Simple off-lattice model to study folding and aggregation of peptides

Nicolas Combe (1) , Daan Frenkel (2)

1 CEMES - Centre d'élaboration de matériaux et d'études structurales
2 AMOLF - FOM Institute for Atomic and Molecular Physics

We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acids interactions. It reproduces the folding of a small protein (peptide) : a morphological analysis of the conformations at low temperature exhibits the two well-known substructures α-helix and β-sheet depending on the chosen sequence. The folding pathway in the scope of this model is studied trough a free energy analysis. We then study the aggregation of proteins. Proteins in the aggregate are mainly bounded trough hydrogen bonds. Performing a free energy analysis, we show that the addition of a peptide in such an aggregate is not favorable. We qualitatively reproduces the abnormal aggregation of proteins in prion diseases.

Mots clés: Physical Sciences

Nicolas Combe, Daan Frenkel. Simple off-lattice model to study folding and aggregation of peptides. Molecular Physics, 2007, 105 (04), pp.375-385. ⟨10.1080/00268970601175483⟩. ⟨hal-00513076⟩