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Volumn 92, Issue 9, 2007, Pages 3032-3039

Structure and dynamics of parallel β-sheets, hydrophobic core, and loops in Alzheimer's Aβ fibrils

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN; SOLVENT;

EID: 34247637243     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.100404     Document Type: Article
Times cited : (118)

References (60)
  • 1
    • 0028170818 scopus 로고
    • Cell biology of the amyloid beta-protein precursor and the mechanism of Alzheimer's disease
    • Selkoe, D. J. 1994. Cell biology of the amyloid beta-protein precursor and the mechanism of Alzheimer's disease. Annu. Rev. Cell Biol. 10:373-403.
    • (1994) Annu. Rev. Cell Biol , vol.10 , pp. 373-403
    • Selkoe, D.J.1
  • 2
    • 1342324027 scopus 로고    scopus 로고
    • Progress towards a molecular-level structural understanding of amyloid fibrils
    • Tycko, R. 2004. Progress towards a molecular-level structural understanding of amyloid fibrils. Curr. Opin. Struct. Biol. 14:96-103.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 96-103
    • Tycko, R.1
  • 3
    • 0031825554 scopus 로고    scopus 로고
    • From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation
    • Sunde, M., and C. C. F. Blake. 1998. From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Q. Rev. Biophys. 31:1-39.
    • (1998) Q. Rev. Biophys , vol.31 , pp. 1-39
    • Sunde, M.1    Blake, C.C.F.2
  • 4
    • 0037551741 scopus 로고    scopus 로고
    • Protofibrils, pores, fibrils, and neurodegeneration: Separating the responsible protein aggregates from the innocent bystanders
    • Caughey, B., and P. T. Lansbury. 2003. Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu. Rev. Neurosci. 26:267-298.
    • (2003) Annu. Rev. Neurosci , vol.26 , pp. 267-298
    • Caughey, B.1    Lansbury, P.T.2
  • 9
    • 0033555275 scopus 로고    scopus 로고
    • Solution structures of micelle-bound amyloid β-(1-40) and β-(1-42) peptides of Alzheimer's disease
    • Shao, H. Y., S. C. Jao, K. Ma, and M. G. Zagorski. 1999. Solution structures of micelle-bound amyloid β-(1-40) and β-(1-42) peptides of Alzheimer's disease. J. Mol. Biol. 285:755-773.
    • (1999) J. Mol. Biol , vol.285 , pp. 755-773
    • Shao, H.Y.1    Jao, S.C.2    Ma, K.3    Zagorski, M.G.4
  • 11
    • 30744433878 scopus 로고    scopus 로고
    • Experimental constraints on quaternary structure in Alzheimer's β-amyloid fibrils
    • Petkova, A. T., W. M. Yau, and R. Tycko. 2006. Experimental constraints on quaternary structure in Alzheimer's β-amyloid fibrils. Biochemistry. 45:498-512.
    • (2006) Biochemistry , vol.45 , pp. 498-512
    • Petkova, A.T.1    Yau, W.M.2    Tycko, R.3
  • 12
    • 26844435756 scopus 로고    scopus 로고
    • Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments
    • Buchete, N. V., R. Tycko, and G. Hummer. 2005. Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments. J. Mol. Biol. 353:804-821.
    • (2005) J. Mol. Biol , vol.353 , pp. 804-821
    • Buchete, N.V.1    Tycko, R.2    Hummer, G.3
  • 13
    • 12244249201 scopus 로고    scopus 로고
    • Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils
    • Petkova, A. T., R. D. Leapman, Z. H. Guo, W. M. Yau, M. P. Mattson, and R. Tycko. 2005. Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils. Science. 307:262-265.
    • (2005) Science , vol.307 , pp. 262-265
    • Petkova, A.T.1    Leapman, R.D.2    Guo, Z.H.3    Yau, W.M.4    Mattson, M.P.5    Tycko, R.6
  • 14
    • 0037457928 scopus 로고    scopus 로고
    • Probing the role of backbone hydrogen bonding in beta-amyloid fibrils with inhibitor peptides containing ester bonds at alternate positions
    • Gordon, D. J., and S. C. Meredith. 2003. Probing the role of backbone hydrogen bonding in beta-amyloid fibrils with inhibitor peptides containing ester bonds at alternate positions. Biochemistry. 42:475-485.
    • (2003) Biochemistry , vol.42 , pp. 475-485
    • Gordon, D.J.1    Meredith, S.C.2
  • 15
    • 33747113591 scopus 로고    scopus 로고
    • Spatial separation of β-sheet domains of β-amyloid: Disruption of each β-sheet by N-methyl amino acids
    • Sciarretta, K. L., A. Boire, D. J. Gordon, and S. C. Meredith. 2006. Spatial separation of β-sheet domains of β-amyloid: disruption of each β-sheet by N-methyl amino acids. Biochemistry. 45:9485-9495.
    • (2006) Biochemistry , vol.45 , pp. 9485-9495
    • Sciarretta, K.L.1    Boire, A.2    Gordon, D.J.3    Meredith, S.C.4
  • 18
    • 33745165393 scopus 로고    scopus 로고
    • Molecular self-assembly of peptide nanostructures: Mechanism of association and potential uses
    • Reches, M., and E. Gazit. 2006. Molecular self-assembly of peptide nanostructures: mechanism of association and potential uses. Curr. Nanosci. 2:105-111.
    • (2006) Curr. Nanosci , vol.2 , pp. 105-111
    • Reches, M.1    Gazit, E.2
  • 20
    • 4444346811 scopus 로고    scopus 로고
    • Kinetic control of dimer structure formation in amyloid fibrillogenesis
    • Hwang, W., S. Zhang, R. D. Kamm, and M. Karplus. 2004. Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc. Natl. Acad. Sci. USA. 101:12916-12921.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12916-12921
    • Hwang, W.1    Zhang, S.2    Kamm, R.D.3    Karplus, M.4
  • 22
    • 11844255790 scopus 로고    scopus 로고
    • 10-35-protein: Assessing the propensity for peptide dimerization
    • 10-35-protein: assessing the propensity for peptide dimerization. J. Mol. Biol. 345:1141-1156.
    • (2005) J. Mol. Biol , vol.345 , pp. 1141-1156
    • Tarus, B.1    Straub, J.E.2    Thirumalai, D.3
  • 23
    • 0037337271 scopus 로고    scopus 로고
    • Dissecting the assembly of Aβ(16-22) amyloid peptides into antiparallel β sheets
    • Klimov, D. K., and D. Thirumalai. 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
    • Klimov, D.K.1    Thirumalai, D.2
  • 24
    • 33644536691 scopus 로고    scopus 로고
    • Atomic-level description of amyloid beta-dimer formation
    • Gnanakaran, S., R. Nussinov, and A. E. García. 2006. Atomic-level description of amyloid beta-dimer formation. J. Am. Chem. Soc. 128:2158-2159.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 2158-2159
    • Gnanakaran, S.1    Nussinov, R.2    García, A.E.3
  • 25
    • 33646192684 scopus 로고    scopus 로고
    • The stability of monomeric intermediates controls amyloid formation: Aβ25-35 and its N27Q mutant
    • Ma, B. Y., and R. Nussinov. 2006. The stability of monomeric intermediates controls amyloid formation: Aβ25-35 and its N27Q mutant. Biophys. J. 90:3365-3374.
    • (2006) Biophys. J , vol.90 , pp. 3365-3374
    • Ma, B.Y.1    Nussinov, R.2
  • 26
    • 15244350752 scopus 로고    scopus 로고
    • Influence of denatured and intermediate states of folding on protein aggregation
    • Fawzi, N. L., V. Chubukov, L. A. Clark, S. Brown, and T. Head-Gordon. 2005. Influence of denatured and intermediate states of folding on protein aggregation. Protein Sci. 14:993-1003.
    • (2005) Protein Sci , vol.14 , pp. 993-1003
    • Fawzi, N.L.1    Chubukov, V.2    Clark, L.A.3    Brown, S.4    Head-Gordon, T.5
  • 27
    • 0036228167 scopus 로고    scopus 로고
    • Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics
    • Dima, R. I., and D. Thirumalai. 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
  • 29
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • Nguyen, H. D., and C. K. Hall. 2004. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA. 101:16180-16185.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16180-16185
    • Nguyen, H.D.1    Hall, C.K.2
  • 30
    • 0033040551 scopus 로고    scopus 로고
    • An atomic model for the pleated β-sheet structure of Aβ amyloid protofilaments
    • Li, L., T. A. Darden, L. Bartolotti, D. Kominos, and L. G. Pedersen. 1999. An atomic model for the pleated β-sheet structure of Aβ amyloid protofilaments. Biophys. J. 76:2871-2878.
    • (1999) Biophys. J , vol.76 , pp. 2871-2878
    • Li, L.1    Darden, T.A.2    Bartolotti, L.3    Kominos, D.4    Pedersen, L.G.5
  • 31
    • 33644821609 scopus 로고    scopus 로고
    • A molecular dynamics approach to the structural characterization of amyloid aggregation
    • Cecchini, M., R. Curcio, M. Pappalardo, R. Melki, and A. Caflisch. 2006. A molecular dynamics approach to the structural characterization of amyloid aggregation. J. Mol. Biol. 357:1306-1321.
    • (2006) J. Mol. Biol , vol.357 , pp. 1306-1321
    • Cecchini, M.1    Curcio, R.2    Pappalardo, M.3    Melki, R.4    Caflisch, A.5
  • 32
    • 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 R. Nussinov. 2002. 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. USA. 99:14126-14131.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14126-14131
    • Ma, B.Y.1    Nussinov, R.2
  • 34
    • 33645513980 scopus 로고    scopus 로고
    • Theoretical approaches to protein aggregation
    • Gsponer, J., and M. Vendruscolo. 2006. Theoretical approaches to protein aggregation. Protein Pept. Lett. 13:287-293.
    • (2006) Protein Pept. Lett , vol.13 , pp. 287-293
    • Gsponer, J.1    Vendruscolo, M.2
  • 35
    • 33751516713 scopus 로고    scopus 로고
    • Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abetal-40 peptide
    • Fawzi, N. L., Y. Okabe, E.-H. Yap, and T. Head-Gordon. 2007. Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abetal-40 peptide. J. Mol. Biol. 365:535-550.
    • (2007) J. Mol. Biol , vol.365 , pp. 535-550
    • Fawzi, N.L.1    Okabe, Y.2    Yap, E.-H.3    Head-Gordon, T.4
  • 37
    • 33744831968 scopus 로고    scopus 로고
    • Polymorphic fibril formation by residues 10-40 of the Alzheimer's β-amyloid peptide
    • Paravastu, A. K., A. T. Petkova, and R. Tycko. 2006. Polymorphic fibril formation by residues 10-40 of the Alzheimer's β-amyloid peptide. Biophys. J. 90:4618-4629.
    • (2006) Biophys. J , vol.90 , pp. 4618-4629
    • Paravastu, A.K.1    Petkova, A.T.2    Tycko, R.3
  • 39
    • 33646088595 scopus 로고    scopus 로고
    • Probing the pressure-temperature stability of amyloid fibrils provides new insights into their molecular properties
    • Meersman, F., and C. M. Dobson. 2006. Probing the pressure-temperature stability of amyloid fibrils provides new insights into their molecular properties. BBA Proteins Proteom. 1764:452-460.
    • (2006) BBA Proteins Proteom , vol.1764 , pp. 452-460
    • Meersman, F.1    Dobson, C.M.2
  • 42
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, W. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
    • MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, W. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
  • 44
    • 36449003554 scopus 로고
    • Constant-pressure molecular-dynamics algorithms
    • Martyna, G. J., D. J. Tobias, and M. L. Klein. 1994. Constant-pressure molecular-dynamics algorithms. J. Chem. Phys. 101:4177-4189.
    • (1994) J. Chem. Phys , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 45
    • 36449007836 scopus 로고
    • Constant-pressure molecular-dynamics simulation - the Langevin piston method
    • Feller, S. E., Y. H. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant-pressure molecular-dynamics simulation - the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 46
    • 33846823909 scopus 로고
    • Particle-mesh Ewald - An Nlog(N) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 1993. Particle-mesh Ewald - An Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
    • (1993) J. Chem. Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 47
    • 33646940952 scopus 로고
    • Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 48
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • Li, A. J., and V. Daggett. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:412-429.
    • (1996) J. Mol. Biol , vol.257 , pp. 412-429
    • Li, A.J.1    Daggett, V.2
  • 49
    • 0036081257 scopus 로고    scopus 로고
    • Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant
    • Massi, F., D. Klimov, D. Thirumalai, and J. E. Straub. 2002. Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci. 11:1639-1647.
    • (2002) Protein Sci , vol.11 , pp. 1639-1647
    • Massi, F.1    Klimov, D.2    Thirumalai, D.3    Straub, J.E.4
  • 50
    • 0037397705 scopus 로고    scopus 로고
    • Emerging ideas on the molecular basis of protein and peptide aggregation
    • Thirumalai, D., D. K. Klimov, and R. I. Dima. 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
  • 51
    • 7244253098 scopus 로고    scopus 로고
    • Proteins associated with diseases show enhanced sequence correlation between charged residues
    • Dima, R. I., and D. Thirumalai. 2004. Proteins associated with diseases show enhanced sequence correlation between charged residues. Bioinformatics. 20:2345-2354.
    • (2004) Bioinformatics , vol.20 , pp. 2345-2354
    • Dima, R.I.1    Thirumalai, D.2
  • 52
    • 1242269712 scopus 로고    scopus 로고
    • Architecture of the Alzheimer's AβP ion channel pore
    • Arispe, N. 2004. Architecture of the Alzheimer's AβP ion channel pore. J. Membr. Biol. 197:33-48.
    • (2004) J. Membr. Biol , vol.197 , pp. 33-48
    • Arispe, N.1
  • 54
    • 22144455300 scopus 로고    scopus 로고
    • Surface behavior and lipid interaction of Alzheimer β-amyloid peptide 1-42: A membrane-disrupting peptide
    • Ambroggio, E. E., D. H. Kim, F. Separovic, C. J. Barrow, K. J. Barnham, L. A. Bagatolli, and G. D. Fidelio. 2005. Surface behavior and lipid interaction of Alzheimer β-amyloid peptide 1-42: a membrane-disrupting peptide. Biophys. J. 88:2706-2713.
    • (2005) Biophys. J , vol.88 , pp. 2706-2713
    • Ambroggio, E.E.1    Kim, D.H.2    Separovic, F.3    Barrow, C.J.4    Barnham, K.J.5    Bagatolli, L.A.6    Fidelio, G.D.7
  • 55
    • 0041825430 scopus 로고    scopus 로고
    • Mixtures of wild-type and a pathogenic (E22G) form of Aβ40 in vitro accumulate protofibrils, including amyloid pores
    • Lashuel, H. A., D. Hartley, B. M. Petre, J. S. Wall, M. N. Simon, T. Walz, and P. T. Lansbury. 2003. Mixtures of wild-type and a pathogenic (E22G) form of Aβ40 in vitro accumulate protofibrils, including amyloid pores. J. Mol. Biol. 332:795-808.
    • (2003) J. Mol. Biol , vol.332 , pp. 795-808
    • Lashuel, H.A.1    Hartley, D.2    Petre, B.M.3    Wall, J.S.4    Simon, M.N.5    Walz, T.6    Lansbury, P.T.7
  • 57
    • 17644397372 scopus 로고    scopus 로고
    • Aβ40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid
    • Sciarretta, K. L., D. J. Gordon, A. T. Petkova, R. Tycko, and S. C. Meredith. 2005. Aβ40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry. 44:6003-6014.
    • (2005) Biochemistry , vol.44 , pp. 6003-6014
    • Sciarretta, K.L.1    Gordon, D.J.2    Petkova, A.T.3    Tycko, R.4    Meredith, S.C.5
  • 58
    • 0035812658 scopus 로고    scopus 로고
    • Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis
    • Kirkitadze, M. D., M. M. Condron, and D. B. Teplow. 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
  • 59
    • 0020485895 scopus 로고
    • Orthogonal packing of β-pleated sheets in proteins
    • Chothia, C., and J. Janin. 1982. Orthogonal packing of β-pleated sheets in proteins. Biochemistry. 21:3955-3965.
    • (1982) Biochemistry , vol.21 , pp. 3955-3965
    • Chothia, C.1    Janin, J.2
  • 60
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman, D., and P. Argos. 1995. Knowledge-based protein secondary structure assignment. Proteins. 23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2


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