Protein Folding, Unfolding and Aggregation Studied Using an All-Atom Model with~a~Simplified Interaction Potential

  • Anders Irbäck
Part of the Lecture Notes in Physics book series (LNP, volume 736)


Finding a suitable transferable energy function for modeling of how different proteins fold into their respective native states is a major challenge in biophysics. Here, we discuss an all-atom protein model with implicit water and some studies based on this model. The model has a simplified and computationally convenient energy function. Despite its simplicity, the model has been found to quite successfully describe the structure and melting behavior of several peptides with about 20 amino acids. The same model, with unchanged parameters, has also been used to investigate the aggregation behavior of a fragment of Alzheimer’s Aβ peptide and the mechanical properties of the 76-residue protein ubiquitin.


Circular Dichroism Melting Behavior Backbone RMSD Helix Content Hydrophobic Attraction 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Anders Irbäck
    • 1
  1. 1.Computational Biology and Biological Physics Group Department of Theoretical PhysicsLund UniversitySölvegatan 14ASweden

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