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Molecules of Life & Mutations - MB151P125

Title:	Molecules of Life & Mutations
Czech title:	Molekuly života & mutace
Guaranteed by:	Department of Cell Biology (31-151)
Faculty:	Faculty of Science
Actual:	from 2023 to 2023
Semester:	summer
E-Credits:	3
Examination process:	summer s.:written
Hours per week, examination:	summer s.:2/3, Ex [DS]
Capacity:	25
Min. number of students:	unlimited
4EU+:	no
Virtual mobility / capacity:	no
State of the course:	taught
Language:	English
Level:	specialized
Explanation:	A tutorial in structural biology and public databases (PDB,OMIM,UniProt,etc.).For students of biology, medicine, chemistry in their 3rd-6th year.Please, enroll in the e-learning Moodle course (e-learning) ASAP - right link
Additional information:	http://www.karger.com/Book/Home/227359
Note:	enabled for web enrollment

Guarantor:	RNDr. Karel Drbal, Ph.D.
Teacher(s):	RNDr. Karel Drbal, Ph.D. Mgr. Marian Novotný, Ph.D. Mgr. Daniel Rozbeský, Ph.D. doc. Ing. Václav Veverka, Ph.D.

Opinion survey results Examination dates SS schedule E-learning course

Annotation -

Last update: RNDr. Karel Drbal, Ph.D. (12.02.2024)

Designed by Professor Siegfried Schwarz, Medical University, Innsbruck/Austria. See: https://www.ncbi.nlm.nih.gov/pubmed/31642707

A practical computer course: molecular modeling and disease explanation as the basis for evidence-based medicine in the future. We will show pathophysiological states in endocrine, nervous and immune systems. The course will help you to understand a health/disease correlation with the use of molecules, their mutations, and interactions with specific drugs.
After the course, you will be able to perform database searches and molecular modeling on your own at the basic level. Here, we use only public domain resources you might be able to exploit in your everyday practice.

Practical training days in the PC room for an introduction to molecular modeling software and how to use PDB and OMIM databases. Computers provided, your personal comps allowed.
It includes an assignment of a single disease case report to each student for your homework on linking the protein structure to the underlying molecular pathophysiology.

Please, enroll in e-learning in Moodle: https://dl2.cuni.cz/course/view.php?id=2266 using your CAS account. Please, find there an example of student's presentations on Moodle.

Program:
3 days in April (15th-17th of April, 2024 at 1 pm - 4,30 pm), presentation 2-3 weeks later: your presentations & discussion. A consensual decision on the date of the final case report presentations of your homework will be taken at the end of the training. The venue is Faculty of Science CUNI - see detailed information in Moodle.

Literature -

Last update: RNDr. Karel Drbal, Ph.D. (27.10.2019)

Literature:

Schwarz S: Molecules of Life & Mutations. Karger, Basel 2002.

Schwarz S, Förster O, Peterlik M, Schauenstein K, Wick G: Pathophysiologie. Molekulare, zelluläre, systemische Grundlagen von Erkrankungen. Maudrich, Wien 2007

Requirements to the exam -

Last update: RNDr. Karel Drbal, Ph.D. (03.04.2024)

Participation at the training, & submission of the homework followed by a 10-minute presentation and discussion on the selected single pathology/molecule case.

Teachers (evaluation committee):
Prof. Dr.Med. Siegfried Schwarz, Doc.Ing. Jiří Hatina, CSc., RNDr. Karel Drbal, Ph.D., Mgr. Daniel Rozbeský, Ph.D., (Mgr. Marian Novotný, Ph.D., Ing. Václav Veverka, Ph.D.)

Syllabus -

Last update: RNDr. Karel Drbal, Ph.D. (27.10.2019)

In collaboration with prof. Siegfried Schwarz, M.D., Division of Experimental Pathophysiology & Immunology, Biocenter, Innsbruck Medical University, CCB, Innrain 80-82, 6020 Innsbruck, Austria, siegfried.schwarz@i-med.ac.at

We would like to welcome undergraduate students of Medicine as well as Biology and Chemistry from the 3rd semester onwards, including PhD students. You are going to learn molecular modelling methods, perform your practical training in the computer room and deliver an individual homework. This homework will be presented as the final 10-minutes presentation in English after 4-day interactive and interdisciplinary course. On the last day of the course (with at least 2 weeks gap), students are going to present their homework in front of all attending colleagues including teachers. As such, everybody learn from the others - kind of a multiplication effect.

This course gives you a general overview on our understanding of the normal as well as abnormal protein structures originating from particular gene mutations and/or allosteric effector function in health as well as in a diseased state. Introduction provides couple of examples of structure-function relationships in human medicine.
Next day we follow with a hands-on course in the computer room where attendees receive a detailed step-by-step description how to perform practical molecular modelling on PC using appropriate open-source software (RasMol, PyMol, LiteMol).
Having the X/Y/Z coordinates of atoms, as deposited in the Brookhaven Protein Data Bank (PDB), students can visualize and manipulate 3D structures of crystallized proteins, alone or after interaction with small or large ligands such as their substrates, drugs, DNA or other proteins.
Attendees will learn also how to use the OMIM (Online Inheritance in Men) database from where they can retrieve the published mutations and a corresponding disease pathology. Thereby, various structural characteristics can be recognized: domains of certain structure or charge, hydrophobicity or shape and other properties, which can serve e.g. as a ligand-binding domain, a DNA-binding domain, a drug-metabolizing pocket or as a domain for any other biological function. The real power of molecular modelling resides in its informative value displaying the molecular structure, in total or in portions thereof, in different formats such as wireframe, protein backbone, atoms, overall surface etc. It is possible to turn the molecule in all directions and to see in real time various aspects of its structure. Most importantly, points of mutation, as documented in the OMIM and other databases, can be mapped into a structural model in order to understand which function of the protein would thus be altered and whether this change in structure would result in loss-of-function or gain-of-function showing recessive or dominant effect. A link between arginine vasopressin precursor (AVP) and Diabetes insipidus serves as an illustrative and informative example.
In the second part of this course, students will get assigned an individual mutated protein and a corresponding disease pathology that they have to elaborate as a homework according to the demo example they have seen in the course. Each student should prepare a short (10 minutes) lecture in Power Point or alternatives and discuss her/his observations, published data and clinical outcomes.

The course is based on a textbook published by Siegfried Schwarz: MOLECULES OF LIFE & MUTATIONS (Karger, Basel 2002, ISBN: 978-3-8055-7395-5), in which structures of 150 most important molecules are displayed. http://www.karger.com/Book/Home/227359

Entry requirements

Last update: RNDr. Karel Drbal, Ph.D. (27.10.2019)

None.

Registration requirements

Last update: RNDr. Karel Drbal, Ph.D. (12.02.2024)

Enrollment in Moodle.

We run the course in the afternoon to allow access also for students from Medical faculties. Erasmus+ students are welcome as well.