Učni načrt predmeta

Predmet:

Od kristalov do 3D strukture makromolekul

Course:

From Crystals to 3D Structure of Macromolecules

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:

NANO3-820

Predavanja Lectures	Seminar Seminar	Vaje Tutorial	Klinične vaje work	Druge oblike študija	Samost. delo Individ. work	ECTS
30	30			30	210	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. Dušan Turk

Sodelavci / Lecturers:

Jeziki / Languages:

Predavanja / Lectures:

slovenščina, angleščina / Slovenian, English

Vaje / Tutorial:

Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:

Prerequisites:

Zaključena druga stopnja bolonjskega študija ali diploma univerzitetnega študijskega programa. Potrebno je poznavanje osnov biokemije, molekularne biologije in fizike. Študent mora biti vključen v raziskave s področja strukturne biologije na osnovi kristalografije.

Completed Bologna second cycle study program or an equivalent pre-Bologna university study program. Basic knowledge of biochemistry, molecular biology and physics is also requested. The student must be involved in structural biology research based on crystallography.

Vsebina:

Content (Syllabus outline):

Preverjanje čistosti in stabilnosti makromolekul

Kristalizacija makromolekul
Snemanje in procesiranje podatkov

Faziranje kristalografskih struktur z vsaj eno od metod:
- molekularne zamenjave
- multi valovna anomalna disperzija (MAD,SAD)
- multipla in enojna izomorfna zamenjava (MIR,SIR)

Modifikacija elektronske gostote:
- identifikacija proteinske regije in topila
- postopki modifikacije regije proteina in topila
- uporaba ne kristalografske simetrije
- povprečenje elektronske gostote

Interpretacija elektronske gostote
- avtomatsko in
- manualno grajenje molekularnih modelov

Fitanje in predelovanje modelov
- tarčne funkcije (metoda najmanjših kvadratov in maksimalne podobnosti)
- počasno in hitro ohlajanje pregretih modelov

Analiza in preverjanje struktur

Biološka interpretacija modelov:
- pisanje članka
- zastavitev nadaljnjih raziskav

Verifying purity and stability of macromolecules

Crystallization of macromolecules
Data collection and processing

Phasing of crystallographic data by at least one method:
- molecular replacement (MR)
- multi-wavelength anomalous dispersion technique (MAD, SAD)
- multiple and single isomorphous replacement (MIR and SIR)

Modifications of density maps:
- identification of protein and solvent regions
- separate procedures for solvent and protein regions
- exploiting non-crystallographic symmetry: electron density averaging

Interpretation of electron density maps:
- automated and
- manual model building

Refinement and model rebuilding
- target functions (least square and maximumlikelihood targets)
- "slow" (simulated annealing) and "fast" cooling minimization techniques

Analysis and validation of 3-D models

Model interpretation:
- manuscript preparation
- basis for further investigations

Temeljna literatura in viri / Readings:

Crystallography of biological macromolecules: International Tables for Crystallography, Volume F, 2nd
Edition, edited by Michael G. Rossmannm, Daniel M. Himmel and Eddy Arnold (2012). Wiley, ISBN 978-0-
470-66078-2.
Protein crystallography. Editors: Wlodawer, Alexander, Dauter, Zbigniew, Jaskolski, Mariusz (Eds.) Springer
International Publishing AG. 2017. ISBN 978-1-4939-7000-1. Methods in Molecular Biology Series Ed.:
Walker, John M. ISSN: 1064-3745.

Tekoča relevantna literatura iz problematike/ Relevant current articles from the field (Biological
Crystallography, Applied Crystallography, Structure, Journal of Molecular Biology, Nature, Science, Current
Opinion of Structural Biology, ...)."

Cilji in kompetence:

Objectives and competences:

Cilj predmeta je, da se študent seznani s teoretičnimi osnovami in praktičnimi pristopi k določevanju 3-dimenzionalne strukture makromolekul v kristalih. Pri svojem delu bo uporabljal najnovejšo tujo strokovno literaturo, kar bo izboljšalo njegove sposobnosti uporabe tujega jezika in kritičnega pogleda na objavljeno
raziskovalno delo.
Po uspešno zaključenem predmetu bi morale kompetence študentov doseči nivo samostojnega določevanja in interpretacije struktur makromolekul v kristalih.

Splošne kompetence:
- obvladanje raziskovalnih metod in postopkov, razvoj kritične in samokritične presoje,
- sposobnost uporabe znanja v praksi,
- razvoj komunikacijskih sposobnosti in spretnosti, posebej komunikacije v mednarodnem okolju,
- kooperativnost, delo v skupini in tudi v mednarodnem okolju.

The goal of the course is to familiarize the student with theoretical background upgraded by practical work on crystal structure determination. During the study the newest scientific literature will be used, which will improve the student's foreign language skills and the ability to study the published research critically.
The competencies of the students completing this course successfully should reach the level of independent determination of crystal structures of macromolecules and their interpretation.

General Competences:
- the student will master research methods and procedures and develop skills for critical assessment of his activities,
- the student will be able to put his knowledge into practice,
- the student will develop communications skills to present research achievement in the international environment,
- training for team work including the work in international environment.

Predvideni študijski rezultati:

Intendeded learning outcomes:

Poznavanje in razumevanje pojmov, metod iz strukturne biologije, s poudarkom na določevanju in interpretaciji 3-dimenzionalnih struktur makromolekul s pomočjo kristalografije.

Pregled različnih pristopov k reševanju relevantnih problemov in razumevanje omejitev metode.

Knowledge and understanding of the concepts and methods of structural biology with the emphasis on macromolecular crystallography.

Overview of different approaches to solving relevant problems and understanding of limitations of the approach.

Metode poučevanja in učenja:

Learning and teaching methods:

Konzultacije/predavanja, seminarji, individualno laboratorijsko delo.

Consultations/lectures, seminar work, individual laboratory work.

Načini ocenjevanja:

Delež v % / Weight in %

Assesment:

Seminarska naloga

20 %

Seminar work

Uspešna določitev strukture makromolekule v kristalu

80 %

Successful completion of macromolecular crystal structure determination

Reference nosilca / Lecturer's references:

1.	TURK, Dušan. MAIN software for density averaging, model building, structure refinement and validation. Acta crystallographica. Section D, Biological crystallography, ISSN 0907-4449, 2013, vol. 69, part 8, str. 1342-1357, doi: 10.1107/S0907444913008408.
2.	TURK, Dušan. Boxes of model building and visualization. V: WLODAWER, Alexander (ur.), DAUTER, Zbigniew (ur.), JASKOLSKI, Mariusz (ur.). Protein crystallography : methods and protocols, (Methods in molecular biology, 1607), (Springer protocols). New York: Humana Press: Springer, 2017, str. 491-548. [COBISS.SI-ID 30667303].
3.	Jure Pražnikar, Miloš Tomić & Dušan Turk (2019) Validation and quality assessment of macromolecular structures using complex network analysis Scientific Reports 9, 1678
4.	Tušar, Livija, Loboda, Jure, Impens, Francis, Sosnowski, Piotr, Van Quickelberghe, Emmy, Vidmar, Robert, Demol, Hans, Sedeyn, Koen, Saelens, X\ avier, Vizovišek, Matej, Mihelič, Marko, Fonović, Marko, Horvat, Jaka, Kosec, Gregor, Turk, Boris, Gevaert, Kris, Turk, Dušan (2023) Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins (2023) Communications Biology, 450, 6, 2399-3642. https://doi.org/10.1038/s42003-023-04772-8
5.	Sara Pintar, Jure Borišek, Aleksandra Usenik, Andrej Perdih & Dušan Turk (2020) Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis. Commun Biol 3, 178.