메뉴 건너뛰기




Volumn 99, Issue 6, 2010, Pages 1949-1958

Mapping conformational ensembles of aβ oligomers in molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77957329138     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.07.008     Document Type: Article
Times cited : (41)

References (50)
  • 1
    • 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
  • 2
    • 0037135111 scopus 로고    scopus 로고
    • The amyloid hypothesis of alzheimer's disease: Progress and problems on the road to therapeutics
    • Hardy, J., and D. J. Selkoe. 2002. The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science. 297: 353-356.
    • (2002) Science , vol.297 , pp. 353-356
    • Hardy, J.1    Selkoe, D.J.2
  • 3
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson, C. M. 2003. Protein folding and misfolding. Nature. 426: 884-890.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 4
    • 0036708168 scopus 로고    scopus 로고
    • Paradigm shifts in alzheimer's disease and other neurodegenerative disorders: The emerging role of oligomeric assemblies
    • Kirkitadze, M. D., G. Bitan, and D. B. Teplow. 2002. Paradigm shifts in Alzheimer's disease and other neurodegenerative disorders: the emerging role of oligomeric assemblies. J. Neurosci. Res. 69: 567-577.
    • (2002) J. Neurosci. Res. , vol.69 , pp. 567-577
    • Kirkitadze, M.D.1    Bitan, G.2    Teplow, D.B.3
  • 5
    • 0036407227 scopus 로고    scopus 로고
    • Peptide aggregation in neurodegenerative disease
    • Murphy, R. M. 2002. Peptide aggregation in neurodegenerative disease. Annu. Rev. Biomed. Eng. 4: 155-174.
    • (2002) Annu. Rev. Biomed. Eng. , vol.4 , pp. 155-174
    • Murphy, R.M.1
  • 6
    • 20444440728 scopus 로고    scopus 로고
    • Structure of the cross-b spine of amyloid-like fibrils
    • Nelson, R., M. R. Sawaya, D. Eisenberg. 2005. Structure of the cross-b spine of amyloid-like fibrils. Nature. 435: 773-778.
    • (2005) Nature , vol.435 , pp. 773-778
    • Nelson, R.1    Sawaya, M.R.2    Eisenberg, D.3
  • 7
    • 12244285938 scopus 로고    scopus 로고
    • Molecular basis for amyloid fibril formation and stability
    • Makin, O. S., E. Atkins, L. C. Serpell. 2005. Molecular basis for amyloid fibril formation and stability. Proc. Natl. Acad. Sci. USA. 102: 315-320.
    • (2005) Proc. Natl. Acad. Sci. USA. , vol.102 , pp. 315-320
    • Makin, O.S.1    Atkins, E.2    Serpell, L.C.3
  • 8
    • 34548291359 scopus 로고    scopus 로고
    • Surface structure of amyloid-b fibrils contributes to cytotoxicity
    • Yoshiike, Y., T. Akagi, and A. Takashima. 2007. Surface structure of amyloid-b fibrils contributes to cytotoxicity. Biochemistry. 46: 9805-9812.
    • (2007) Biochemistry , vol.46 , pp. 9805-9812
    • Yoshiike, Y.1    Akagi, T.2    Takashima, A.3
  • 9
    • 0242668337 scopus 로고    scopus 로고
    • Common structure of soluble amyloid oligomers implies common mechanism of pathogen-esis
    • Kayed, R., E. Head, C. G. Glabe. 2003. Common structure of soluble amyloid oligomers implies common mechanism of pathogen-esis. Science. 300: 486-489.
    • (2003) Science , vol.300 , pp. 486-489
    • Kayed, R.1    Head, E.2    Glabe, C.G.3
  • 10
    • 33847662852 scopus 로고    scopus 로고
    • Soluble protein oligomers in neuro-degeneration: Lessons from the alzheimer's amyloid b-peptide
    • Haass, C., and D. J. Selkoe. 2007. Soluble protein oligomers in neuro-degeneration: lessons from the Alzheimer's amyloid b-peptide. Nat. Rev. Mol. Cell Biol. 8: 101-112.
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 101-112
    • Haass, C.1    Selkoe, D.J.2
  • 11
    • 49149124343 scopus 로고    scopus 로고
    • Amyloid-b protein dimers isolated directly fromalzheimer's brains impairsy napticplasticity and memory
    • Shankar, G. M., S. Li, D. J. Selkoe. 2008. Amyloid-b protein dimers isolateddirectlyfromAlzheimer's brains impairsynapticplasticityand memory. Nat. Med. 14: 837-842.
    • (2008) Nat. Med. , vol.14 , pp. 837-842
    • Shankar, G.M.1    Li, D.J.2    Selkoe, S.3
  • 12
    • 23144459082 scopus 로고    scopus 로고
    • Molecular recycling with in amyloid fibrils
    • Carulla, N., G. L. Caddy, C. M. Dobson. 2005. Molecularrecycling within amyloid fibrils. Nature. 436: 554-558.
    • (2005) Nature , vol.436 , pp. 554-558
    • Carulla, N.1    Caddy, G.L.2    Dobson, C.M.3
  • 13
    • 0033863220 scopus 로고    scopus 로고
    • Activation barriers to structural transition determine deposition rates of alzheimer's disease a beta amyloid
    • Esler, W. P., A. M. Felix, J. E. Maggio. 2000. Activation barriers to structural transition determine deposition rates of Alzheimer's disease a beta amyloid. J. Struct. Biol. 130: 174-183.
    • (2000) J. Struct. Biol. , vol.130 , pp. 174-183
    • Esler, W.P.1    Felix, A.M.2    Maggio, J.E.3
  • 14
    • 0035173352 scopus 로고    scopus 로고
    • NMR studies in aqueous solution fail to identify significant conformational differences between the monomeric forms of two alzheimer peptides with widely different plaque-competence, a β(1-40)(ox) and a β(1-42)(ox)
    • Riek, R., P. Güntert, ...,K. Wüthrich. 2001. NMR studies in aqueous solution fail to identify significant conformational differences between the monomeric forms of two Alzheimer peptides with widely different plaque-competence, A β(1-40)(ox) and A β(1-42)(ox). Eur. J. Biochem. 268: 5930-5936.
    • (2001) Eur. J. Biochem. , vol.268 , pp. 5930-5936
    • Riek, R.1    Güntert, P.2    Wüthrich, K.3
  • 15
    • 10744219665 scopus 로고    scopus 로고
    • Solution NMR studies of the a β(1-40) and a β(1-42) peptides establish that the met35 oxidation state affects the mechanism of amyloid formation
    • Hou, L., H. Shao, M. G. Zagorski. 2004. Solution NMR studies of the A β(1-40) and A β(1-42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formation. J. Am. Chem. Soc. 126: 1992-2005.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 1992-2005
    • Hou, L.1    Shao, H.2    Zagorski, M.G.3
  • 16
  • 17
    • 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
  • 18
    • 28444442999 scopus 로고    scopus 로고
    • 3d structure of alzheimers amyloid-β(1-42) fibrils
    • Luhrs, T., C. Ritter, R. Riek. 2005. 3D structure of Alzheimers amyloid-β(1-42) fibrils. Proc. Natl. Acad. Sci. USA. 102: 17342-17347.
    • (2005) Proc. Natl. Acad. Sci. USA. , vol.102 , pp. 17342-17347
    • Luhrs, T.1    Ritter, C.2    Riek, R.3
  • 19
    • 13444310701 scopus 로고    scopus 로고
    • Characterization of chemical exchange between soluble and aggregated states of β-amyloid by solution-state NMR upon variation of salt conditions
    • Narayanan, S., and B. Reif. 2005. Characterization of chemical exchange between soluble and aggregated states of β-amyloid by solution-state NMR upon variation of salt conditions. Biochemistry. 44: 1444-1452.
    • (2005) Biochemistry , vol.44 , pp. 1444-1452
    • Narayanan, S.1    Reif, B.2
  • 20
    • 70349295278 scopus 로고    scopus 로고
    • Structure-neurotox-icity relationships of amyloid β-protein oligomers
    • Ono, K., M. M. Condron, and D. B. Teplow. 2009. Structure-neurotox-icity relationships of amyloid β-protein oligomers. Proc. Natl. Acad. Sci. USA. 106: 14745-14750.
    • (2009) Proc. Natl. Acad. Sci. USA. , vol.106 , pp. 14745-14750
    • Ono, K.1    Condron, M.M.2    Teplow, D.B.3
  • 21
    • 33748689799 scopus 로고    scopus 로고
    • Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    • Ma, B., and R. Nussinov. 2006. Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr. Opin. Chem. Biol. 10: 445-452.
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 445-452
    • Ma, B.1    Nussinov, R.2
  • 22
    • 34247234602 scopus 로고    scopus 로고
    • The alzheimer's peptides AB40 and 42 adopt distinct conformations in water: A combined MD/NMR study
    • Sgourakis, N. G., Y. Yan, A. E. Garcia. 2007. The Alzheimer's peptides Ab40 and 42 adopt distinct conformations in water: a combined MD/NMR study. J. Mol. Biol. 368: 1448-1457.
    • (2007) J. Mol. Biol. , vol.368 , pp. 1448-1457
    • Sgourakis, N.G.1    Yan, Y.2    Garcia, A.E.3
  • 23
    • 84954358028 scopus 로고    scopus 로고
    • Amyloid β-protein monomer folding: Free-energy surfaces reveal alloform-specific differences
    • Yang, M., and D. B. Teplow. 2008. Amyloid β-protein monomer folding: free-energy surfaces reveal alloform-specific differences. J. Mol. Biol. 384: 450-464.
    • (2008) J. Mol. Biol. , vol.384 , pp. 450-464
    • Yang, M.1    Teplow, D.B.2
  • 24
    • 33644821609 scopus 로고    scopus 로고
    • A molecular dynamics approach to the structural characterization of amyloid aggregation
    • Cecchini, M., R. Curcio, 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    Caflisch, A.3
  • 25
    • 33748121600 scopus 로고    scopus 로고
    • Folding landscapes of the alzheimer amyloid-β(12-28) peptide
    • Baumketner, A., and J.-E. Shea. 2006. Folding landscapes of the Alzheimer amyloid-β(12-28) peptide. J. Mol. Biol. 362: 567-579.
    • (2006) J. Mol. Biol. , vol.362 , pp. 567-579
    • Baumketner, A.1    Shea, J.-E.2
  • 26
    • 66149189211 scopus 로고    scopus 로고
    • Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
    • Lu, Y., P. Derreumaux, G. Wei. 2009. Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent. Proteins. 75: 954-963.
    • (2009) Proteins , vol.75 , pp. 954-963
    • Lu, Y.1    Derreumaux, P.2    Wei, G.3
  • 27
    • 70349246463 scopus 로고    scopus 로고
    • In silico study of full-length amyloid β 1-42 tri-and penta-oligomers in solution
    • Masman, M. F., U. L. M. Eisel, P. G. Luiten. 2009. In silico study of full-length amyloid β 1-42 tri-and penta-oligomers in solution. J. Phys. Chem. B. 113: 11710-11719.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 11710-11719
    • Masman, M.F.1    Eisel, U.L.M.2    Luiten, P.G.3
  • 28
    • 69549145714 scopus 로고    scopus 로고
    • Interpeptide interactions induce helix to strand structural transition in aβ peptides
    • Takeda, T., and D. K. Klimov. 2009. Interpeptide interactions induce helix to strand structural transition in Aβ peptides. Proteins. 77: 1-13.
    • (2009) Proteins , vol.77 , pp. 1-13
    • Takeda, T.1    Klimov, D.K.2
  • 29
    • 66749092410 scopus 로고    scopus 로고
    • Structures and thermodynamics of alzheimer's amyloid-beta aβ(16-35) monomer and dimer by replica exchange molecular dynamics simulations: Implication for full-length aβ fibrillation
    • Chebaro, Y., N. Mousseau, and P. Derreumaux. 2009. Structures and thermodynamics of Alzheimer's amyloid-beta Aβ(16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Aβ fibrillation. J. Phys. Chem. B. 113: 7668-7675.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 7668-7675
    • Chebaro, Y.1    Mousseau, N.2    Derreumaux, P.3
  • 30
    • 56849108519 scopus 로고    scopus 로고
    • The alzheimer beta-amyloid (aβ (1-39)) dimer in an implicit solvent
    • Anand, P., F. S. Nandel, and U. H. E. Hansmann. 2008. The Alzheimer beta-amyloid (Aβ (1-39)) dimer in an implicit solvent. J. Chem. Phys. 129: 195102.
    • (2008) J. Chem. Phys. , vol.129 , pp. 195102
    • Anand, P.1    Nandel, F.S.2    Hansmann, U.H.E.3
  • 31
    • 77950219248 scopus 로고    scopus 로고
    • Elucidation of amyloid β-protein oligomerization mechanisms: Discrete molecular dynamics study
    • Urbanc, B., M. Betnel, D. B. Teplow. 2010. Elucidation of amyloid β-protein oligomerization mechanisms: discrete molecular dynamics study. J. Am. Chem. Soc. 132: 4266-4280.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 4266-4280
    • Urbanc, B.1    Betnel, M.2    Teplow, D.B.3
  • 32
    • 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
  • 33
    • 0041816383 scopus 로고    scopus 로고
    • Elucidation of primary structure elements controlling early amyloid β-protein oligomeriza-tion
    • Bitan, G., S. S. Vollers, and D. B. Teplow. 2003. Elucidation of primary structure elements controlling early amyloid β-protein oligomeriza-tion. J. Biol. Chem. 278: 34882-34889.
    • (2003) J. Biol. Chem. , vol.278 , pp. 34882-34889
    • Bitan, G.1    Vollers, S.S.2    Teplow, D.B.3
  • 34
    • 67650079408 scopus 로고    scopus 로고
    • Probing the effect of amino-terminal truncation for aβ1-40 peptides
    • Takeda, T., and D. K. Klimov. 2009. Probing the effect of amino-terminal truncation for Aβ1-40 peptides. J. Phys. Chem. B. 113: 6692-6702.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 6692-6702
    • Takeda, T.1    Klimov, D.K.2
  • 35
    • 84986512474 scopus 로고
    • Charmm: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B. R., R. E. Bruccoleri, M. Karplus. 1982. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4: 187-217.
    • (1982) J. Comput. Chem. , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Karplus, M.3
  • 36
    • 0036138028 scopus 로고    scopus 로고
    • Evaluation of a fast implicit solvent model for molecular dynamics simulations
    • Ferrara, P., J. Apostolakis, and A. Caflisch. 2002. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins. 46: 24-33.
    • (2002) Proteins , vol.46 , pp. 24-33
    • Ferrara, P.1    Apostolakis, J.2    Caflisch, A.3
  • 37
    • 68949122827 scopus 로고    scopus 로고
    • Probing energetics of aβ fibril elongation by molecular dynamics simulations
    • Takeda, T., and D. K. Klimov. 2009. Probing energetics of Aβ fibril elongation by molecular dynamics simulations. Biophys. J. 96: 4428-4437.
    • (2009) Biophys. J. , vol.96 , pp. 4428-4437
    • Takeda, T.1    Klimov, D.K.2
  • 38
    • 69549113121 scopus 로고    scopus 로고
    • Side chain interactions can impede amyloid fibril growth: Replica exchange simulations of aβ peptide mutant
    • Takeda, T., and D. K. Klimov. 2009. Side chain interactions can impede amyloid fibril growth: replica exchange simulations of Aβ peptide mutant. J. Phys. Chem. B. 113: 11848-11857.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 11848-11857
    • Takeda, T.1    Klimov, D.K.2
  • 39
    • 0034718553 scopus 로고    scopus 로고
    • Folding simulations of a three-stranded antiparallel β-sheet peptide
    • Ferrara, P., and A. Caflisch. 2000. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. USA. 97: 10780-10785.
    • (2000) Proc. Natl. Acad. Sci. USA. , vol.97 , pp. 10780-10785
    • Ferrara, P.1    Caflisch, A.2
  • 40
    • 0034324385 scopus 로고    scopus 로고
    • Free energy surface of the helical peptide y(meara)6
    • Hiltpold, A., P. Ferrara, A. Caflisch. 2000. Free energy surface of the helical peptide Y(MEARA)6. J. Phys. Chem. B. 104: 10080-10086.
    • (2000) J. Phys. Chem. B. , vol.104 , pp. 10080-10086
    • Hiltpold, A.1    Ferrara, P.2    Caflisch, A.3
  • 41
    • 10844230140 scopus 로고    scopus 로고
    • Replica exchange molecular dynamics simulations of amyloid peptide aggregation
    • Cecchini, M., F. Rao, A. Caflisch. 2004. Replica exchange molecular dynamics simulations of amyloid peptide aggregation. J. Chem. Phys. 121: 10748-10756.
    • (2004) J. Chem. Phys. , vol.121 , pp. 10748-10756
    • Cecchini, M.1    Rao, F.2    Caflisch, A.3
  • 42
    • 58849114585 scopus 로고    scopus 로고
    • Replica exchange simulations of the thermodynamics of aβ fibril growth
    • Takeda, T., and D. K. Klimov. 2009. Replica exchange simulations of the thermodynamics of Aβ fibril growth. Biophys. J. 96: 442-452.
    • (2009) Biophys. J. , vol.96 , pp. 442-452
    • Takeda, T.1    Klimov, D.K.2
  • 43
    • 77953584016 scopus 로고    scopus 로고
    • Globular state in the oligomers formed by aβ peptides
    • Kim, S., T. Takeda, and D. K. Klimov. 2010. Globular state in the oligomers formed by Aβ peptides. J. Chem. Phys. 132: 225101.
    • (2010) J. Chem. Phys. , vol.132 , pp. 225101
    • Kim, S.1    Takeda, T.2    Klimov, D.K.3
  • 44
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 114: 141-151.
    • (1999) Chem. Phys. Lett. , vol.114 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 45
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 46
    • 33646987405 scopus 로고
    • Optimized monte carlo data analysis
    • Ferrenberg, A. M., and R. H. Swendsen. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63: 1195-1198.
    • (1989) Phys. Rev. Lett. , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 47
    • 77950671357 scopus 로고    scopus 로고
    • Computational backbone muta-genesis of aβ peptides: Probing the role of backbone hydrogen bonds in aggregation
    • Takeda, T., and D. K. Klimov. 2010. Computational backbone muta-genesis of Aβ peptides: probing the role of backbone hydrogen bonds in aggregation. J. Phys. Chem. B. 114: 4755-4762.
    • (2010) J. Phys. Chem. B. , vol.114 , pp. 4755-4762
    • Takeda, T.1    Klimov, D.K.2
  • 48
    • 28844441969 scopus 로고    scopus 로고
    • Secondary structure of α-synuclein oligomers: Characterization by raman and atomic force microscopy
    • Apetri, M. M., N. C. Maiti, V. E. Anderson. 2006. Secondary structure of α-synuclein oligomers: characterization by Raman and atomic force microscopy. J. Mol. Biol. 355: 63-71.
    • (2006) J. Mol. Biol. , vol.355 , pp. 63-71
    • Apetri, M.M.1    Maiti, N.C.2    Anderson, V.E.3
  • 49
    • 63649103441 scopus 로고    scopus 로고
    • Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations
    • Mo, Y., Y. Lu, P. Derreumaux. 2009. Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations. J. Chem. Phys. 130: 125101.
    • (2009) J. Chem. Phys. , vol.130 , pp. 125101
    • Mo, Y.1    Lu Derreumaux P, Y.2
  • 50
    • 4444221565 scopus 로고    scopus 로고
    • Ucsf chimera-a visualization system for exploratory research and analysis
    • Pettersen, E. F., T. D. Goddard, T. E. Ferrin. 2004. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605-1612.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1    Goddard, T.D.2    Ferrin, T.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.