The Molecules of Life

Structural biology – a subject for people with imagination

Lecture course: 7 meetings, 96 min each
Journal Club: 6 meetings, 100 min each
Lecturer: Prof. Mariusz Jaskolski
Laboratory practicals: 6 meetings, 225 min each
Tutor for practical exercises: Andrii Pyrih, MSc.

Lectures: Monday and Wednesday, 9:00
Beginning: March 2, 2020
Venue: Room 3.52, Coll. Chemicum

Journal Club: Wednesday, 17:00
Beginning: March 18, 2020
Venue: Room 2.4, Coll. Chemicum

Practicals: Thursday, 9:00
Beginning: March 19, 2020
Venue: contact your tutor before each class!

Student consultations:
 - Prof. Mariusz Jaskolski: Monday 11:00-12:00, Room 4.103, Coll. Chemicum

Material covered

• Principles of protein structure
• Classification of protein folds
• Anatomy and taxonomy of nucleic acids and macromolecular complexes
• Overview of experimental methods of structural biology: cryo-EM
• Principles of macromolecular crystallography
• Protein handling and crystallization
• Modern diffraction techniques
• Phasing methods in protein crystallography
• Electron density maps and model building
• Protein Data Bank (PDB) and validation of protein models
• Examples of structure-based drug design

Practicals

• Introduction to practicals classes
• 1. Protein handling and crystallization, including robotic crystallization
• 2: Protein crystal handling, cryoprotection and X-ray diffraction
• 5: Electron density maps and their interpretation
• 3: Protein Data Bank (PDB) and bioinformatics tools for protein structure analysis
• 4: An exercise in structure-guided drug design
• 6: Protein model building

Textbooks

• Arthur Lesk, Introduction to Protein Science: Architecture, Function, and Genomics. Oxford U. Press 2010.
• Gale Rhodes, Crystallography Made Crystal Clear, 3rd edition. Academic Press, 2006.
• Bernhard Rupp, Biomolecular Crystallography, Garland Science, 2010.
• A.Wlodawer, Z.Dauter, M.Jaskolski (editors), Protein Crystallography, Springer, 2017.
• V.Ramakrishnan, Gene Machine, Basic Books, 2018.

Literature

• A. Lesk, Introduction to Protein Science: Architecture, Function, and Genomics. Oxford U. Press 2010.
• C. Branden, J. Tooze, Introduction to Protein Structure, Garland Publishing, New York 1998 (2nd edition).
• G. Rhodes, Crystallography Made Crystal Clear, Academic Press, New York 2006.
• B. Rupp, Biomolecular Crystallography, Garland Science, 2010.
• A. Wlodawer, Z. Dauter, M. Jaskolski (editors), Protein Crystallography, Springer, 2017.
• A. Wlodawer, W. Minor, Z. Dauter, M. Jaskolski, Crystallography for non-crystallographers. FEBS J. 275, 1-20 (2007).
  A PDF file is available here
• M. Jaskolski, From atomic resolution to molecular giants: an overview of crystallographic studies of biological macromolecules with synchrotron radiation. Acta Phys. Polon. A 117, 257-263 (2010).
  A PDF file is available here

Assessment

Written multiple-choice test examination
First term: May 20, 2020, 9:00-10:15, Room 3.52, Coll. Chemicum
Second term (only if failed first test): May 27, 2020, 9:00-10:15, Room 3.52, Coll. Chemicum

Last modification: Feb 21, 2020 (SW+MJ)