Bi9410cen Structural Biology - practice

Faculty of Science
Autumn 2024
Extent and Intensity
0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).
In-person direct teaching
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (seminar tutor)
Mgr. Jana Horáčková (seminar tutor)
MUDr. Jan Mičan (seminar tutor)
Saltuk Mustafa Eyrilmez, Ph.D. (seminar tutor)
Anthony Thomas P Legrand, Ph.D. (seminar tutor)
Joan Planas Iglesias (seminar tutor)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 16:00–17:50 B09/316
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular biology.
Course Enrolment Limitations
The course is offered to students of any study field.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 13/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24
Course objectives
The aim of the course is to teach students how to operate a number of selected and freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.
Learning outcomes
Upon the successful completion of the course, students will be able to:
- operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of biomacromolecules, interaction of proteins with proteins, nucleic acids and small organic molecules.
- visualize the 3D structure of biomolecules
- identify functionally relevant regions of proteins
- predict the structure of proteins and their complexes
- evaluate an effect of mutations on the protein function
Syllabus
  • 1. Introduction to structural biology - introduction to PyMOL3, PDB, and UniProt databases
  • 2. The structure of biomacromolecules - different types of structures of proteins and nucleic acids and how to assess them
  • 3. Evaluation of the quality of experimental structures - visualization of electron density, validation of crystallographic and NMR structures
  • 4. Protein structure prediction - prediction of secondary structure and surface area, structure prediction with homology modeling and AlphaFold 3, assessment of model quality
  • 5. Protein stability and dynamics - protein stability databases, protein dynamics assessment, databases, and visualization
  • 6. Protein structure analysis - analysis of molecular interactions, identification of functional regions
  • 7. Protein-ligand complexes - identification of binding sites and druggability, molecular docking, docking analysis, binding through protein tunnels
  • 8. Macromolecular complexes and interactions - oligomeric states in crystals, protein-nucleic acids complexes, macromolecular complex prediction and analysis, hot-spot prediction
  • 9. Engineering of protein structures I - annotation of mutated residues, prediction of mutant structures, prediction of mutational effect on protein properties
  • 10. Engineering of protein structures II - prediction of mutational effect on protein properties (continued), design and optimization of proteins, mutational impact on dynamics
  • 11. Applications of structural biology - discussion of practical use cases and personalized examples from the students
Literature
    recommended literature
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Teaching methods
Individual practice in the computer lab
Assessment methods
Written practical test, 11 exercises awarding 100 points in total, 70 points are needed to pass.
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Teacher's information
http://loschmidt.chemi.muni.cz/sbiol
All the teachers are part of the Loschmidt Laboratories: https://loschmidt.chemi.muni.cz/
  • Enrolment Statistics (recent)
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