The aim of the course is to offer basic information about structure determination of biomacromolecules (especially proteins and nucleic acids). The course is designed as a general overview offered to students who do not plan to enter this research area, but it may serve as an introduction to advanced courses of structure analysis.
Students who successfully finish the course will be able to apply methods of structure-related database searching, to analyze structural models, to make decision which structure determination method is applicable in a given case, and to understand basic principles of structure determination and of analyzing the underlaying data.
1-4. Structure of macromolecules, basic structural motifs of proteins and nucleic acids, structure of saccharides and membranes.
5. Computational methods, molecular mechanics and dynamics, simulated annealing.
6. Sample preparation, sequencing of nucleic acids, proteins, and saccharides.
7. Optical methods of characterization of biomacromolecules: circular dichroism, infrared spectroscopy.
8-9. X-ray crystallography. Crystal preparation, diffraction experiment, methods of solving phase problem, electron density maps, structure model building.
10-11. Nuclear magnetic resonance. Isotope labeling, NMR experiment, spectral frequency assignment, determination of geometry (NOE, coupling constants), protein dynamics.
12. Databases of structures, bioinformatics, computer prediction and modeling.
LESK, Arthur M. Introduction to protein architecture :the structural biology of proteins. New York: Oxford University Press, 2001. xii, 347 s. ISBN 0-19-850474-8. info
FINKELSTEIN, Alexei V. and O. B. PTITSYN. Protein physics :a course of lectures. Amsterdam: Academic Press, 2002. xix, 354 s. ISBN 0-12-256781-1. info
DAUNE, Michel. Molecular biophysics : structures in motion. Oxford: Oxford University Press, 1999. xxii, 499. ISBN 0-19-857783-4. info
MAREK, Jaromír and Z. TRÁVNÍČEK. Monokrystalová rentgenová strukturní analýza (Single crystal X-ray structure analysis). první. Olomouc: Vydavatelství Univerzity Palackého, 2002. 169 pp. nedělí se na edice. ISBN 80-244-0551-2. info
RHODES, Gale. Crystallography made crystal clear :a guide for users of macromolecular models. 2nd ed. San Diego, Calif.: Academic Press, 2000. xix, 269 s. ISBN 0-12-587072-8. info
Protein NMR spectroscopy :principles and practice. Edited by John Cavanagh. 2nd ed. Amsterdam: Elsevier, 2007. xxv, 885 s. ISBN 978-0-12-164491. info
ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999. xx, 218 s. ISBN 0-582-32788-1. info
The basic principles are explained in lectures complemented with presentation of model examples and opened for discussion. All lectures are collected with additional examples in an electronic textbook, available to students for free.
Exam is based on "open-book" solving practical problems, followed by a short oral examination.
Further comments (probably available only v češtině)
The course can also be completed outside the examination period.
The course is taught annually.