Research in the Strodel group focuses on the misfolding and subsequent aggregation of proteins occurring in neurodegenerative diseases like Alzheimer’s and Parkinson’s disease. It is our aim to elucidate the aggregation pathways of such amyloid proteins.

To this end, we perform computer studies using the molecular dynamics (MD) technique, which provide movies of the biomolecular motions over a time scale of microseconds, with femtosecond time resolution and atomistic spatial resolution. Such simulations allow us to follow the aggregation from monomers into amyloid oligomers. These are non-fibrillar assemblies whose toxicity has been demonstrated in various cell studies and animal models and which are difficult to characterise by experimental techniques due to their inherent instability.

We further employ different simulation techniques for elucidating interactions between amyloid proteins and potential anti-amyloid inhibitors, which helps towards the rational design of the latter.

Our long-term goal is to simulate the aggregation process under consideration of different physiological and pathological factors, such as alterations in neuronal membrane composition and ion concentrations, oxidative stress or glycation of the amyloid proteins.

1. B. Barz, Q. Liao, B. Strodel. Pathways of amyloid-β aggregation depend on oligomer shape. J. Am. Chem. Soc. 140: 319–327 (2018) PubMed
2. M. Wolff, B. Zhang-Haagen, C. Decker, B. Barz, M. Schneider, R. Biehl, A. Radulescu, B. Strodel, D. Willbold, L. Nagel-Steger. Aβ42 pentamers/hexamers are the smallest detectable oligomers in solution. Sci. Rep. 7: 2493 (2017) PubMed
3. Q. Liao, M. C. Owen, O. O. Olubiyi, B. Barz, B. Strodel. Conformational Transitions of the Amyloid-β Peptide Upon Copper(II) Binding and pH Changes. Israel J. Chem. 57: 771-784 (2017) Wiley Online Library
4. B. Barz and B. Strodel. Understanding Amyloid-β Oligomerization at the Molecular Level: the Role of the Fibril Surface. Chem. Eur. J. 22, 8768-8772 (2016) PubMed
5. C. Wallin, Y.S. Kulkarni, A. Abelein, J. Jarvet, Q. Liao, B. Strodel, L. Olsson, J. Luo, J.P. Abrahams, S.B. Sholts, P.M. Roos, S.C.L. Kamerlin, A. Gräslund, S.K.T.S. Wärmländer. Characterization of Mn(II) ion Binding to the Amyloid-β Peptide in Alzheimer’s Disease. J. Trace Elem. Med. Biol. 38: 183-193 (2016) PubMed
6. M. Carballo-Pacheco, B. Strodel. Advances in the Simulation of Protein Aggregation at the Atomistic Scale. J. Phys. Chem. B 120: 2991–2999 (2016) PubMed
7. L. Nagel-Steger, M. C. Owen, & B. Strodel. An account of amyloid oligomers: facts and figures obtained from experiments and simulations. ChemBioChem. 17: 657-676 (2016) PubMed
8. J. Nasica-Labouze, P.H. Nguyen, F. Sterpone, O. Berthoumieu, N.V. Buchete, S. Coté, A. DeSimone, A.J. Doig, P. Faller, A. Garcia, A. Laio, S.L. Mai, S. Melchionna, N. Mousseau, Y. Mu, A. Paravastu, S. Pasquali, D.J. Rosenman, B. Strodel, B. Tarus, J.H. Viles, T. Zhang, C. Wang, P. Derreumaux. Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev. 115: 3518-3563 (2015) PubMed