메뉴 건너뛰기




Volumn 7, Issue 5, 2011, Pages

A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide gnnqqny from the yeast prion sup-35

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; GLYCOPROTEINS; MOLECULAR DYNAMICS; OLIGOMERS;

EID: 79958122197     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002051     Document Type: Article
Times cited : (75)

References (92)
  • 1
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid and human disease
    • Chiti F, Dobson CM, (2006) Protein misfolding, functional amyloid and human disease. Annu Rev Biochem 75: 333-366.
    • (2006) Annu Rev Biochem , vol.75 , pp. 333-366
    • Chiti, F.1    Dobson, C.M.2
  • 2
    • 3142514201 scopus 로고    scopus 로고
    • Protein aggregation and neurodegenerative disease
    • Ross CA, Poirier MA, (2004) Protein aggregation and neurodegenerative disease. Nat Med 10: S10-S17.
    • (2004) Nat Med , vol.10
    • Ross, C.A.1    Poirier, M.A.2
  • 3
    • 1842533373 scopus 로고    scopus 로고
    • Unzipping the mysteries of amyloid fibril formation
    • Miranker AD, (2004) Unzipping the mysteries of amyloid fibril formation. Proc Natl Acad Sci U S A 101: 4335-4336.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 4335-4336
    • Miranker, A.D.1
  • 4
    • 0036377156 scopus 로고    scopus 로고
    • Amyloid-fibril formation. Proposed mechanisms and relevance to conformational disease
    • Zerovnik E, (2002) Amyloid-fibril formation. Proposed mechanisms and relevance to conformational disease. Eur J Biochem 269: 3362-3371.
    • (2002) Eur J Biochem , vol.269 , pp. 3362-3371
    • Zerovnik, E.1
  • 5
    • 0033200063 scopus 로고    scopus 로고
    • Protein misfolding, evolution and disease
    • Dobson CM, (1999) Protein misfolding, evolution and disease. Trends Biochem Sci 24: 329-332.
    • (1999) Trends Biochem Sci , vol.24 , pp. 329-332
    • Dobson, C.M.1
  • 6
    • 34249290108 scopus 로고    scopus 로고
    • Atomic structures of amyloid cross-β spines reveal varied steric zippers
    • Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, et al. (2007) Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447: 453-457.
    • (2007) Nature , vol.447 , pp. 453-457
    • Sawaya, M.R.1    Sambashivan, S.2    Nelson, R.3    Ivanova, M.I.4    Sievers, S.A.5
  • 7
    • 20444440728 scopus 로고    scopus 로고
    • Structure of the cross-β spine of amyloid-like fibrils
    • Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, et al. (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435: 773-778.
    • (2005) Nature , vol.435 , pp. 773-778
    • Nelson, R.1    Sawaya, M.R.2    Balbirnie, M.3    Madsen, A.4    Riekel, C.5
  • 8
    • 0242668337 scopus 로고    scopus 로고
    • Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
    • Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, et al. (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
  • 9
    • 0037397705 scopus 로고    scopus 로고
    • Emerging ideas on the molecular basis of protein and peptide aggregation
    • Thirumalai D, Klimov DK, Dima RI, (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
  • 10
    • 0031592945 scopus 로고    scopus 로고
    • Common structure of amyloid fibrils by synchrotron X-ray diffraction
    • Sunde M, Serpell LC, Bartlam M, Fraser PE, Pepys MB, et al. (1997) Common structure of amyloid fibrils by synchrotron X-ray diffraction. J Mol Biol 273: 729-739.
    • (1997) J Mol Biol , vol.273 , pp. 729-739
    • Sunde, M.1    Serpell, L.C.2    Bartlam, M.3    Fraser, P.E.4    Pepys, M.B.5
  • 11
    • 70349568356 scopus 로고    scopus 로고
    • Structural polymorphism of Alzheimer Aβ and other amyloid fibrils
    • Fändrich M, Meinhardt J, Grigorieff N, (2009) Structural polymorphism of Alzheimer Aβ and other amyloid fibrils. Prion 3: 89-93.
    • (2009) Prion , vol.3 , pp. 89-93
    • Fändrich, M.1    Meinhardt, J.2    Grigorieff, N.3
  • 12
    • 68249093598 scopus 로고    scopus 로고
    • A triple emission fluorescent probe reveals distinctive amyloid fibrillar polymorphism of wild-type α-synuclein and its familial Parkinsons disease-mutants
    • Celej MS, Caarls W, Demchenko AP, Jovin TM, (2009) A triple emission fluorescent probe reveals distinctive amyloid fibrillar polymorphism of wild-type α-synuclein and its familial Parkinsons disease-mutants. Biochem 48: 7465-7472.
    • (2009) Biochem , vol.48 , pp. 7465-7472
    • Celej, M.S.1    Caarls, W.2    Demchenko, A.P.3    Jovin, T.M.4
  • 13
    • 59649110455 scopus 로고    scopus 로고
    • Aβ(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils
    • Meinhardt J, Sachse C, Hortschansky P, Grigorieff N, Fändrich M, (2009) Aβ(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils. J Mol Biol 386: 869-877.
    • (2009) J Mol Biol , vol.386 , pp. 869-877
    • Meinhardt, J.1    Sachse, C.2    Hortschansky, P.3    Grigorieff, N.4    Fändrich, M.5
  • 14
    • 57449091884 scopus 로고    scopus 로고
    • Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils
    • Paravastu AK, Leapman RD, Yau WM, Tycko R, (2008) Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils. Proc Natl Acad Sci U S A 105: 18349-54.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 18349-18354
    • Paravastu, A.K.1    Leapman, R.D.2    Yau, W.M.3    Tycko, R.4
  • 15
    • 57349120654 scopus 로고    scopus 로고
    • Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction
    • Madine J, Jack E, Stockley PG, Radford SE, Serpell LC, et al. (2008) Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction. J Am Chem Soc 130: 14990-5001.
    • (2008) J Am Chem Soc , vol.130 , pp. 14990-15001
    • Madine, J.1    Jack, E.2    Stockley, P.G.3    Radford, S.E.4    Serpell, L.C.5
  • 17
    • 33846160381 scopus 로고    scopus 로고
    • Polymorphism in the intermediates and products of amyloid assembly
    • Kodali R, Wetzel R, (2007) Polymorphism in the intermediates and products of amyloid assembly. Curr Opin Struct Biol 17: 48-57.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 48-57
    • Kodali, R.1    Wetzel, R.2
  • 18
    • 30744433878 scopus 로고    scopus 로고
    • Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils
    • Petkova AT, Yau WM, Tycko R, (2006) Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. Biochem 45: 498-512.
    • (2006) Biochem , vol.45 , pp. 498-512
    • Petkova, A.T.1    Yau, W.M.2    Tycko, R.3
  • 19
    • 33845637320 scopus 로고    scopus 로고
    • From the polymorphism of amyloid fibrils to their assembly mechanism and cytotoxicity
    • Kreplak L, Aebi U, (2006) From the polymorphism of amyloid fibrils to their assembly mechanism and cytotoxicity. Adv Protein Chem 73: 217-33.
    • (2006) Adv Protein Chem , vol.73 , pp. 217-233
    • Kreplak, L.1    Aebi, U.2
  • 20
    • 33646093028 scopus 로고    scopus 로고
    • Polymorphism and ultrastructural organizations of prion protein amyloid fibrils: an insight from high-resolution atomic force microscopy
    • Anderson M, Bocharova OV, Makarava N, Breydo L, Salnikov VV, et al. (2006) Polymorphism and ultrastructural organizations of prion protein amyloid fibrils: an insight from high-resolution atomic force microscopy. J Mol Biol 358: 580-96.
    • (2006) J Mol Biol , vol.358 , pp. 580-596
    • Anderson, M.1    Bocharova, O.V.2    Makarava, N.3    Breydo, L.4    Salnikov, V.V.5
  • 21
    • 12244249201 scopus 로고    scopus 로고
    • Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils
    • Petkova AT, Leapman RD, Guo WM, Mattson MP, Tycko R, (2005) Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils. Science 307: 262-5.
    • (2005) Science , vol.307 , pp. 262-265
    • Petkova, A.T.1    Leapman, R.D.2    Guo, W.M.3    Mattson, M.P.4    Tycko, R.5
  • 22
    • 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, Lu Y, Wei G, Derreumaux P, (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, Y.2    Wei, G.3    Derreumaux, P.4
  • 23
    • 70349658765 scopus 로고    scopus 로고
    • Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine
    • Park J, Kahng B, Hwang W, (2009) Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine. PLoS Comput Biol 5: e1000492.
    • (2009) PLoS Comput Biol , vol.5
    • Park, J.1    Kahng, B.2    Hwang, W.3
  • 24
    • 68849107584 scopus 로고    scopus 로고
    • Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation
    • Berryman JT, Radford SE, Harris SA, (2009) Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation. Biophys J 97: 1-11.
    • (2009) Biophys J , vol.97 , pp. 1-11
    • Berryman, J.T.1    Radford, S.E.2    Harris, S.A.3
  • 25
    • 2542455537 scopus 로고    scopus 로고
    • Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease
    • Klein WL, Stine WB, Teplow DB, (2004) Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease. Neurobiol Aging 25: 569-580.
    • (2004) Neurobiol Aging , vol.25 , pp. 569-580
    • Klein, W.L.1    Stine, W.B.2    Teplow, D.B.3
  • 26
    • 0037041420 scopus 로고    scopus 로고
    • Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases
    • Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, et al. (2002) Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416: 507-511.
    • (2002) Nature , vol.416 , pp. 507-511
    • Bucciantini, M.1    Giannoni, E.2    Chiti, F.3    Baroni, F.4    Formigli, L.5
  • 27
    • 49149124343 scopus 로고    scopus 로고
    • Amyloid-β protein dimers isolated directly from Alzheimer's brains impair synaptic plasticity and memory
    • Shankar GM, Li S, Mehta TH, Garcia-Munoz A, Shepardson NE, et al. (2008) Amyloid-β protein dimers isolated directly from Alzheimer's brains impair synaptic plasticity and memory. Nat Med 14: 837-842.
    • (2008) Nat Med , vol.14 , pp. 837-842
    • Shankar, G.M.1    Li, S.2    Mehta, T.H.3    Garcia-Munoz, A.4    Shepardson, N.E.5
  • 28
    • 70349295278 scopus 로고    scopus 로고
    • Structure-neurotoxicity relationships of amyloid beta-protein oligomers
    • Ono K, Condron MM, Teplow DB, (2009) Structure-neurotoxicity relationships of amyloid beta-protein oligomers. Proc Natl Acad Sci U S A 106: 14745-50.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 14745-14750
    • Ono, K.1    Condron, M.M.2    Teplow, D.B.3
  • 30
    • 0033771793 scopus 로고    scopus 로고
    • Is there a cause-and-effect relationship between alpha-synuclein fibrillization and Parkinson's disease?
    • Goldberg MS, Lansbury PT, (2000) Is there a cause-and-effect relationship between alpha-synuclein fibrillization and Parkinson's disease? Nature Cell Biol 2: E115-E119.
    • (2000) Nature Cell Biol , vol.2
    • Goldberg, M.S.1    Lansbury, P.T.2
  • 31
    • 0033616682 scopus 로고    scopus 로고
    • Evolution of amyloid: what normal protein folding may tell us about fibrillogenesis and disease
    • Lansbury PT, (1999) Evolution of amyloid: what normal protein folding may tell us about fibrillogenesis and disease. Proc Natl Acad Sci U S A 96: 3342-3344.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 3342-3344
    • Lansbury, P.T.1
  • 32
    • 46749113483 scopus 로고    scopus 로고
    • Annular structures as intermediates in fibril formation of Alzheimer's Aβ-17-42
    • Zheng J, Jang H, Ma B, Nussinov R, (2008) Annular structures as intermediates in fibril formation of Alzheimer's Aβ-17-42. J Phys Chem B 112: 6856-6865.
    • (2008) J Phys Chem B , vol.112 , pp. 6856-6865
    • Zheng, J.1    Jang, H.2    Ma, B.3    Nussinov, R.4
  • 34
    • 72149118250 scopus 로고    scopus 로고
    • An analytical solution to the kinetics of breakable filament assembly
    • Knowles TP, Waudby CA, Devlin GL, Cohen SI, Aguzzi A, et al. (2009) An analytical solution to the kinetics of breakable filament assembly. Science 326: 1533-1537.
    • (2009) Science , vol.326 , pp. 1533-1537
    • Knowles, T.P.1    Waudby, C.A.2    Devlin, G.L.3    Cohen, S.I.4    Aguzzi, A.5
  • 35
    • 0035956924 scopus 로고    scopus 로고
    • An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid
    • Balbirnie M, Grothe R, Eisenberg DS, (2001) An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid. Proc Natl Acad Sci U S A 98: 2375-2380.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 2375-2380
    • Balbirnie, M.1    Grothe, R.2    Eisenberg, D.S.3
  • 36
    • 0038690113 scopus 로고    scopus 로고
    • Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide
    • Diaz-Avalos R, Long C, Fontano E, Balbirnie M, Grothe R, et al. (2003) Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide. J Mol Biol 330: 1165-1175.
    • (2003) J Mol Biol , vol.330 , pp. 1165-1175
    • Diaz-Avalos, R.1    Long, C.2    Fontano, E.3    Balbirnie, M.4    Grothe, R.5
  • 37
    • 34247504580 scopus 로고    scopus 로고
    • Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p
    • Van der Wel PCA, Lewandowski JR, Griffin R G, (2006) Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p. J Am Chem Soc 129: 5117-5130.
    • (2006) J Am Chem Soc , vol.129 , pp. 5117-5130
    • van der Wel, P.C.A.1    Lewandowski, J.R.2    Griffin, R.G.3
  • 38
    • 52049119509 scopus 로고    scopus 로고
    • Self-assembly of amyloid-forming peptides using molecular dynamics simulations and the OPEP coarse-grained force field
    • Wei G, Song W, Derreumaux P, Mousseau N, (2008) Self-assembly of amyloid-forming peptides using molecular dynamics simulations and the OPEP coarse-grained force field. Frontiers in Biosciences 13: 5681-5692.
    • (2008) Frontiers in Biosciences , vol.13 , pp. 5681-5692
    • Wei, G.1    Song, W.2    Derreumaux, P.3    Mousseau, N.4
  • 39
    • 46449133376 scopus 로고    scopus 로고
    • Self-assembly of the beta2-microglobulin NHVTLSQ peptide using coarse-grained protein model reveals β-barrel species
    • Song W, Wei G, Mousseau N, Derreumaux P, (2008) Self-assembly of the beta2-microglobulin NHVTLSQ peptide using coarse-grained protein model reveals β-barrel species. J Phys Chem B 112: 4410-4418.
    • (2008) J Phys Chem B , vol.112 , pp. 4410-4418
    • Song, W.1    Wei, G.2    Mousseau, N.3    Derreumaux, P.4
  • 40
    • 40549089901 scopus 로고    scopus 로고
    • Spontaneous β-barrel formation: an all-atom Monte-Carlo study of Aβ-16-22 oligomerization
    • Irbäck A, Mitternacht S, (2007) Spontaneous β-barrel formation: an all-atom Monte-Carlo study of Aβ-16-22 oligomerization. Proteins 71: 207-214.
    • (2007) Proteins , vol.71 , pp. 207-214
    • Irbäck, A.1    Mitternacht, S.2
  • 41
    • 77952324067 scopus 로고    scopus 로고
    • Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent
    • De Simone A, Derreumaux P, (2010) Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent. J Chem Phys 132: 165103.
    • (2010) J Chem Phys , vol.132 , pp. 165103
    • De Simone, A.1    Derreumaux, P.2
  • 42
    • 61949163833 scopus 로고    scopus 로고
    • Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide
    • Periole X, Rampioni A, Vendruscolo M, Mark AE, (2009) Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. J Phys Chem B 113: 1728-1737.
    • (2009) J Phys Chem B , vol.113 , pp. 1728-1737
    • Periole, X.1    Rampioni, A.2    Vendruscolo, M.3    Mark, A.E.4
  • 43
    • 58149360794 scopus 로고    scopus 로고
    • All-atom simulations of amyloid fibrils disaggregation
    • Wang J, Tan C, Chen HF, Luo R, (2008) All-atom simulations of amyloid fibrils disaggregation. Biophys J 95: 5037-5047.
    • (2008) Biophys J , vol.95 , pp. 5037-5047
    • Wang, J.1    Tan, C.2    Chen, H.F.3    Luo, R.4
  • 44
    • 44849096158 scopus 로고    scopus 로고
    • Investigating the mechanism of peptide aggregation: Insights from mixed Monte-Carlo molecular dynamics simulations
    • Meli M, Morra G, Colombo G, (2008) Investigating the mechanism of peptide aggregation: Insights from mixed Monte-Carlo molecular dynamics simulations. Biophys J 94: 4414-4426.
    • (2008) Biophys J , vol.94 , pp. 4414-4426
    • Meli, M.1    Morra, G.2    Colombo, G.3
  • 45
    • 34548627237 scopus 로고    scopus 로고
    • Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35
    • Zhang Z, Chen H, Bai H, Lai L, (2007) Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35. Biophys J 93: 1484-1492.
    • (2007) Biophys J , vol.93 , pp. 1484-1492
    • Zhang, Z.1    Chen, H.2    Bai, H.3    Lai, L.4
  • 46
    • 37549055108 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of aggregation for the GNNQQNY peptide
    • Strodel B, Whittleston CS, Wales DJ, (2007) Thermodynamics and kinetics of aggregation for the GNNQQNY peptide. J Am Chem Soc 129: 16005-16014.
    • (2007) J Am Chem Soc , vol.129 , pp. 16005-16014
    • Strodel, B.1    Whittleston, C.S.2    Wales, D.J.3
  • 47
    • 77949612059 scopus 로고    scopus 로고
    • GNNQQNY-investigation of early steps during amyloid formation
    • Reddy AS, Chopra M, de Pablo JJ, (2010) GNNQQNY-investigation of early steps during amyloid formation. Biophys J 98: 1038-1045.
    • (2010) Biophys J , vol.98 , pp. 1038-1045
    • Reddy, A.S.1    Chopra, M.2    de Pablo, J.J.3
  • 48
    • 56349091416 scopus 로고    scopus 로고
    • Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association
    • Vitagliano L, Esposito L, Pedone C, De Simone A, (2008) Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association. Biochem Biophys Res Commun 377: 1036-1041.
    • (2008) Biochem Biophys Res Commun , vol.377 , pp. 1036-1041
    • Vitagliano, L.1    Esposito, L.2    Pedone, C.3    De Simone, A.4
  • 49
    • 33746765060 scopus 로고    scopus 로고
    • Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion Sup35
    • Zheng J, Ma B, Tsai CJ, Nussinov R, (2006) Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion Sup35. Biophys J 91: 824-833.
    • (2006) Biophys J , vol.91 , pp. 824-833
    • Zheng, J.1    Ma, B.2    Tsai, C.J.3    Nussinov, R.4
  • 50
    • 33746800825 scopus 로고    scopus 로고
    • Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation
    • Esposito L, Pedone C, Vitagliano L, (2006) Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation. Proc Natl Acad Sci U S A 103: 11533-11538.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 11533-11538
    • Esposito, L.1    Pedone, C.2    Vitagliano, L.3
  • 51
    • 0037627715 scopus 로고    scopus 로고
    • The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
    • Gsponer J, Haberthür U, Caflisch A, (2003) The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc Natl Acad Sci U S A 100: 5154-5159.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 5154-5159
    • Gsponer, J.1    Haberthür, U.2    Caflisch, A.3
  • 52
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y, (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314: 141-151.
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 53
    • 34548809141 scopus 로고    scopus 로고
    • A coarse-grained protein force field for folding and structure prediction
    • Maupetit J, Tufféry P, Derreumaux P, (2007) A coarse-grained protein force field for folding and structure prediction. Proteins 69: 394-408.
    • (2007) Proteins , vol.69 , pp. 394-408
    • Maupetit, J.1    Tufféry, P.2    Derreumaux, P.3
  • 54
    • 0001418816 scopus 로고    scopus 로고
    • From polypeptide sequences to structures using Monte-Carlo simulations and an optimized potential
    • Derreumaux P, (1999) From polypeptide sequences to structures using Monte-Carlo simulations and an optimized potential. J Chem Phys 111: 2301-2310.
    • (1999) J Chem Phys , vol.111 , pp. 2301-2310
    • Derreumaux, P.1
  • 55
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient load-balanced, scalable molecular simulation
    • Hess B, Kutzner C, Van Der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for highly efficient load-balanced, scalable molecular simulation. J Chem Theory Comput 4: 435-447.
    • (2008) J Chem Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 56
    • 33748277992 scopus 로고    scopus 로고
    • The conformations of the amyloid-beta(21-30) fragment can be described by three families in solution
    • Chen W, Mousseau N, Derreumaux P, (2006) The conformations of the amyloid-beta(21-30) fragment can be described by three families in solution. J Chem Phys 125: 084911.
    • (2006) J Chem Phys , vol.125 , pp. 084911
    • Chen, W.1    Mousseau, N.2    Derreumaux, P.3
  • 57
    • 45249089694 scopus 로고    scopus 로고
    • Role of the region 23-28 in Abeta fibril formation: insights from simulations of the monomers and dimmers of Alzheimer's peptides Abeta40 and Abeta42
    • Melquiond A, Dong X, Mousseau N, Derreumaux P, (2008) Role of the region 23-28 in Abeta fibril formation: insights from simulations of the monomers and dimmers of Alzheimer's peptides Abeta40 and Abeta42. Curr Alzheimer Res 5: 244-250.
    • (2008) Curr Alzheimer Res , vol.5 , pp. 244-250
    • Melquiond, A.1    Dong, X.2    Mousseau, N.3    Derreumaux, P.4
  • 58
    • 67849130555 scopus 로고    scopus 로고
    • PEP-FOLD: an online resource for de novo peptide structure prediction
    • Maupetit J, Derreumaux P, Tufféry P, (2009) PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res 37: W498-503.
    • (2009) Nucleic Acids Res , vol.37
    • Maupetit, J.1    Derreumaux, P.2    Tufféry, P.3
  • 59
    • 76249128506 scopus 로고    scopus 로고
    • A fast method for large-scale de novo peptide and miniprotein structure prediction
    • Maupetit J, Derreumaux P, Tufféry P, (2010) A fast method for large-scale de novo peptide and miniprotein structure prediction. J Comput Chem 31: 726-738.
    • (2010) J Comput Chem , vol.31 , pp. 726-738
    • Maupetit, J.1    Derreumaux, P.2    Tufféry, P.3
  • 61
    • 33846234246 scopus 로고    scopus 로고
    • Coarse-grained protein molecular dynamics simulations
    • Derreumaux P, Mousseau N, (2007) Coarse-grained protein molecular dynamics simulations. J Chem Phys 126: 025101.
    • (2007) J Chem Phys , vol.126 , pp. 025101
    • Derreumaux, P.1    Mousseau, N.2
  • 62
    • 61749091340 scopus 로고    scopus 로고
    • Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent
    • Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N, (2009) Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. J Phys Chem B 113: 267-274.
    • (2009) J Phys Chem B , vol.113 , pp. 267-274
    • Chebaro, Y.1    Dong, X.2    Laghaei, R.3    Derreumaux, P.4    Mousseau, N.5
  • 63
    • 0042622443 scopus 로고    scopus 로고
    • DSSPcont: Continuous secondary structure assignments for proteins
    • Carter P, Andersen CA, Rost B, (2003) DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res 31: 3293-3295.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3293-3295
    • Carter, P.1    Andersen, C.A.2    Rost, B.3
  • 64
    • 63649101084 scopus 로고    scopus 로고
    • Comparison between integrated and parallel tempering methods in enhanced sampling simulations
    • Yang L, Shao Q, Goa YQ, (2009) Comparison between integrated and parallel tempering methods in enhanced sampling simulations. J Chem Phys 130: 124111.
    • (2009) J Chem Phys , vol.130 , pp. 124111
    • Yang, L.1    Shao, Q.2    Goa, Y.Q.3
  • 65
    • 0025978283 scopus 로고
    • Database algorithm for generating protein backbone and side-chain co-ordinates from a C-alpha trace application to model building and detection of co-ordinate errors
    • Holm L, Sander C, (1991) Database algorithm for generating protein backbone and side-chain co-ordinates from a C-alpha trace application to model building and detection of co-ordinate errors. J Mol Biol 218: 183-194.
    • (1991) J Mol Biol , vol.218 , pp. 183-194
    • Holm, L.1    Sander, C.2
  • 66
    • 34250792960 scopus 로고    scopus 로고
    • IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models
    • Hartmann C, Antes I, Lengauer T, (2007) IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci 16: 294-1307.
    • (2007) Protein Sci , vol.16 , pp. 294-1307
    • Hartmann, C.1    Antes, I.2    Lengauer, T.3
  • 67
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack RL Jr, Cohen FE, (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 6: 1661-1681.
    • (1997) Protein Sci , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 70
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
    • Miyamoto S, Kollman PA, (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comp Chem 13: 952-962.
    • (1992) J Comp Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 71
    • 0029633168 scopus 로고
    • GROMACS: A message passing parallel molecular dynamics implementation
    • Berendsen HJC, van der Spoel D, van Drunen R, (1995) GROMACS: A message passing parallel molecular dynamics implementation. Comp Phys Comm 91: 43-56.
    • (1995) Comp Phys Comm , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 72
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D, (2001) Gromacs 3.0: A package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
    • (2001) J Mol Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 78
    • 25444481354 scopus 로고    scopus 로고
    • Replica exchange with solute tempering: a method for sampling biological systems in explicit water
    • Liu P, Friesner RA, Berne BJ, (2005) Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Natl Acad Sci U S A 102: 13749-13754.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13749-13754
    • Liu, P.1    Friesner, R.A.2    Berne, B.J.3
  • 79
    • 34250323902 scopus 로고    scopus 로고
    • Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange
    • Kubitzki MB, de Groot BL, (2007) Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophys J 92: 4262-4270.
    • (2007) Biophys J , vol.92 , pp. 4262-4270
    • Kubitzki, M.B.1    de Groot, B.L.2
  • 80
    • 33745184030 scopus 로고    scopus 로고
    • Protein folding kinetics and thermodynamics from atomistic simulations
    • van der Spoel D, Seibert MM, (2006) Protein folding kinetics and thermodynamics from atomistic simulations. Phys Rev E 96: 238102.
    • (2006) Phys Rev E , vol.96 , pp. 238102
    • van der Spoel, D.1    Seibert, M.M.2
  • 81
    • 34548804689 scopus 로고    scopus 로고
    • Computational simulations of the early steps of protein aggregation
    • Wei G, Mousseau N, Derreumaux P, (2007) Computational simulations of the early steps of protein aggregation. Prion 1: 3-8.
    • (2007) Prion , vol.1 , pp. 3-8
    • Wei, G.1    Mousseau, N.2    Derreumaux, P.3
  • 82
    • 3142568651 scopus 로고    scopus 로고
    • Pathway complexity of Alzheimer's beta-amyloid Abeta16-22 peptide assembly
    • Santini S, Wei G, Mousseau N, Derreumaux P, (2004) Pathway complexity of Alzheimer's beta-amyloid Abeta16-22 peptide assembly. Structure 12: 1245-1255.
    • (2004) Structure , vol.12 , pp. 1245-1255
    • Santini, S.1    Wei, G.2    Mousseau, N.3    Derreumaux, P.4
  • 83
    • 77958491288 scopus 로고    scopus 로고
    • Amyloid fibril polymorphism is under kinetic control
    • Pellarin R, Schuetz P, Guarnera E, Caflisch A, (2010) Amyloid fibril polymorphism is under kinetic control. J Am Chem Soc 132: 14960-14970.
    • (2010) J Am Chem Soc , vol.132 , pp. 14960-14970
    • Pellarin, R.1    Schuetz, P.2    Guarnera, E.3    Caflisch, A.4
  • 84
    • 4544283591 scopus 로고    scopus 로고
    • In silico assembly of Alzheimer's Abeta16-22 peptide into beta-sheets
    • Santini S, Mousseau N, Derreumaux P, (2004) In silico assembly of Alzheimer's Abeta16-22 peptide into beta-sheets. J Am Chem Soc 126: 11509-11516.
    • (2004) J Am Chem Soc , vol.126 , pp. 11509-11516
    • Santini, S.1    Mousseau, N.2    Derreumaux, P.3
  • 85
    • 58149174069 scopus 로고    scopus 로고
    • Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment
    • Li DW, Mohanty S, Irbäck A, Huo S, (2008) Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment. PLoS Comput Biol 4: e1000238.
    • (2008) PLoS Comput Biol , vol.4
    • Li, D.W.1    Mohanty, S.2    Irbäck, A.3    Huo, S.4
  • 86
    • 67650022104 scopus 로고    scopus 로고
    • Evidence for novel beta-sheet structures in Iowa mutant beta-amyloid fibrils
    • Tycko R, Sciarretta KL, Orgel JP, Meredith SC, (2009) Evidence for novel beta-sheet structures in Iowa mutant beta-amyloid fibrils. Biochemistry 48: 6072-6084.
    • (2009) Biochemistry , vol.48 , pp. 6072-6084
    • Tycko, R.1    Sciarretta, K.L.2    Orgel, J.P.3    Meredith, S.C.4
  • 87
    • 0019880372 scopus 로고
    • Conformational and geometrical properties of beta-sheets in proteins. I. Parallel beta-sheets
    • Salemme FR, Weatherford DW, (1981) Conformational and geometrical properties of beta-sheets in proteins. I. Parallel beta-sheets. J Mol Biol 146: 101-117.
    • (1981) J Mol Biol , vol.146 , pp. 101-117
    • Salemme, F.R.1    Weatherford, D.W.2
  • 88
    • 0019880377 scopus 로고
    • Conformational and geometrical properties of beta-sheets in proteins. II. Antiparallel and mixed beta-sheets
    • Salemme FR, Weatherford DW, (1981) Conformational and geometrical properties of beta-sheets in proteins. II. Antiparallel and mixed beta-sheets. J Mol Biol 146: 119-141.
    • (1981) J Mol Biol , vol.146 , pp. 119-141
    • Salemme, F.R.1    Weatherford, D.W.2
  • 89
    • 0034700129 scopus 로고    scopus 로고
    • Multiple quantum solid-state NMW indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils
    • Antzutkin ON, Balbach JJ, Leapman RD, Rizzo NW, Reed J, et al. (2000) Multiple quantum solid-state NMW indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils. Proc Natl Acad Sci U S A 97: 13045-13050.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 13045-13050
    • Antzutkin, O.N.1    Balbach, J.J.2    Leapman, R.D.3    Rizzo, N.W.4    Reed, J.5
  • 90
    • 33746405081 scopus 로고    scopus 로고
    • Destruction or potentiation of different prions catalyzed by similar Hsp104 remodeling activities
    • Shorter J, Lindquist S, (2006) Destruction or potentiation of different prions catalyzed by similar Hsp104 remodeling activities. Mol Cell 23: 425-438.
    • (2006) Mol Cell , vol.23 , pp. 425-438
    • Shorter, J.1    Lindquist, S.2
  • 91
    • 33748561495 scopus 로고    scopus 로고
    • Chaperonin TRiC promotes the assembly of polyQ expansion proteins into nontoxic oligomers
    • Behrends C, Langer CA, Boteva R, Böttcher UM, Stemp MJ, et al. (2006) Chaperonin TRiC promotes the assembly of polyQ expansion proteins into nontoxic oligomers. Mol Cell 23: 887-97.
    • (2006) Mol Cell , vol.23 , pp. 887-897
    • Behrends, C.1    Langer, C.A.2    Boteva, R.3    Böttcher, U.M.4    Stemp, M.J.5
  • 92


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.