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Articles

Two major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils

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Pages 1370-1376 | Received 15 Feb 2017, Accepted 17 Jul 2017, Published online: 22 Aug 2017

References

  • Valastyan JS, Lindquist S. Mechanisms of protein-folding diseases at a glance. Dis Models Mech. 2014;7:9–14.
  • Sipe JD, Cohen AS. Review: history of the amyloid fibril. J Struct Biol. 2000;130:88–98.
  • Selkoe DJ. Folding proteins in fatal ways. Nature. 2003;426:900–904.
  • Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Ann Rev Biochem. 2006;75:333–366.
  • Chiti F, Dobson CM. Amyloid formation by globular proteins under native conditions. Nat Chem Biol. 2009;5:15–22.
  • Hiramatsu H, Goto Y, Naiki H, et al. Structural model of the amyloid fibril formed by β2-microglobulin 21–31 fragment based on vibrational spectroscopy. J Amer Chem Soc. 2005;127:7988–7989.
  • Yoshimura Y, Lin Y, Yagi H, et al. Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation. Proc Nat Acad Sci USA. 2012;109:14446–14451.
  • Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, et al. Amyloid fibril formation by Abeta16-22, a seven-residue fragment of the Alzheimer ’s beta-amyloid peptide, and structural characterization by solid state NMR. Biochemistry. 2000;39:13748–13759.
  • Childers WS, Mehta AK, Ni R, et al. Peptides organized as bilayer membranes. Angew Chem. 2010;49:4104–4107.
  • Nishino M, Sugita Y, Yoda T, et al. Structures of a peptide fragment of β2-microglobulin studied by replica-exchange molecular dynamics simulations-towards the understanding of the mechanism of amyloid formation. FEBS Lett. 2005;579:5425–5429.
  • Wei G, Song W, Derreumaux P, et al. Self-assembly of amyloid-forming peptides by molecular dynamics simulations. Front Biosci. 2008;13:5681–5692.
  • Li MS, Reddy G, Hu CK, et al. Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. Phys Rev Lett. 2010;105:218101.
  • 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.
  • Itoh SG, Okumura H. Dimerization process of amyloid-β (29–42) studied by the Hamiltonian replica-permutation molecular dynamics simulations. J Phys Chem B. 2014;118:11428–11436.
  • Nishikawa N, Nguyen PH, Derreumaux P, et al. Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol Simul. 2015;40:1041–1044.
  • Nishikawa N, Sakae Y, Okamoto Y. Molecular dynamics simulations to clarify the concentration dependency of protein aggregation. J. Math. 2015;1:011020.
  • Nasica-Labouze J, Nguyen PH, Sterpone F, et al. Amyloid β protein and Alzheimer’s disease: when computer simulations complement experimental studies. Chem Rev. 2015;115:3518–3563.
  • Straub JE, Thirumalai D. Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Ann Rev Phys Chem. 2011;62:437–463.
  • Naiki H, Hashimoto N, Suzuki S, et al. Establishment of a kinetic model of dialysis-related amyloid fibril extension in vitro. Amyloid. 1997;4:223–232.
  • Koch KM. Dialysis-related amyloidosis. Kidney Int. 1992;41:1416–1429.
  • Yamamoto S, Gejyo F. Historical background and clinical treatment of dialysis-related amyloidosis, Biochim Biophys Acta (BBA)- Proteins. Proteomics. 2005;1753:4–10.
  • Iwata K, Matsuura T, Sakurai K, et al. High-resolution crystal structure of β2-microglobulin formed at pH 70. J Biochem. 2007;142:413–419.
  • Hasegawa K, Ohhashi Y, Yamaguchi I, et al. Amyloidogenic synthetic peptides of β2-microglobulin-a role of the disulfide bond. Biochem Biophys Res Commun. 2003;304:101–106.
  • Hiramatsu H, Goto Y, Naiki H, et al. Core structure of amyloid fibril proposed from IR-microscope linear dichroism. J Amer Chem Soc. 2004;126:3008–3009.
  • Hiramatsu H, Kitagawa T. FT-IR approaches on amyloid fibril structure, Biochim Biophys Acta (BBA)-Proteins. Proteomics. 2005;1753:100–107.
  • Mitsutake A, Sugita Y, Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers. 2001;60:96–123.
  • Okumura H, Itoh SG, Okamoto Y. Generalized-ensemble algorithms for simulations of complex molecular systems. In: Leszczynski J, Shukla MK, editors. Practical aspects of computational chemistry II: an overview of the last two decades and current trends. Dordrecht: Springer; 2012. p. 69–101.
  • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314:141–151.
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38.
  • Case DA, Darden TA, Cheatham III TE, et al. AMBER 12. San Francisco (CA): University of California; 2012.
  • Pearlman DA, Case DA, Caldwell JW, et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun. 1995;91:1–41.
  • Case DA, Cheatham TE, Darden T, et al. The Amber biomolecular simulation programs. J Comput Chem. 2005;26:1668–1688.
  • Kollman P, Dixon R, Cornell W, et al. The development/application of a minimalist’organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: Gunsterenvan WF, Weiner PK, editors. Computer simulation of biomolecular systems. Dordrecht: Springer; 1997. p. 83–96.
  • Calimet N, Schaefer M, Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins Struct Funct Bioinform. 2001;45:144–158.
  • Dominy BN, Brooks CL. Development of a generalized Born model parametrization for proteins and nucleic acids. J Phys Chem B. 1999;103:3765–3773.
  • Onufriev A, Bashford D, Case DA. Modification of the generalized Born model suitable for macromolecules. J Phys Chem B. 2000;104:3712–3720.
  • Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins Struct Funct Bioinform. 2004;55:383–394.
  • Tsui V, Case DA. Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J Amer Chem Soc. 2000;122:2489–2498.
  • Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem. 1999;20:217–230.
  • Shell MS, Ritterson R, Dill KA. A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B. 2008;112:6878–6886.
  • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.
  • Sindhikara DJ, Kim S, Voter AF, et al. Bad seeds sprout perilous dynamics: stochastic thermostat induced trajectory synchronization in biomolecules. J Chem Theory Comput. 2009;5:1624–1631.
  • Uberuaga BP, Anghel M, Voter AF. Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation. J Chem Phys. 2004;120:6363–6374.
  • Brooks BR, Bruccoleri RE, Olafson BD, et al. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983;4:187–217.
  • Becker OM, MacKerell AD Jr, Roux B, et al. editors. Computational biochemistry and biophysics. New York (NY): Marcel Dekker; 2001.
  • Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys. 2008;129:124105.
  • Berg BA. Multicanonical simulations step by step. Comput Phys Commun. 2003;153:397–406.
  • Joosten RP, Te Beek TAH, Krieger E, et al. A series of PDB related databases for everyday needs. Nucleic Acids Res. 2011;39:D411–D419.
  • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical eatures. Biopolymers. 1983;22:2577–2637.

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