-Rottinghaus, S.M.2    Murphy, K.P.3
  • 22
    • 0032554078 scopus 로고    scopus 로고
    • Hydrophobic interactions in aqueous urea solutions with implications for the mechanism of protein denaturation
    • Wallqvist A, Covell DG, Thirumalai D. Hydrophobic interactions in aqueous urea solutions with implications for the mechanism of protein denaturation. J Amer Chem Soc 1998;120:427-428.
    • (1998) J Amer Chem Soc , vol.120 , pp. 427-428
    • Wallqvist, A.1    Covell, D.G.2    Thirumalai, D.3
  • 23
    • 0037442337 scopus 로고    scopus 로고
    • Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution
    • Mountain RD, Thirumalai D. Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Amer Chem Soc 2003;125:1950-1957.
    • (2003) J Amer Chem Soc , vol.125 , pp. 1950-1957
    • Mountain, R.D.1    Thirumalai, D.2
  • 24
    • 0024115760 scopus 로고    scopus 로고
    • Denaturation of globular-proteins by urea-breakdown of hydrogen or hydrophobic bonds
    • Kamoun PP. Denaturation of globular-proteins by urea-breakdown of hydrogen or hydrophobic bonds. Trends Biochem Sci 1998;13:424-425.
    • (1998) Trends Biochem Sci , vol.13 , pp. 424-425
    • Kamoun, P.P.1
  • 25
    • 0742286773 scopus 로고    scopus 로고
    • Computer simulations of urea-water mixtures: A test of force field parameters for use in biomolecular simulations
    • Smith LJ, Berendsen HJC, van Gunsteren WF. Computer simulations of urea-water mixtures: a test of force field parameters for use in biomolecular simulations. J Phys Chem A 2004;108:1065-1071.
    • (2004) J Phys Chem A , vol.108 , pp. 1065-1071
    • Smith, L.J.1    Berendsen, H.J.C.2    Van Gunsteren, W.F.3
  • 26
    • 1542743738 scopus 로고    scopus 로고
    • Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9M aqueous urea solution
    • Trzesniak D, van der Vegt NFA, van Gunsteren WF. Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9M aqueous urea solution. Phys Chem Chem Phys 2004;6:697-702.
    • (2004) Phys Chem Chem Phys , vol.6 , pp. 697-702
    • Trzesniak, D.1    Van Der Vegt, N.F.A.2    Van Gunsteren, W.F.3
  • 27
    • 0033548540 scopus 로고    scopus 로고
    • Side-chain conformational disorder in a molten globule: Molecular dynamics simulations of the A-state of human α-lactalbumin
    • Smith LJ, Dobson CM, van Gunsteren WF. Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human α-lactalbumin. J Mol Biol 1999;286:1567-1580.
    • (1999) J Mol Biol , vol.286 , pp. 1567-1580
    • Smith, L.J.1    Dobson, C.M.2    Van Gunsteren, W.F.3
  • 28
    • 0032538350 scopus 로고    scopus 로고
    • Peptide models of local and long-range interactions in the molten globule state of human alpha-lactalbumin
    • Demarest SJ, Fairman R, Raleigh DP. Peptide models of local and long-range interactions in the molten globule state of human alpha-lactalbumin. J Mol Biol 1998;283:279-291.
    • (1998) J Mol Biol , vol.283 , pp. 279-291
    • Demarest, S.J.1    Fairman, R.2    Raleigh, D.P.3
  • 29
    • 0033584978 scopus 로고    scopus 로고
    • Defining the core structure of the alpha-lactalbumin molten globule state
    • Demarest SJ, Boice JA, Fairman R, Raleigh DP. Defining the core structure of the alpha-lactalbumin molten globule state. J Mol Biol 1999;294:213-221.
    • (1999) J Mol Biol , vol.294 , pp. 213-221
    • Demarest, S.J.1    Boice, J.A.2    Fairman, R.3    Raleigh, D.P.4
  • 31
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman B, editor. Dordrecht, The Netherlands: Reidel
    • Berendsen HJC, Postma, JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht, The Netherlands: Reidel; 1981 p. 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 34
    • 0742268867 scopus 로고    scopus 로고
    • Viscometric and volumetric studies of some amino acids in binary aqueous solutions of urea at various temperatures
    • Pal A, Kumar S. Viscometric and volumetric studies of some amino acids in binary aqueous solutions of urea at various temperatures. J Mol Liq 2004;109:23-31.
    • (2004) J Mol Liq , vol.109 , pp. 23-31
    • Pal, A.1    Kumar, S.2
  • 36
    • 33646940952 scopus 로고
    • Numerical intergration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical intergration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 37
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics-methodology, applications, and perspectives in chemistry
    • van Gunsteren WF, Berendsen HJC. Computer simulation of molecular dynamics-methodology, applications, and perspectives in chemistry. Angew Chem Int Ed Eng 1990;29:992-1023.
    • (1990) Angew Chem Int Ed Eng , vol.29 , pp. 992-1023
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 38
    • 2242491482 scopus 로고
    • Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300K
    • Smith PE, van Gunsteren WF. Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300K. J Chem Phys 1994;100:3169-3174.
    • (1994) J Chem Phys , vol.100 , pp. 3169-3174
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 39
    • 0003742069 scopus 로고
    • Departments of Biochemistry and Molecular Biology, University College London
    • Hubbard SJ, Thornton JM. NACCESS computer program. Departments of Biochemistry and Molecular Biology, University College London 1993.
    • (1993) NACCESS Computer Program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 40
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 41
    • 0033168453 scopus 로고    scopus 로고
    • Molecular dynamics simulations of human alpha-lactalbumin: Changes to the structural and dynamical properties of the protein at low pH
    • Smith LJ, Dobson CM, van Gunsteren WF. Molecular dynamics simulations of human alpha-lactalbumin: Changes to the structural and dynamical properties of the protein at low pH. Proteins 1999;36:77-86.
    • (1999) Proteins , vol.36 , pp. 77-86
    • Smith, L.J.1    Dobson, C.M.2    Van Gunsteren, W.F.3
  • 42
    • 0026509005 scopus 로고
    • X-ray structural evidence for a local helix-loop transition in α-lactalbumin
    • Harata K, Muraki M. X-ray structural evidence for a local helix-loop transition in α-lactalbumin. J Biol Chem 1992;267:1419-1421.
    • (1992) J Biol Chem , vol.267 , pp. 1419-1421
    • Harata, K.1    Muraki, M.2
  • 43
    • 0028774041 scopus 로고
    • Solution structure of a peptide fragment of human alpha-lactalbumin in trifluoroethanol - A model for local structure in the molten globule
    • Smith LJ, Alexandrescu AT, Pitkeathly M, Dobson CM. Solution structure of a peptide fragment of human alpha-lactalbumin in trifluoroethanol - a model for local structure in the molten globule. Structure 1994;2:703-712.
    • (1994) Structure , vol.2 , pp. 703-712
    • Smith, L.J.1    Alexandrescu, A.T.2    Pitkeathly, M.3    Dobson, C.M.4
  • 44
    • 0029894160 scopus 로고    scopus 로고
    • A synthetic peptide study on the molten globule of alpha-lactalbumin
    • Shimizu A, Ikeguchi M, Kobayashi T, Sugai S. A synthetic peptide study on the molten globule of alpha-lactalbumin. J Biochem 1996;119:947-952.
    • (1996) J Biochem , vol.119 , pp. 947-952
    • Shimizu, A.1    Ikeguchi, M.2    Kobayashi, T.3    Sugai, S.4
  • 45
    • 0034141812 scopus 로고    scopus 로고
    • Solution structure of a peptide model of a region important for the folding of alpha-lactalbumin provides evidence for the formation of non-native structure in the denatured state
    • Demarest SJ, Raleigh DP. Solution structure of a peptide model of a region important for the folding of alpha-lactalbumin provides evidence for the formation of non-native structure in the denatured state. Proteins 2000;38:189-196.
    • (2000) Proteins , vol.38 , pp. 189-196
    • Demarest, S.J.1    Raleigh, D.P.2
  • 47
    • 0033153245 scopus 로고    scopus 로고
    • Local interactions drive the formation of nonnative structure in the denatured state of human alpha-lactalbumin: A high resolution structural characterization of a peptide model in aqueous solution
    • Demarest SJ, Hua YX, Raleigh DP. Local interactions drive the formation of nonnative structure in the denatured state of human alpha-lactalbumin: A high resolution structural characterization of a peptide model in aqueous solution. Biochemistry 1999;38: 7380-7387.
    • (1999) Biochemistry , vol.38 , pp. 7380-7387
    • Demarest, S.J.1    Hua, Y.X.2    Raleigh, D.P.3
  • 48
    • 0034696753 scopus 로고    scopus 로고
    • Hierarchical unfolding of the alpha-lactalbumin molten globule: Presence of a compact intermediate without a unique tertiary fold
    • Chakraborty S, Peng ZY. Hierarchical unfolding of the alpha-lactalbumin molten globule: Presence of a compact intermediate without a unique tertiary fold. J Mol Biol 2000;298:1-6.
    • (2000) J Mol Biol , vol.298 , pp. 1-6
    • Chakraborty, S.1    Peng, Z.Y.2
  • 49
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ. Molscript: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991;24:946-950.
    • (1991) J Appl Cryst , vol.24 , pp. 946-950
    • Kraulis, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.