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Molecular Simulation Volume 41, 2015 - Issue 10-12: Proceedings of the 3rd International Conference on Molecular Simulation
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Proceedings of the 3rd International Conference on Molecular Simulation

Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation

Naohiro NishikawaDepartment of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, JapanCorrespondence[email protected]
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,
Phuong H. NguyenLaboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005Paris, FranceView further author information
,
Philippe DerreumauxLaboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005Paris, FranceView further author information
&
Yuko OkamotoDepartment of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan;Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan;Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi464-8603, Japan;Information Technology Center, Nagoya University, Nagoya, Aichi464-8601, JapanView further author information
Pages 1041-1044 | Received 29 May 2014, Accepted 20 Jun 2014, Published online: 15 Sep 2014

References

  • Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Ann Rev Biochem. 2006;75:333–366.
  • Lührs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Dobeli H, Schubert D, Riek R. 3D structure of Alzheimer's amyloid-beta(1–42) fibrils. Proc Natl Acad Sci USA. 2005;102:17342–17347.
  • Serpell LC. Alzheimer's amyloid fibrils: structure and assembly. Biochim Biophys Acta. 2000;1502:16–30.
  • Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. J Phys Chem B. 2009;113:267–274.
  • Chebaro Y, Mousseau N, Derreumaux P. Structures and thermodynamics of Alzheimer's amyloid-beta Abeta(16–35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Abeta fibrillation. J Phys Chem B. 2009;113:7668–7675.
  • Wei G, Song W, Derreumaux P, Mousseau N. Self-assembly of amyloid-forming peptides by molecular dynamics simulations. Front Biosci. 2008;13:5681–5692.
  • Itoh SG, Okamoto Y. Amyloid-beta(29–42) dimer formations studied by a multicanonical–multioverlap molecular dynamics simulation. J Phys Chem B. 2008;112:2767–2770.
  • Baumketner A, Shea JE. The structure of the Alzheimer amyloid beta 10–35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent. J Mol Biol. 2007;366:275–285.
  • Baumketner A, Shea JE. Folding landscapes of the Alzheimer amyloid-beta(12–28) peptide. J Mol Biol. 2006;362:567–579.
  • Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R. Amyloid fibril formation by Abeta(16–22), a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Biochemistry. 2000;39:13748–13759.
  • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314:141–151.
  • Maupetit J, Tuffery P, Derreumaux P. A coarse-grained protein force field for folding and structure prediction. Proteins. 2007;69:394–408.
  • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22:2577–2637.

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