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

Abstract

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.KeywordsCircular DichroismMelting BehaviorBackbone RMSDHelix ContentHydrophobic AttractionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.