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

Abstract

We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acid interactions. It reproduces the folding of a small protein (peptide): morphological analysis of the conformations at low temperature shows 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 through a free-energy analysis. We then study the aggregation of proteins. Proteins in the aggregate are mainly bound via hydrogen bonds. Performing a free-energy analysis we show that the addition of a peptide to such an aggregate is not favourable. We qualitatively reproduce the abnormal aggregation of proteins in prion diseases.

Keywords:

• Peptides folding
• Aggregation
• Molecular dynamics simulation

Acknowledgements

We gratefully acknowledge discussions with P.R. ten Wolde. This research was supported by a Marie Curie Fellowship of the European Community program ‘Improving Human Research Potential and the Socio-economic Knowledge Base’ under contract number HPMF-CT-2001-01212. Disclaimer: the authors are solely responsible for the information communicated and the European Commission is not responsible for any views or result expressed. The work of the FOM Institute is part of the research program of FOM and is made possible by financial support from the Netherlands Organization for Scientific Research (NWO).