Your browser has javascript turned off or blocked. This will lead to some parts of our website to not work properly or at all. Turn on javascript for best performance.

The browser you are using is not supported by this website. All versions of Internet Explorer are no longer supported, either by us or Microsoft (read more here:

Please use a modern browser to fully experience our website, such as the newest versions of Edge, Chrome, Firefox or Safari etc.

Anders Irbäck. Photo.

Anders Irbäck


Anders Irbäck. Photo.

Protein dynamics: aggregation and mechanical unfolding


  • Simon Mitternacht

Summary, in English

The subject of this thesis is protein dynamics. Papers I--IV and VI study either of two different processes: mechanical unfolding and aggregation. Paper V presents a computationally efficient all-atom model for proteins, variants of which are used to perform Monte Carlo simulations in the other papers.

Mechanical unfolding experiments probe properties of proteins at the single molecule level. The only information obtained the experiments is the extension and resisting force of the molecule. We perform all-atom simulations to generate a detailed description of the unfolding process. Papers I and II discuss the mechanical and thermal unfolding of the protein ubiquitin. The principal finding of Paper I is that ubiquitin unfolds through a well-defined pathway and that the experimentally observed non-obligatory unfolding intermediate lies on this pathway. Paper II compares mechanical unfolding pathways with thermal unfolding pathways. In Paper IV we study the mechanical unfolding of the protein FNIII-10 and find that it has three important, mutually exclusive, unfolding pathways and that the balance between the three can be shifted by changing the pulling


Paper III describes oligomerization of six-chain systems of the disease-related peptide Abeta(16-22). We find that disordered oligomers of different sizes dominate at high temperatures and as temperature is lowered, larger, more structured, oligomers form. In particular a very stable beta-barrel structure forms. Paper VI is an investigation of the effect of mutations on the folding properties of the peptide Abeta42 from Alzheimer's disease. Small aggregates of this peptide are believedto be important toxic agents. We find that a disease-related mutant peptide, with an elevated aggregation propensity, has a larger conformational diversity than the wild-type peptide, whereas a mutation that is known to inhibit aggregation has the opposite effect.


  • Computational Biology and Biological Physics

Publishing year




Document type



  • Biophysics


  • Monte Carlo simulations
  • All-atom protein models
  • Mechanical unfolding
  • Protein aggregation




  • Anders Irbäck


  • ISBN: 978-91-628-7714-9

Defence date

17 April 2009

Defence time


Defence place

Lecture hall F, Department of Theoretical Physics


  • Guido Tiana (Dr)