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Mini Review

Computational Simulations of the Early Steps of Protein Aggregation

Guanghong Wei
,
Normand Mousseau
&
Philippe Derreumaux
Pages 3-8 | Received 12 Jan 2007, Accepted 05 Feb 2007, Published online: 01 Mar 2007

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Valeriya M. Trusova & Galyna P. Gorbenko. (2018) Molecular dynamics simulations of lysozyme–lipid systems: probing the early steps of protein aggregation. Journal of Biomolecular Structure and Dynamics 36:9, pages 2249-2260.
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Priya Yadav, Ganesh Shahane & Sushama Gaikwad. (2018) Amaranthus caudatus lectin with polyproline II fold: conformational and functional transitions and molecular dynamics. Journal of Biomolecular Structure and Dynamics 36:9, pages 2203-2215.
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Phuong Hoang Nguyen, Pierre Tufféry & Philippe Derreumaux. 2022. Computational Peptide Science. Computational Peptide Science 95 113 .
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Size Zheng, Katherine S. Shing & Muhammad Sahimi. (2018) Dynamics of proteins aggregation. II. Dynamic scaling in confined media. The Journal of Chemical Physics 148:10.
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B.R. Ginn. (2017) The thermodynamics of protein aggregation reactions may underpin the enhanced metabolic efficiency associated with heterosis, some balancing selection, and the evolution of ploidy levels. Progress in Biophysics and Molecular Biology 126, pages 1-21.
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Cindie Eugene, Rozita Laghaei & Normand Mousseau. (2014) Early oligomerization stages for the non-amyloid component of α-synuclein amyloid. The Journal of Chemical Physics 141:13.
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Gaetano Invernizzi, Elena Papaleo, Raimon Sabate & Salvador Ventura. (2012) Protein aggregation: Mechanisms and functional consequences. The International Journal of Biochemistry & Cell Biology 44:9, pages 1541-1554.
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Workalemahu M. Berhanu & Ulrich H. E. Hansmann. (2012) Structure and Dynamics of Amyloid-β Segmental Polymorphisms. PLoS ONE 7:7, pages e41479.
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Yan Lu, Guanghong Wei & Philippe Derreumaux. (2012) Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations. The Journal of Chemical Physics 137:2, pages 025101.
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Matthew S. Church, Christine E. Ferry & Alan E. van Giessen. (2012) Thermodynamics of peptide dimer formation. The Journal of Chemical Physics 136:24.
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Sébastien Côté, Rozita Laghaei, Philippe Derreumaux & Normand Mousseau. (2012) Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ 1–40 , Aβ 1–42 , and Aβ 1–40 (D23N) . The Journal of Physical Chemistry B 116:13, pages 4043-4055.
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Tuomas P. J. Knowles & Markus J. Buehler. (2011) Nanomechanics of functional and pathological amyloid materials. Nature Nanotechnology 6:8, pages 469-479.
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Jessica Nasica-Labouze, Massimiliano Meli, Philippe Derreumaux, Giorgio Colombo & Normand Mousseau. (2011) A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35. PLoS Computational Biology 7:5, pages e1002051.
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Maria T. Panteva, Reza Salari, Monica Bhattacharjee & Lillian T. Chong. (2011) Direct Observations of Shifts in the β-Sheet Register of a Protein-Peptide Complex Using Explicit Solvent Simulations. Biophysical Journal 100:9, pages L50-L52.
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Guanbo Wang, Rinat R. Abzalimov & Igor A. Kaltashov. (2011) Direct Monitoring of Heat-Stressed Biopolymers with Temperature-Controlled Electrospray Ionization Mass Spectrometry. Analytical Chemistry 83:8, pages 2870-2876.
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Yan Lu, Guanghong Wei & Philippe Derreumaux. (2010) Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-β Fragment 29−42 by Replica Exchange Molecular Dynamics Simulations. The Journal of Physical Chemistry B 115:5, pages 1282-1288.
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Phuong H. Nguyen, Mai Suan Li & Philippe Derreumaux. (2011) Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer. Physical Chemistry Chemical Physics 13:20, pages 9778.
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Cezary Czaplewski, Adam Liwo, Mariusz Makowski, Stanisław Ołdziej & Harold A. Scheraga. 2011. Multiscale Approaches to Protein Modeling. Multiscale Approaches to Protein Modeling 35 83 .
Jennifer S. Laurence & C. Russell Middaugh. 2010. Aggregation of Therapeutic Proteins. Aggregation of Therapeutic Proteins 1 61 .
Brian R. Ginn. (2010) The implications of gene heterozygosity for protein folding and protein turnover. Journal of Theoretical Biology 265:4, pages 554-564.
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Xin Liu. (2010) Outline and computational approaches of protein misfolding. Frontiers in Biology 5:3, pages 211-218.
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Nikolay Blinov, Lyudmyla Dorosh, David Wishart & Andriy Kovalenko. (2010) Association Thermodynamics and Conformational Stability of β-Sheet Amyloid β(17-42) Oligomers: Effects of E22Q (Dutch) Mutation and Charge Neutralization. Biophysical Journal 98:2, pages 282-296.
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Naoyuki Miyashita, John E. Straub & D. Thirumalai. (2009) Structures of β-Amyloid Peptide 1−40, 1−42, and 1−55—the 672−726 Fragment of APP—in a Membrane Environment with Implications for Interactions with γ-Secretase. Journal of the American Chemical Society 131:49, pages 17843-17852.
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Takeshi Yamazaki, Nikolay Blinov, David Wishart & Andriy Kovalenko. (2008) Hydration Effects on the HET-s Prion and Amyloid-β Fibrillous Aggregates, Studied with Three-Dimensional Molecular Theory of Solvation. Biophysical Journal 95:10, pages 4540-4548.
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Jean-Francois St-Pierre, Normand Mousseau & Philippe Derreumaux. (2008) The complex folding pathways of protein A suggest a multiple-funnelled energy landscape. The Journal of Chemical Physics 128:4.
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Chungwen Liang, Philippe Derreumaux & Guanghong Wei. (2007) Structure and Aggregation Mechanism of β2-Microglobulin (83–99) Peptides Studied by Molecular Dynamics Simulations. Biophysical Journal 93:10, pages 3353-3362.
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Julien Maupetit, P. Tuffery & Philippe Derreumaux. (2007) A coarse-grained protein force field for folding and structure prediction. Proteins: Structure, Function, and Bioinformatics 69:2, pages 394-408.
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