Učni načrt predmeta

Predmet:
Mehanizem in biološke implikacije agregacije proteinov
Course:
Mechanism and Biological Implications of Protein Aggregation
Študijski program in stopnja /
Study programme and level		 Študijska smer /
Study field		 Letnik /
Academic year		 Semester /
Semester
Nanoznanosti in nanotehnologije, 3. stopnja Bioznanosti 1 1
Nanosciences and Nanotechnologies, 3rd cycle Biosciences 1 1
Vrsta predmeta / Course type
Izbirni
Univerzitetna koda predmeta / University course code:
NANO3-810
Predavanja
Lectures		 Seminar
Seminar		 Vaje
Tutorial		 Klinične vaje
work		 Druge oblike
študija		 Samost. delo
Individ. work		 ECTS
30 30 30 21 10

*Navedena porazdelitev ur velja, če je vpisanih vsaj 15 študentov. Drugače se obseg izvedbe kontaktnih ur sorazmerno zmanjša in prenese v samostojno delo. / This distribution of hours is valid if at least 15 students are enrolled. Otherwise the contact hours are linearly reduced and transfered to individual work.

Nosilec predmeta / Course leader:
prof. dr. Eva Žerovnik
Sodelavci / Lecturers:
Jeziki / Languages:
Predavanja / Lectures:
Slovenščina, angleščina / Slovenian, English
Vaje / Tutorial:
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Končan študij druge stopnje biokemije, biologije, medicine, veterine ali katerekoli druge naravoslovne smeri.

Second cycle degree in biochemistry, biology, medicine, vet-medicine or any other natural sciences discipline.

Vsebina:
Content (Syllabus outline):

Poglavja:
1. Biofizikalne osnove agregacije proteinov. Modeli za amiloidno fibrilacijo proteinov.
2. Struktura amiloidnih fibril.
3. Eksperimentalne tehnike za študij termodinamike in kinetike procesa fibrilacije. Študij primerov iz literature: A-beta, beta-microglobulin, alfa-sinuklein, stefin B.
4. Korelacija med zvijanjem proteinov in tvorjenjem amiloidnih fibril. Vloga vmesnih stanj zvitja pri tvorbi amiloidov. Vloga šaperonov pri obrambi pred agregati.
5. Citotoksičnost amiloidnih fibril. Interakcija z lipidi in tvorjenje por.
6. Proteinska agregacija v celici. Akumulacija in transport agregatov. Čiščenje celice – razgradnja agregatov preko ubikvitin proteasomalnega sistema in autofagije.
7. Reverzibilna agregacija proteinov v telesca brez membran
8. Amiloidoze in nevrodegenerativne boleznim - Seminar.

Topics:
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. Role of chaperones in defence against aggregates.
5. Citotoxicity 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. Reversible protein aggregation into membrane-less bodies
8. Amyloidoses and neurodegenerative diseases - Seminar.

Temeljna literatura in viri / Readings:

Books:
Protein Folding-Misfolding: some current concepts of protein chemistry. Zbilut JP and Scheibel T (eds.), Nova Sci Publi., New York, 2007.
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:
K¨uffner et al., 2021. Sequestration within biomolecular condensates inhibits Aβ-42 amyloid formation. Chem Sci, 2021 Feb 18;12(12):4373-4382. doi: 10.1039/d0sc04395h.
Lion et al., 2021. A framework for understanding the functions of biomolecular condensates across scales. Nat Rev Mol Cell Biol, 2021 Mar;22(3):215-235. doi: 10.1038/s41580-020-00303-z.
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.
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.
Žerovnik E. (2010).Protein conformational pathology in Alzheimer's and other neurodegenerative diseases; new targets for therapy. Curr Alzheimer Res. 7: 74-83. Review.
Žerovnik E, Stoka V, Mirtič A, Gunčar G, Grdadolnik J, Staniforth RA, Turk D, Turk V. (2011). Mechanisms of amyloid fibril formation--focus on domain-swapping. FEBS J. 278:2263-82. doi: 10.1111/j.1742-4658.2011.08149.x. Epub 2011 May 31. Review.
Di Scala e tal., (2016) Common molecular mechanism of amyloid pore formation by Alzheimer's b- amyloid peptide and a-synuclein Scien. Reports, DOI: 10.1038/srep28781.
Sengupta U, Nilson N.A., Kayed R., The role of amyloid-b oligomers in toxicity, propagation, and immunotherapy EBioMedicine , 2016, vol6, 42-49.

Cilji in kompetence:
Objectives and competences:

CILJI: Razumeti proces agregacije proteinov do amiloidnih fibril. Ti procesi se pojavljajo v nevrodegenerativnih boleznih, kot so Alzheimerjeva, Parkinsonova, razne demence in prionske bolezni. Z boljšim razumevanjem molekularnih in celičnih osnov proteinske agregacije bo možno priti do novih terapij za nevrodegenerativne bolezni. Predmet bo vključeval molekularne, celične in izbrane klinične vidike.

KOMPETENCE: Spoznavanje z interdisciplinarnimi področji molekularne in celične biologije, biokemije in biofizike. Samostojno mišljenje, formuliranje problemov in vprašanj.

OBJECTIVES: 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.

COMPETENCES: get to know interdisciplinary fields of molecular and cell biology, biochemistry and biophysics. Independent and creative thinking; be able to formulate problems and open questions.

Predvideni študijski rezultati:
Intendeded learning outcomes:

Znanje in razumevanje:
- študent bo razumel osnove fenomena urejene agregacije proteinov do amiloidnih fibril,
- študent bo pridobil razumevanje, kako se ta osnovna znanja prenašajo v prakso, t.j. v iskanje novih terapij za nevrodegenerativne bolezni,
- pridobil bo dodatno razumevanje molekularnih in celičnih vidikov proteinske agregacije.

Splošni rezultati:
- poznavanje raziskovalnih metod, postopkov in procesov, ki se uporabljajo na področju zvijanja in agregacije proteinov, ki obsegajo biofizikalne metode, mikroskopije (AFM, TEM, fluorescence in konfokalni m), biokemijske metode frakcioniranja oligomer, kot npr. SEC in DLS, in spektroskopije, kot npr. CD, FTIR, NMR in fluorescenca,
- razvoj kritične in samokritične presoje,
- razvoj komunikacijskih sposobnosti in spretnosti, posebej predstavitve raziskovalnih rezultatov,
- kooperativnost, delo v skupini v stimulativnem okolju; možna mednarodna izmenjava.

Predmetnospecifični rezultati:
- predmet pripravlja študente za delo na interdisciplinarnih bazičnih projektih,
- povezanost z biomedicino,
- uporabna znanja tudi za biotehnologijo in živilsko tehnologijo.

Knowledge and understanding:
- the student will understand basics of the phenomenon of protein ordered aggregation into amyloid fibrils,
- he also will get to know ways, how this basic knowledge is being used in search for therapy of neurodegenerative diseases,
- additional understanding of molecular and cellular aspects of protein aggregation.

General Ouitcomess:
- the student will get to know research methods, procedures and processes used in the field of protein folding and aggregation, which comprise biophysical methods, microscopies: AFM and TEM, fluorescent and confocal m., biochemical methods of oligomer fractionation, such as SEC and DLS and spectroscopies, such as CD, FTIR, NMR and fluorescence,
- the student will develop critical thinking,
- the student will develop communication skills to present research achievenment,
- cooperation, team work in competitive environment; possible international exchange.

Course Specific Results:
- this course prepares students to work on interdisciplinary projects,
- is connected to biomedicine,
- useful for biotechnology and food technology.

Metode poučevanja in učenja:
Learning and teaching methods:

Predavanja, konzultacije, individualno delo, laboratorijsko delo (samo v primeru mentorstva).

Lectures, consultations, individual work, laboratory work (If supervising the student).

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Ustno preverjanje
50 %
Oral assessment
Pisni e-seminar
50 %
Written e-seminar
Reference nosilca / Lecturer's references:
1. ŽEROVNIK, Eva (2019). Possible mechanisms by which Stefin B could regulate proteostasis and oxidative stress. Cells, ISSN 2073-4409, 2019, vol. 8, no. 1, str. 70-1-70-8, doi: 10.3390/cells8010070.
2. Jahić Mujkić A, Tušek Žnidarič M, Berbić S, Žerovnik E. (2021) Synergy of the Inhibitory Action of Polyphenols Plus Vitamin C on Amyloid Fibril Formation: Case Study of Human Stefin B. Antioxidants (Basel). 2021 Sep 15;10(9):1471. doi: 10.3390/antiox10091471.
3. ŽEROVNIK, EVA (2022). Human stefin B: from its structure, folding, and aggregation to its function in health and disease. Front Mol Neurosci. 2022 Oct 21;15:1009976. doi: 10.3389/fnmol.2022.1009976. eCollection 2022. review
4. Žganec M, Taler Verčič A, Muševič I, Škarabot M, Žerovnik E. (2023). Amyloid Fibrils of Stefin B Show Anisotropic Properties. Int J Mol Sci. 2023 Feb 13;24(4):3737. doi: 10.3390/ijms24043737.
5. Venko K, Žerovnik E. (2023). Protein Condensates and Protein Aggregates: In Vitro, in the Cell, and In Silico. Front Biosci (Landmark Ed). 2023 Aug 28;28(8):183. doi: 10.31083/j.fbl2808183.