Jun 13 – 19, 2015
University of Alberta
America/Edmonton timezone
Welcome to the 2015 CAP Congress! / Bienvenue au congrès de l'ACP 2015!

Coarse-Grained computer simulations of Alzheimer’s beta-amyloid peptides, using the Mercedes-Benz Hydrogen Bond Potential

Jun 16, 2015, 4:15 PM
CAB 239 (University of Alberta)

CAB 239

University of Alberta

Oral (Non-Student) / orale (non-étudiant) Medical and Biological Physics / Physique médicale et biologique (DMBP-DPMB) T3-9 Molecular Biophysics (DMBP) / Biophysique moléculaire (DPMB)


Dr Apichart Linhananta (Lakehead University)


Protein aggregation is a medically relevant phenomenon that can lead to protein-folding diseases such as Alzheimer’s and Prion’s. The aggregation process is largely determined by hydrogen bonds (HB), involving hundreds of peptides, over a period of days or even months. This rules out molecular dynamics (MD) simulations of all-atom protein models in explicit solvents. However, coarse-grained models of protein aggregation must accurately represent HB. This work considers the coarse-grained model used by Head- Gordon and coworkers to study the beta-amyloid (Aβ) peptides that forms plaques in Alzheimer’s diseases [1]. The model represents one amino-acid residue by a single bead, and used the Mercedes-Benz (MB) model to describes backbone HB. This has been adapted to study residue 25 to 35 of the peptide, Aβ_{25-35}, which is believed to be the most toxic stretch of Aβ. Preliminary work has obtained data on Langevin dynamics of 100 Aβ_{25-35} in a 100A ×100A ×100A box. The model peptides will be immersed in the MB water model of Dias and coworkers [2], used previously to study cold denaturation of proteins. The final model will be used to accurately identify the structure of Aβ intermediates believed to the neurotoxin agents in Alzheimer’s disease. [1] Hui, Fawzi, Head-Gordon, Proteins 70, 626 (2008) [2] Dias, Alla-Nissila, Grant, Kartunnen, J. Chem. Phys. 131, 054505 (2009)

Primary author

Dr Apichart Linhananta (Lakehead University)


Mr Girardin Robert (Lakehead University)

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