메뉴 건너뛰기




Volumn 65, Issue 1, 2006, Pages 180-191

Structures of soluble amyloid oligomers from computer simulations

Author keywords

Activation relaxation technique; Aggregation; Amyloid fibril formation; Coarse grained force field; Molecular dynamics; Protein simulations; Soluble oligomers

Indexed keywords

AMYLOID;

EID: 33748278029     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21100     Document Type: Article
Times cited : (56)

References (50)
  • 1
    • 0033621165 scopus 로고    scopus 로고
    • Amyloid diseases: Abnormal protein aggregation in neurodegeneration
    • Koo EH, Lansbury PT, Jr, Kelly JW. Amyloid diseases: abnormal protein aggregation in neurodegeneration. Proc Natl Acad Sci USA 1999;96:9989,9990.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9989
    • Koo, E.H.1    Lansbury Jr., P.T.2    Kelly, J.W.3
  • 2
    • 0037174618 scopus 로고    scopus 로고
    • Alzheimer's disease is a synaptic failure
    • Selkoe DJ. Alzheimer's disease is a synaptic failure. Science 2002;298:789-791.
    • (2002) Science , vol.298 , pp. 789-791
    • Selkoe, D.J.1
  • 3
    • 0030822582 scopus 로고    scopus 로고
    • Prion diseases and the BSE crisis
    • Prusiner SB. Prion diseases and the BSE crisis. Science 1997;278: 245-251.
    • (1997) Science , vol.278 , pp. 245-251
    • Prusiner, S.B.1
  • 5
    • 12244249201 scopus 로고    scopus 로고
    • Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils
    • Petkova AT, Leapman RD, Guo Z, Yau WM, Mattson MP, Tycko R. Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils. Science 2005;307:262-265.
    • (2005) Science , vol.307 , pp. 262-265
    • Petkova, A.T.1    Leapman, R.D.2    Guo, Z.3    Yau, W.M.4    Mattson, M.P.5    Tycko, R.6
  • 11
    • 4143067019 scopus 로고    scopus 로고
    • Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease
    • Armen RS, DeMarco ML, Alonso DO, Daggett V. Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease. Proc Natl Acad Sci USA 2004;101:11622-11627.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11622-11627
    • Armen, R.S.1    DeMarco, M.L.2    Alonso, D.O.3    Daggett, V.4
  • 13
    • 11844291405 scopus 로고    scopus 로고
    • A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single β-sheet model with a small hydrophobic core
    • Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single β-sheet model with a small hydrophobic core. J Mol Biol 2005;345:1213-1227.
    • (2005) J Mol Biol , vol.345 , pp. 1213-1227
    • Haspel, N.1    Zanuy, D.2    Ma, B.3    Wolfson, H.4    Nussinov, R.5
  • 14
    • 22144432561 scopus 로고    scopus 로고
    • MD simulations indicate a possible role of parallel β-helices in seeded aggregation of poly-Gln
    • Stork M, Giese A, Kretzschmar HA, Tavan P. MD simulations indicate a possible role of parallel β-helices in seeded aggregation of poly-Gln. Biophys J 2005;88:2442-2451.
    • (2005) Biophys J , vol.88 , pp. 2442-2451
    • Stork, M.1    Giese, A.2    Kretzschmar, H.A.3    Tavan, P.4
  • 15
    • 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 2005;345:1141-1156.
    • (2005) J Mol Biol , vol.345 , pp. 1141-1156
    • Tarus, B.1    Straub, J.E.2    Thirumalai, D.3
  • 16
    • 19544375553 scopus 로고    scopus 로고
    • Sequence dependence of amyloid fibril formation: Insights from molecular dynamics simulations
    • Lopez de la Paz M, de Mori GM, Serrano L, Colombo G. Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol 2005;349: 583-596.
    • (2005) J Mol Biol , vol.349 , pp. 583-596
    • Lopez De La Paz, M.1    De Mori, G.M.2    Serrano, L.3    Colombo, G.4
  • 17
    • 17844362202 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water
    • Colombo G, Daidone I, Gazit E, Amadei A, Di Nola A. Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water. Proteins 2005;59:519-527.
    • (2005) Proteins , vol.59 , pp. 519-527
    • Colombo, G.1    Daidone, I.2    Gazit, E.3    Amadei, A.4    Di Nola, A.5
  • 18
    • 15444364664 scopus 로고    scopus 로고
    • Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations
    • Soto P, Cladera J, Mark AE, Daura X. Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations. Angew Chem Int Ed Engl 2005;44:1065-1067.
    • (2005) Angew Chem Int Ed Engl , vol.44 , pp. 1065-1067
    • Soto, P.1    Cladera, J.2    Mark, A.E.3    Daura, X.4
  • 19
    • 20444363123 scopus 로고    scopus 로고
    • Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
    • Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci USA 2005;102:8174-8179.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 8174-8179
    • Tsai, H.H.1    Reches, M.2    Tsai, C.J.3    Gunasekaran, K.4    Gazit, E.5    Nussinov, R.6
  • 20
    • 0037337271 scopus 로고    scopus 로고
    • 16-22 amyloid peptides into antiparallel β sheets
    • 16-22 amyloid peptides into antiparallel β sheets. Structure 2003;11: 295-307.
    • (2003) Structure , vol.11 , pp. 295-307
    • Klimov, D.K.1    Thirumalai, D.2
  • 21
    • 2942707921 scopus 로고    scopus 로고
    • Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin
    • Paci E, Gsponer J, Salvatella X, Vendruscolo M. Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin. J Mol Biol 2004;340:555-569.
    • (2004) J Mol Biol , vol.340 , pp. 555-569
    • Paci, E.1    Gsponer, J.2    Salvatella, X.3    Vendruscolo, M.4
  • 22
    • 22144448838 scopus 로고    scopus 로고
    • The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent
    • Wu C, Lei H, Duan Y. The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophys J 2005;88:2897-2906.
    • (2005) Biophys J , vol.88 , pp. 2897-2906
    • Wu, C.1    Lei, H.2    Duan, Y.3
  • 23
    • 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, Haberthur U, Caflisch A. 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 USA 2003;100:5154-5159.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 5154-5159
    • Gsponer, J.1    Haberthur, U.2    Caflisch, A.3
  • 24
    • 4444346811 scopus 로고    scopus 로고
    • Kinetic control of dimer structure formation in amyloid fibrillogenesis
    • Hwang W, Zhang S, Kamm RD, Karplus M. Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc Natl Acad Sci USA 2004;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
  • 25
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • Nguyen ND, Hall CK. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc Natl Acad Sci USA 2004;101:16180-16185.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 16180-16185
    • Nguyen, N.D.1    Hall, C.K.2
  • 27
    • 0037044732 scopus 로고    scopus 로고
    • Charge attraction and β propensity are necessary for amyloid fibril formation from tetrapeptides
    • Tjernberg L, Hosia W, Bark N, Thyberg J, Johansson J. Charge attraction and β propensity are necessary for amyloid fibril formation from tetrapeptides. J Biol Chem 2002;277:43243-43246.
    • (2002) J Biol Chem , vol.277 , pp. 43243-43246
    • Tjernberg, L.1    Hosia, W.2    Bark, N.3    Thyberg, J.4    Johansson, J.5
  • 28
    • 34548067360 scopus 로고    scopus 로고
    • Following the aggregation of amyloid-forming peptides by computer simulations
    • Melquiond A, Boucher G, Mousseau N, Derreumaux P. Following the aggregation of amyloid-forming peptides by computer simulations. J Chem Phys 2005;122:174904.
    • (2005) J Chem Phys , vol.122 , pp. 174904
    • Melquiond, A.1    Boucher, G.2    Mousseau, N.3    Derreumaux, P.4
  • 29
    • 10044289451 scopus 로고    scopus 로고
    • Sampling the self-assembly pathways of KFFE hexamers
    • Wei GH, Mousseau N, Derreumaux P. Sampling the self-assembly pathways of KFFE hexamers. Biophys J 2004;87:3648-3656.
    • (2004) Biophys J , vol.87 , pp. 3648-3656
    • Wei, G.H.1    Mousseau, N.2    Derreumaux, P.3
  • 33
    • 4043157260 scopus 로고    scopus 로고
    • Event-based relaxation of continuous disordered systems
    • Barkema GT, Mousseau N. Event-based relaxation of continuous disordered systems. Phys Rev Lett 1996;77:4358-4361.
    • (1996) Phys Rev Lett , vol.77 , pp. 4358-4361
    • Barkema, G.T.1    Mousseau, N.2
  • 34
    • 0034505723 scopus 로고    scopus 로고
    • Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique
    • Malek R, Mousseau N. Dynamics of Lennard-Jones clusters: a characterization of the activation-relaxation technique. Phys Rev E 2000;62:7723-7728.
    • (2000) Phys Rev E , vol.62 , pp. 7723-7728
    • Malek, R.1    Mousseau, N.2
  • 35
    • 3142737884 scopus 로고    scopus 로고
    • Complex folding pathways in a simple β-hairpin
    • Wei GH, Mousseau N, Derreumaux P. Complex folding pathways in a simple β-hairpin. Proteins 2004;56:464-474.
    • (2004) Proteins , vol.56 , pp. 464-474
    • Wei, G.H.1    Mousseau, N.2    Derreumaux, P.3
  • 36
    • 28844499140 scopus 로고    scopus 로고
    • Exploring the early steps of amyloid peptide aggregation by computers
    • Mousseau N, Derreumaux P. Exploring the early steps of amyloid peptide aggregation by computers. Acc Chem Res 2005;38: 885-891.
    • (2005) Acc Chem Res , vol.38 , pp. 885-891
    • Mousseau, N.1    Derreumaux, P.2
  • 37
    • 10044227276 scopus 로고    scopus 로고
    • 16-22 peptides using hydrogen bonds and hydrophobicity forces
    • 16-22 peptides using hydrogen bonds and hydrophobicity forces. Biophys J 2004;87:3657-3664.
    • (2004) Biophys J , vol.87 , pp. 3657-3664
    • Favrin, G.1    Irback, A.2    Mohanty, S.3
  • 38
    • 27744547951 scopus 로고    scopus 로고
    • Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique
    • Mousseau N, Derreumaux P, Gilbert G. Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique. Phys Biol 2005;2:S101-S107.
    • (2005) Phys Biol , vol.2
    • Mousseau, N.1    Derreumaux, P.2    Gilbert, G.3
  • 39
    • 0001418816 scopus 로고    scopus 로고
    • From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential
    • Derreumaux P. From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential. J Chem Phys 1999;111:2301-2310.
    • (1999) J Chem Phys , vol.111 , pp. 2301-2310
    • Derreumaux, P.1
  • 40
    • 0034214823 scopus 로고    scopus 로고
    • Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations
    • Derreumaux P. Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations. Phys Rev Lett 2000;85:206-209.
    • (2000) Phys Rev Lett , vol.85 , pp. 206-209
    • Derreumaux, P.1
  • 41
    • 0037103928 scopus 로고    scopus 로고
    • Role of supersecondary structural elements in protein G folding
    • Derreumaux P. Role of supersecondary structural elements in protein G folding. J Chem Phys 2002;117:3499-3503.
    • (2002) J Chem Phys , vol.117 , pp. 3499-3503
    • Derreumaux, P.1
  • 42
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 46
    • 25844456992 scopus 로고    scopus 로고
    • Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent
    • Wu C, Lei H, Duan Y. Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent. J Am Chem Soc 2005;127:13530-13537.
    • (2005) J Am Chem Soc , vol.127 , pp. 13530-13537
    • Wu, C.1    Lei, H.2    Duan, Y.3
  • 47
    • 27744538230 scopus 로고    scopus 로고
    • Interplay between structure and size in a critical crystal nucleus
    • Moroni D, ten Wolde PR, Bolhuis PG. Interplay between structure and size in a critical crystal nucleus. Phys Rev Lett 2005;94: 235703.
    • (2005) Phys Rev Lett , vol.94 , pp. 235703
    • Moroni, D.1    Ten Wolde, P.R.2    Bolhuis, P.G.3
  • 48
    • 0037039394 scopus 로고    scopus 로고
    • Structure determination of micelle-like intermediates in amyloid β-protein fibril assembly by using small angle neutron scattering
    • Yong W, Lomakin A, Kirkitadze MD, Teplow DB, Chen SH, Benedek GB. Structure determination of micelle-like intermediates in amyloid β-protein fibril assembly by using small angle neutron scattering. Proc Natl Acad Sci USA 2002;99:150-154.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 150-154
    • Yong, W.1    Lomakin, A.2    Kirkitadze, M.D.3    Teplow, D.B.4    Chen, S.H.5    Benedek, G.B.6
  • 49
    • 0036415838 scopus 로고    scopus 로고
    • α-synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils
    • Lashuel HA, Petre BM, Wall J, Simon M, Nowak RJ, Walz T, Lansbury PT, Jr. α-synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils. J Mol Biol 2002;322:1089-1102.
    • (2002) J Mol Biol , vol.322 , pp. 1089-1102
    • Lashuel, H.A.1    Petre, B.M.2    Wall, J.3    Simon, M.4    Nowak, R.J.5    Walz, T.6    Lansbury Jr., P.T.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.