All-Atom Monte Carlo Simulations of Protein Folding and Aggregation

  • Anders Irbäck
  • Sandipan Mohanty
Part of the Springer Series in Bio-/Neuroinformatics book series (SSBN, volume 1)


The ability to aggregate into β-sheet-rich fibrillar structures is a common property shared by many proteins. However, the propensity to aggregate and the precise mechanisms involved vary from protein to protein. Two currently intensely studied proteins are the Alzheimer’s-related amyloid β-peptide (Aβ) and the Parkinson’s-related α-synuclein (αS), both of which are disordered as free monomers and form fibrils. Here, we present studies of Aβ monomers and dimers and monomeric αS, based on an implicit solvent all-atom Monte Carlo (MC) approach. Somewhat unexpectedly, in the αS study, two distinct phases are observed. As a result, in the simulations, disordered αS has to overcome a rather large free-energy barrier in order to acquire a fibril-like fold. No corresponding barrier is observed in the Aβ simulations. Recently, the same computational model was used to study the folding of the Top7 protein, with > 90 residues and a mixed α + β fold. This chapter provides a summary of these Aβ , αS and Top7 studies.


Monte Carlo Conformational Ensemble Replica Exchange Backbone RMSD Folding Simulation 
These 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.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Department of Astronomy and Theoretical PhysicsLund UniversityLundSweden
  2. 2.Institute for Advanced Simulation, Jülich Supercomputing CentreForschungszentrum JülichJülichGermany

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