C9530 Structure of biomacromolecules

Faculty of Science
Autumn 2024
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
prof. Mgr. Lukáš Žídek, Ph.D. (lecturer)
doc. Mgr. Pavel Plevka, Ph.D. (lecturer)
Mgr. Viktor Bartošík (assistant)
Mgr. Tomáš Brom (assistant)
Mgr. Michaela Mikysková (assistant)
Mgr. Dávid Tužinčin (assistant)
Guaranteed by
prof. Mgr. Lukáš Žídek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. Mgr. Lukáš Žídek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Wed 14:00–15:50 B11/205
Prerequisites
The course is offered to students of biochemistry and related areas (molecular biology, biophysics) and to all who are interested in modern methods of structure determination of biomacromolecules.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
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.
Learning outcomes
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.
Syllabus
  • 1-4. Structure of macromolecules, basic structural motifs of proteins and nucleic acids, structure of saccharides.
  • . 5. Sample preparation, sequencing of nucleic acids, proteins, and saccharides.
  • 6. Optical methods of characterization of biomacromolecules: circular dichroism, infrared spectroscopy. Small angle X-ray scattering
  • 7. Computational methods, molecular mechanics and dynamics, simulated annealing.
  • 8-9. X-ray crystallography. Crystal preparation, diffraction experiment, methods of solving phase problem, electron density maps, structure model building. Electron microscopy. Electron microscope, sample preparation for cryo-electron microscopy, data processing, reconstruction of the shape of the molecule.
  • 10-11. Nuclear magnetic resonance. Isotope labeling, NMR experiment, spectral frequency assignment, determination of geometry (NOE, coupling constants), protein dynamics.
  • 12. Bioinformatics, databases, computer prediction and modelling.
Literature
  • LESK, Arthur M. Introduction to protein architecture : the structural biology of proteins. Oxford: Oxford University Press, 2001, xii, 347. ISBN 0198504748. info
  • FINKEL‘ŠTEJN, Aleksej Vital‘jevič and Oleg Borisovič PTICYN. Protein physics : a course of lectures. Amsterdam: Academic Press, 2002, xix, 354. ISBN 0122567811. 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. ISBN 0125870728. info
  • CAVANAGH, John. Protein NMR spectroscopy : principles and practice. 2nd ed. Amsterdam: Elsevier, 2007, xxv, 885. ISBN 9780121644918. info
  • ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
Teaching methods
The basic principles are explained in interactive 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.
Assessment methods
Exam is based on a written test (solving practical problems), followed by an oral examination. The practical course C9531 prepares students for the final test. Students who successfully passed all test during the course C9531, do not write the final test of C9530. The mark is based on the oral exam.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
Listed among pre-requisites of other courses
Teacher's information
http://ncbr.chemi.muni.cz/~lzidek/C9530/C9530.html
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2010 - only for the accreditation, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.
  • Enrolment Statistics (recent)
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