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Volumn 14, Issue 3, 2005, Pages 653-662

Protein aggregation determinants from a simplified model: Cooperative folders resist aggregation

Author keywords

Aggregate structure; Aggregation oligomers; Folding cooperativity; Protein aggregation; Protein simulation

Indexed keywords

MUTANT PROTEIN; OLIGOMER; PROTEIN G; PROTEIN L; UNCLASSIFIED DRUG;

EID: 14144256476     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041017305     Document Type: Article
Times cited : (24)

References (56)
  • 2
    • 0028865843 scopus 로고
    • 3D domain swapping - A mechanism for oligomer assembly
    • Bennett, M.J., Schlunegger, M.P., and Eisenberg, D. 1995. 3D domain swapping - A mechanism for oligomer assembly. Protein Sci. 4: 2455-2468.
    • (1995) Protein Sci. , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3
  • 3
    • 0035151879 scopus 로고    scopus 로고
    • Competition between protein folding and aggregation: A three-dimensional lattice-model simulation
    • Bratko, D. and Blanch, H.W. 2001. Competition between protein folding and aggregation: A three-dimensional lattice-model simulation. J. Chem. Phys. 114: 561-569.
    • (2001) J. Chem. Phys. , vol.114 , pp. 561-569
    • Bratko, D.1    Blanch, H.W.2
  • 4
    • 0037444764 scopus 로고    scopus 로고
    • On-lattice modeling of protein aggregation: The effect of secondary structure
    • _. 2003. On-lattice modeling of protein aggregation: The effect of secondary structure. J. Chem. Phys. 118: 5185-5194.
    • (2003) J. Chem. Phys. , vol.118 , pp. 5185-5194
  • 6
    • 0034598954 scopus 로고    scopus 로고
    • Nature disfavors sequences of alternating polar and non-polar amino acids: Implications for amyloidogenesis
    • Broome, B.M. and Hecht, M.H. 2000. Nature disfavors sequences of alternating polar and non-polar amino acids: Implications for amyloidogenesis. J. Mol. Biol. 296: 961-968.
    • (2000) J. Mol. Biol. , vol.296 , pp. 961-968
    • Broome, B.M.1    Hecht, M.H.2
  • 7
    • 1842454761 scopus 로고    scopus 로고
    • Intermediates and the folding of proteins L and G
    • Brown, S. and Head-Gordon, T. 2004. Intermediates and the folding of proteins L and G. Protein Sci. 13: 958-970.
    • (2004) Protein Sci. , vol.13 , pp. 958-970
    • Brown, S.1    Head-Gordon, T.2
  • 8
    • 0141480046 scopus 로고    scopus 로고
    • Coarse-grained sequences for protein folding and design
    • Brown, S., Fawzi, N.J., and Head-Gordon, T. 2003. Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci. 100: 10712-10717.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 10712-10717
    • Brown, S.1    Fawzi, N.J.2    Head-Gordon, T.3
  • 10
    • 0141567459 scopus 로고    scopus 로고
    • Physical stability of proteins in aqueous solution: Mechanism and driving forces in normative protein aggregation
    • Chi, E.Y., Krishnan, S., Randolph, T.W., and Carpenter, J.F. 2003. Physical stability of proteins in aqueous solution: Mechanism and driving forces in normative protein aggregation. Pharmaceutical Res. 20: 1325-1336.
    • (2003) Pharmaceutical Res. , vol.20 , pp. 1325-1336
    • Chi, E.Y.1    Krishnan, S.2    Randolph, T.W.3    Carpenter, J.F.4
  • 12
    • 0042467550 scopus 로고    scopus 로고
    • Rationalization of the effects of mutations on peptide and protein aggregation rates
    • Chiti, F., Stefani, M., Taddei, N., Ramponi, G., and Dobson, C.M. 2003. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424: 805-808.
    • (2003) Nature , vol.424 , pp. 805-808
    • Chiti, F.1    Stefani, M.2    Taddei, N.3    Ramponi, G.4    Dobson, C.M.5
  • 13
    • 0035313135 scopus 로고    scopus 로고
    • Protein refolding for industrial processes
    • Clark, E.D. 2001. Protein refolding for industrial processes. Curr. Opin. Struct. Biol. 12: 202-207.
    • (2001) Curr. Opin. Struct. Biol. , vol.12 , pp. 202-207
    • Clark, E.D.1
  • 14
    • 0036228167 scopus 로고    scopus 로고
    • Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics
    • Dima, R.I. and Thirumalai, D. 2002. Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics. Protein Sci. 11: 1036-1049.
    • (2002) Protein Sci. , vol.11 , pp. 1036-1049
    • Dima, R.I.1    Thirumalai, D.2
  • 15
    • 0036923039 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
    • Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., and Shakhnovich, E.I. 2002. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J. Mol. Biol. 324: 851-857.
    • (2002) J. Mol. Biol. , vol.324 , pp. 851-857
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 16
    • 0033121095 scopus 로고    scopus 로고
    • Factors that affect the folding ability of proteins
    • Dinner, A.R., Abkevich, V., Shakhnovich, E., and Karplus, M. 1999. Factors that affect the folding ability of proteins. Proteins 35: 34-40.
    • (1999) Proteins , vol.35 , pp. 34-40
    • Dinner, A.R.1    Abkevich, V.2    Shakhnovich, E.3    Karplus, M.4
  • 17
    • 0035961329 scopus 로고    scopus 로고
    • The structural basis of protein folding and its links with human disease
    • Dobson, C.M. 2001. The structural basis of protein folding and its links with human disease. Phil. Trans. R. Soc. Lond. B 356: 133-145.
    • (2001) Phil. Trans. R. Soc. Lond. B , vol.356 , pp. 133-145
    • Dobson, C.M.1
  • 18
    • 0035253217 scopus 로고    scopus 로고
    • Macromolecular crowding: An important but neglected aspect of the intracellular environment
    • Ellis, R.J. 2001. Macromolecular crowding: An important but neglected aspect of the intracellular environment. Curr. Opin. Struct. Biol. 11: 114-119.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 114-119
    • Ellis, R.J.1
  • 20
    • 4243819810 scopus 로고
    • New Monte Carlo technique for studying phase transitions
    • Ferrenberg, A.M. and Swendsen, R.H. 1988. New Monte Carlo technique for studying phase transitions. Phys. Rev. Lett. 61: 2635-2638.
    • (1988) Phys. Rev. Lett. , vol.61 , pp. 2635-2638
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 21
    • 0031932169 scopus 로고    scopus 로고
    • Protein aggregation: Folding aggregates, inclusion bodies and amyloid
    • Fink, A.L. 1998. Protein aggregation: Folding aggregates, inclusion bodies and amyloid. Fold. Des. 3: R9-R23.
    • (1998) Fold. Des. , vol.3
    • Fink, A.L.1
  • 22
    • 0037473750 scopus 로고    scopus 로고
    • Prevention of transthyretin amyloid disease by changing protein misfolding energetics
    • Hammarstrom, P., Wiseman, R.L., Powers, E.T., and Kelly, J.W. 2003. Prevention of transthyretin amyloid disease by changing protein misfolding energetics. Science 299: 713-716.
    • (2003) Science , vol.299 , pp. 713-716
    • Hammarstrom, P.1    Wiseman, R.L.2    Powers, E.T.3    Kelly, J.W.4
  • 23
    • 0033582587 scopus 로고    scopus 로고
    • Thermodynamics of model prions and its implications for the problem of prion protein folding
    • Harrison, P.M., Chan, H.S., Prusiner, S.B., and Cohen, F.E. 1999. Thermodynamics of model prions and its implications for the problem of prion protein folding. J. Mol. Biol. 286: 593-606.
    • (1999) J. Mol. Biol. , vol.286 , pp. 593-606
    • Harrison, P.M.1    Chan, H.S.2    Prusiner, S.B.3    Cohen, F.E.4
  • 24
    • 0035079856 scopus 로고    scopus 로고
    • Conformational propagation with prion-like characteristics in a simple model of protein folding
    • Harrison, P.M., Chan, H.S., Prusiner, S.B., and Cohen, F.E. 2001. Conformational propagation with prion-like characteristics in a simple model of protein folding. Protein Sci. 10: 819-835.
    • (2001) Protein Sci. , vol.10 , pp. 819-835
    • Harrison, P.M.1    Chan, H.S.2    Prusiner, S.B.3    Cohen, F.E.4
  • 25
    • 0036841958 scopus 로고    scopus 로고
    • Protein aggregation in disease: A role for folding intermediates forming specific multimeric interactions
    • Horwich, A. 2002. Protein aggregation in disease: A role for folding intermediates forming specific multimeric interactions. J. Clin. Invest. 110: 1221-1232.
    • (2002) J. Clin. Invest. , vol.110 , pp. 1221-1232
    • Horwich, A.1
  • 26
    • 0028305304 scopus 로고
    • A role for destabilizing amino-acid replacements in light-chain amyloidosis
    • Hurle, M.R., Helms, L.R., Li, L., Chan, W.N., and Wetzel, R. 1994. A role for destabilizing amino-acid replacements in light-chain amyloidosis. Proc. Natl. Acad. Sci. 91: 5446-5450.
    • (1994) Proc. Natl. Acad. Sci. , vol.91 , pp. 5446-5450
    • Hurle, M.R.1    Helms, L.R.2    Li, L.3    Chan, W.N.4    Wetzel, R.5
  • 27
    • 0032994142 scopus 로고    scopus 로고
    • Lattice simulations of aggregation funnels for protein folding
    • Istrail, S., Schwartz, R., and King, J. 1999. Lattice simulations of aggregation funnels for protein folding. J. Comp. Biol. 6: 143-162.
    • (1999) J. Comp. Biol. , vol.6 , pp. 143-162
    • Istrail, S.1    Schwartz, R.2    King, J.3
  • 29
    • 0033998280 scopus 로고    scopus 로고
    • A new approach to the design of uniquely folded thermally stable proteins
    • Jiang, X., Farid, H., Pistor, E., and Farid, R.S. 2000. A new approach to the design of uniquely folded thermally stable proteins. Protein Sci. 9: 403-416.
    • (2000) Protein Sci. , vol.9 , pp. 403-416
    • Jiang, X.1    Farid, H.2    Pistor, E.3    Farid, R.S.4
  • 30
    • 0242668337 scopus 로고    scopus 로고
    • Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
    • Kayed, R., Head, E., Thompson, J.L., Mcintire, T.M., Milton, S.C., Cotman, C.W., and Glabe, C.G. 2003. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300: 486-489.
    • (2003) Science , vol.300 , pp. 486-489
    • Kayed, R.1    Head, E.2    Thompson, J.L.3    Mcintire, T.M.4    Milton, S.C.5    Cotman, C.W.6    Glabe, C.G.7
  • 31
    • 0033793872 scopus 로고    scopus 로고
    • Mechanisms of amyloidogenesis
    • Kelly, J.W. 2000. Mechanisms of amyloidogenesis. Nat. Struct. Biol. 7: 824-826.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 824-826
    • Kelly, J.W.1
  • 32
    • 0035812658 scopus 로고    scopus 로고
    • Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis
    • Kirkitadze, M.D., Condron, M.M., and Teplow, D.B. 2001. Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis. J. Mol. Biol. 312: 1103-1119.
    • (2001) J. Mol. Biol. , vol.312 , pp. 1103-1119
    • Kirkitadze, M.D.1    Condron, M.M.2    Teplow, D.B.3
  • 33
    • 4243572706 scopus 로고    scopus 로고
    • Criterion that determines the foldability of proteins
    • Klimov, D.K. and Thirumalai, D. 1996. Criterion that determines the foldability of proteins. Phys. Rev. Lett. 76: 4070-4073.
    • (1996) Phys. Rev. Lett. , vol.76 , pp. 4070-4073
    • Klimov, D.K.1    Thirumalai, D.2
  • 34
    • 0001504441 scopus 로고    scopus 로고
    • Cooperatively in protein folding: From lattice models with sidechains to real proteins
    • _. 1998. Cooperatively in protein folding: From lattice models with sidechains to real proteins. Fold. Des. 3: 127-139.
    • (1998) Fold. Des. , vol.3 , pp. 127-139
  • 35
    • 0037337271 scopus 로고    scopus 로고
    • Dissecting the assembly of Aβ (16-22) amyloid peptides into antiparallel β sheets
    • _. 2003. Dissecting the assembly of Aβ (16-22) amyloid peptides into antiparallel β sheets. Structure 11: 295-307.
    • (2003) Structure , vol.11 , pp. 295-307
  • 36
    • 0033813424 scopus 로고    scopus 로고
    • A glimpse of a possible amyloidogenic intermediate of transthyretin
    • Liu, K., Cho, H.S., Lashuel, H.A., Kelly, J.W., and Wemmer, D.E. 2000. A glimpse of a possible amyloidogenic intermediate of transthyretin. Nat. Struct. Biol. 7: 754-757.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 754-757
    • Liu, K.1    Cho, H.S.2    Lashuel, H.A.3    Kelly, J.W.4    Wemmer, D.E.5
  • 37
    • 0035127031 scopus 로고    scopus 로고
    • A domain-swapped RNase a dimer with implications for amyloid formation
    • Liu, Y.S., Gotte, G., Libonati, M., and Eisenberg, D. 2001. A domain-swapped RNase a dimer with implications for amyloid formation. Nat. Struct. Biol. 8: 211-214.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 211-214
    • Liu, Y.S.1    Gotte, G.2    Libonati, M.3    Eisenberg, D.4
  • 38
    • 9044229145 scopus 로고    scopus 로고
    • On the nucleation and growth of amyloid β-protein fibrils: Detection of nuclei and quantitation of rate constants
    • Lomakin, A., Chung, D.S., Benedek, G.B., Kirschner, D.A., and Teplow, D.B. 1996. On the nucleation and growth of amyloid β-protein fibrils: Detection of nuclei and quantitation of rate constants. Proc. Natl. Acad. Sci. 93: 1125-1129.
    • (1996) Proc. Natl. Acad. Sci. , vol.93 , pp. 1125-1129
    • Lomakin, A.1    Chung, D.S.2    Benedek, G.B.3    Kirschner, D.A.4    Teplow, D.B.5
  • 39
    • 0037195098 scopus 로고    scopus 로고
    • Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ 16-22, Aβ 16-35, and Aβ 10-35): Sequence effects
    • Ma, B.Y. and Nussinov, R. 2002a. Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ 16-22, Aβ 16-35, and Aβ 10-35): Sequence effects. Proc. Natl. Acad. Sci. 99: 14126-14131.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 14126-14131
    • Ma, B.Y.1    Nussinov, R.2
  • 40
    • 0036784617 scopus 로고    scopus 로고
    • Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation
    • _. 2002b. Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation. Protein Sci. 11: 2335-2350.
    • (2002) Protein Sci. , vol.11 , pp. 2335-2350
  • 41
    • 0035815743 scopus 로고    scopus 로고
    • The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
    • Minton, A.P. 2001. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 276: 10577-10580.
    • (2001) J. Biol. Chem. , vol.276 , pp. 10577-10580
    • Minton, A.P.1
  • 42
    • 0346500469 scopus 로고    scopus 로고
    • The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process
    • Monti, M., Garolla di Bard, B.L., Calloni, G., Chili, F., Amoresano, A., Ramponi, G., and Pucci, P. 2004. The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process. J. Mol. Biol. 336: 253-262.
    • (2004) J. Mol. Biol. , vol.336 , pp. 253-262
    • Monti, M.1    Garolla Di Bard, B.L.2    Calloni, G.3    Chili, F.4    Amoresano, A.5    Ramponi, G.6    Pucci, P.7
  • 43
    • 0033869084 scopus 로고    scopus 로고
    • Characterization of the oligomeric states of insulin in self-assembly and amyloid fibril formation by mass spectrometry
    • Nettleton, E.J., Tito, P., Sunde, M., Bouchard, M., Dobson, C.M., and Robinson, C.V. 2000. Characterization of the oligomeric states of insulin in self-assembly and amyloid fibril formation by mass spectrometry. Biophys. J. 79: 1053-1065.
    • (2000) Biophys. J. , vol.79 , pp. 1053-1065
    • Nettleton, E.J.1    Tito, P.2    Sunde, M.3    Bouchard, M.4    Dobson, C.M.5    Robinson, C.V.6
  • 45
    • 0035190116 scopus 로고    scopus 로고
    • Single-site mutations induce 3D domain swapping in the B1 domain of protein 1 from Peptostreptococcus magnus
    • O'Neill, J.W., Kim, D.E., Johnsen, K., Baker, D., and Zhang, K.Y.J. 2001. Single-site mutations induce 3D domain swapping in the B1 domain of protein 1 from Peptostreptococcus magnus. Structure 9: 1017-1027.
    • (2001) Structure , vol.9 , pp. 1017-1027
    • O'Neill, J.W.1    Kim, D.E.2    Johnsen, K.3    Baker, D.4    Zhang, K.Y.J.5
  • 46
    • 0037421836 scopus 로고    scopus 로고
    • Kinetics of irreversible protein aggregation: Analysis of extended Lumry-Eyring models and implications for predicting protein shelf life
    • Roberts, C.J. 2003. Kinetics of irreversible protein aggregation: Analysis of extended Lumry-Eyring models and implications for predicting protein shelf life. J. Phys. Chem. B 107: 1194-1207.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 1194-1207
    • Roberts, C.J.1
  • 47
    • 0347987853 scopus 로고    scopus 로고
    • Folding proteins in fatal ways
    • Selkoe, D.J. 2003. Folding proteins in fatal ways. Nature 426: 900-904.
    • (2003) Nature , vol.426 , pp. 900-904
    • Selkoe, D.J.1
  • 48
    • 0035880742 scopus 로고    scopus 로고
    • Statistical mechanics of solvophobic aggregation: Additive and cooperative effects
    • Shimizu, S. and Chan, H.S. 2001. Statistical mechanics of solvophobic aggregation: Additive and cooperative effects. J. Chem. Phys. 115: 3424-3431.
    • (2001) J. Chem. Phys. , vol.115 , pp. 3424-3431
    • Shimizu, S.1    Chan, H.S.2
  • 49
    • 0035823222 scopus 로고    scopus 로고
    • Protein refolding versus aggregation: Computer simulations on an intermediate-resolution protein model
    • Smith, A.V. and Hall, C.K. 2001. Protein refolding versus aggregation: Computer simulations on an intermediate-resolution protein model. J. Mol. Biol. 312: 187-202.
    • (2001) J. Mol. Biol. , vol.312 , pp. 187-202
    • Smith, A.V.1    Hall, C.K.2
  • 50
    • 0032726519 scopus 로고    scopus 로고
    • Redesigning the hydrophobic core of a model β-sheet protein: Destabilizing traps through a threading approach
    • Sorenson, J.M. and Head-Gordon, T. 1999. Redesigning the hydrophobic core of a model β-sheet protein: Destabilizing traps through a threading approach. Proteins 37: 582-591.
    • (1999) Proteins , vol.37 , pp. 582-591
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 51
    • 14144252729 scopus 로고    scopus 로고
    • Matching simulation and experiment: A new simplified model for simulating protein folding
    • _. 2000. Matching simulation and experiment: A new simplified model for simulating protein folding. J. Comp. Biol. 7: 3-4.
    • (2000) J. Comp. Biol. , vol.7 , pp. 3-4
  • 52
    • 0036207492 scopus 로고    scopus 로고
    • Protein engineering study of protein 1 by simulation
    • _. 2002. Protein engineering study of protein 1 by simulation. J. Comp. Biol. 9: 35-54.
    • (2002) J. Comp. Biol. , vol.9 , pp. 35-54
  • 53
    • 0031021542 scopus 로고    scopus 로고
    • Conformation of P22 tailspike folding and aggregation intermediates probed by monoclonal antibodies
    • Speed, M.A., Morshead, T., Wang, D.I., and King, J. 1997. Conformation of P22 tailspike folding and aggregation intermediates probed by monoclonal antibodies. Protein Sci. 6: 99-108.
    • (1997) Protein Sci. , vol.6 , pp. 99-108
    • Speed, M.A.1    Morshead, T.2    Wang, D.I.3    King, J.4
  • 54
    • 3042584515 scopus 로고    scopus 로고
    • The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates
    • Tartaglia, G.G., Cavalli, A., Pellarin, R., and Caflisch, A. 2004. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Sci. 7: 1939-1941.
    • (2004) Protein Sci. , vol.7 , pp. 1939-1941
    • Tartaglia, G.G.1    Cavalli, A.2    Pellarin, R.3    Caflisch, A.4
  • 55
    • 0037397705 scopus 로고    scopus 로고
    • Emerging ideas on the molecular basis of protein and peptide aggregation
    • Thirumalai, D., Klimov, D.K., and Dima, R.I. 2003. Emerging ideas on the molecular basis of protein and peptide aggregation. Curr. Opin. Struct. Biol. 13: 146-159.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 146-159
    • Thirumalai, D.1    Klimov, D.K.2    Dima, R.I.3
  • 56
    • 0037041426 scopus 로고    scopus 로고
    • Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo
    • Walsh, D.M., Klyubin, I., Fadeeva, J.V., Cullen, W.K., Anwyl, R., Wolfe, M.S., Rowan, M.J., and Selkoe, D.J. 2002. Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416: 535-539.
    • (2002) Nature , vol.416 , pp. 535-539
    • Walsh, D.M.1    Klyubin, I.2    Fadeeva, J.V.3    Cullen, W.K.4    Anwyl, R.5    Wolfe, M.S.6    Rowan, M.J.7    Selkoe, D.J.8


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