MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description

Mechanism and Biological Implications of Protein Aggregation


Nanosciences and Nanotechnologies, third-level study programme


prof. dr. Eva Žerovnik


To understand the phenomenon of protein ordered aggregation into amyloid fibrils. These processes are involved in neurodegenerative diseases such as Alzheimer’s, Parkinson’s, various dementias and prion diseases. Additional understanding of molecular and cellular bases of protein aggregation will help in search for new therapies for neurodegenerative diseases. The course will cover molecular, cellular and selected clinical aspects.



1. Biophysical background of protein aggregation (Models describing amyloid-fibrillation of proteins)

2. The structure of amyloid-fibrils

3. Experimental means to study thermodynamics and kinetics of the process of fibrillation (Case studies from the literature: A-beta, beta-microglobulin, alpha-synuclein, stefin B)

4. Correlation between protein folding and amyloid-fibril formation (Role of folding intermediates in amyloid-fibril formation; Role of chaperones in defence against aggregates)

5. Cytotoxicity of amyloid fibrils (Interaction with lipids and pore formation)

6. Protein aggregation in the cell (Accumulation and transport of the aggregates; Means of clearance: ubiquitin proteasome system and autophagy)

7. Amyloidoses and neurodegenerative diseases (Seminar)

Course literature:


Textbook: Methods Enzymol. 309, Amyloids, Prions and other protein aggregates, ed. Wetzel R.,(1999) Academic Press.

Textbook: Amyloid Proteins; Methods and Protocols Ed. Sigurdsson EM, Series: Methods in Molecular Biology Vol 299, Humana Press 2005.

Texbook: Molecular Chaperones in the Cell, Frontiers in Mol.Biology series, ed. P. Lund, Oxford Univ.Press, 2001

Textbook: R.H. Pain: Mechanisms of Protein Folding, 2nd edn., (2000) R. H. Pain (ed.), Oxford University Press, ISBN 0 19 963788, selected chapters.

Additional Textbook: Protein Folding-Misfolding: some current concepts of protein chemistry. (2007) Zbilut JP and Scheibel T (eds.), Nova Sci Publi., New York.

Additional Textbook: Protein misfolding diseases; current and emerging therapies. eds Raminez-Alvarado, J.W. Kelly, C.M. Dobson, Wiley Series in Protein and Peptide Science, Series Ed. V.N. Uversky. John Wiley & Sons, New Jersey 2010.

Review papers :

Rochet JC and Lansbury PT (2000) Amyloid fibrillogenesis: themes and variations. Curr.Opin.Struct.Biol. 10, 60 – 68.

Sherman MY and Goldberg AL (2001) Cellular defences against unfolded proteins : a cell biologist thinks about neurodegenerative diseases. Neuron 29, 15-32.

Žerovnik E (2002) Amyloid-fibril formation; Proposed mechanisms and relevance to conformational disease. Eur.J.Biochem. 269, 3362- 3371.

Lansbury PT, Lashuel HA. (2006) A century-old debate on protein aggregation and neurodegeneration enters the clinic. Nature 443: 774-779. Review.

Lashuel HA, Lansbury PT Jr. (2006) Are amyloid diseases caused by protein aggregates that mimic bacterial pore-forming toxins? Q Rev Biophys. 39, 167-201.

David C. Rubinsztein (2006) The roles of intracellular protein-degradation pathways in neurodegeneration NATURE 443, 780-786.

Haass C, Selkoe DJ. 2007. Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid beta-peptide. Nat Rev Mol Cell Biol. 2007 Feb;8(2):101-12. Review.

M, Ueno T, Waguri S et al. 2007. Constitutive autophagy:vital role in clearance of unfavorable proteins in neurons. Cell Death Differ. 1-8.

Irvine CB, El-Agnaf OM, Shankar GM and Walsh DM (2008). Protein aggregation in the brain. The molecular basis for Alzheimer’s and Parkinson’s diseases. Mol.Med. 14, 451 – 464.

Additional references available for students.

Significant publications and references:

1. Book chapter: Žerovnik, E, Giannini, S, Stoka, V, Tušek-Žnidarič, M, Pompe-Novak, M, Staniforth, RA. (2006) On the mechanism of amyloid-fibrillation: stefin B as a good model protein. In: Žerovnik, E, Kopitar-Jerala, N (eds.). Human stefins and cystatins. New York: Nova Sci.Publ., Inc., 2006, pp. 97-114.

2. Rabzelj, S., Viero, G., Gutiérrez-Aguirre, I., Turk, V., Dalla Serra, M., Anderluh, G., Žerovnik, E. (2008) Interaction with model membranes and pore formation by human stefin B - Studying the native and prefibrillar states. FEBS Journal, 275, 2455-2466.

3. Čeru S et al., Žerovnik E. (2008) Size and morphology of toxic oligomers of amyloidogenic proteins: a case study of human stefin B. Amyloid, 15, 147–159.

4. Žerovnik, E., Škarabot, M., Škerget, K., Giannini, S., Stoka, V., Jenko-Kokalj, S., Staniforth, R.A. (2007) Amyloid fibril formation by human stefin B: Influence of pH and TFE on fibril growth and morphology Amyloid, 14, 237-247.

5. Rabzelj, S., Turk, V., Žerovnik, E. (2005) In vitro study of stability and amyloid-fibril formation of two mutants of human stefin B (cystatin B) occurring in patients with EPM1. Protein Science, 14 (10), pp. 2713-2722.

6. Jenko, S., Škarabot, M., Kenig, M., Gunčar, G., Muševič, I., Turk, D., Žerovnik, E. (2004) Different Propensity to Form Amyloid Fibrils by Two Homologous Proteins - Human Stefins A and B: Searching for an Explanation (2004) Proteins: Structure, Function and Genetics, 55, 417-425.

7. Žerovnik, E., Pompe-Novak, M., Škarabot, M., Ravnikar, M., Muševič, I., Turk, V. (2002a) Human stefin B readily forms amyloid fibrils in vitro (2002) Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology, 1594, 1-5.

Additional, new References:

8. Jelinska C, Davis PJ, Kenig M, et al. (2011) Modulation of Contact Order Effects in the Two-State Folding of Stefins A and B. Biophys.J. 100: 2268-2274.

9. Taler-Verčič A, Žerovnik E (2010) Binding of amyloid peptides to domain-swapped dimers of other amyloid-forming proteins may prevent their neurotoxicity. BIOESSAYS 32: 1020-1024.

10. Škerget K, Taler-Verčič A, Bavdek A, et al. Žerovnik E (2010) Interaction between Oligomers of Stefin B and Amyloid-beta in Vitro and in Cells. J.Biol.Chem. 285: 3201-3210.

11. Čeru S, Layfield R, Zavasnik-Bergant T, et al. Žerovnik E (2010). Intracellular aggregation of human stefin B: confocal and electron microscopy study. Biol.Cell 102: 319-334.

12. Žerovnik E, Staniforth RA, Turk D. (2010). Amyloid fibril formation by human stefins: Structure, mechanism & putative functions. BIOCHIMIE 92: 1597-1607.

13. Žerovnik E (2010) Protein Conformational Pathology in Alzheimer's and Other Neurodegenerative Diseases; New Targets for Therapy. Curr. Alz. Res. 7: 74-83.

14. Žerovnik E (2009) The emerging role of cystatins in Alzheimer's disease. BIOESSAYS 31: 597-599.

15. Škerget K, Vilfan A, Pompe-Novak M, et al. Žerovnik E (2009). The mechanism of amyloid-fibril formation by stefin B: Temperature and protein concentration dependence of the rates. PROTEINS: Structure Function and Bioinformatics 74: 425-436.

16. Morgan GJ, Giannini S, Hounslow AM, et al. (2008) Exclusion of the native alpha-helix from the amyloid fibrils of a mixed alpha/beta protein. J. Mol. Biol. 375: 487-498

17. Jenko Kokalj S, Guncar G, Stern I, et al. (2007) Essential role of proline isomerization in stefin B tetramer formation. J.Mol.Biol. 366: 1569-1579.

18. Žerovnik E, Skarabot M, Skerget K, et al. (2007). Amyloid fibril formation by human stefin B: influence of pH and TFE on fibril growth and morphology. AMYLOID 14: 237-247.


• oral assessment
• written e-seminar

Students obligations:

• regular coursework, oral examination, e-seminar