FA602 Biophysical aspects of structural biology

Faculty of Science
Spring 2020
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
doc. Mgr. Lukáš Trantírek, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Josef Humlíček, CSc.
Department of Condensed Matter Physics – Physics Section – Faculty of Science
Contact Person: doc. Mgr. Karel Kubíček, PhD.
Supplier department: Department of Condensed Matter Physics – Physics Section – Faculty of Science
Timetable
Wed 11:00–11:50 Kontaktujte učitele
Prerequisites
Knowledge of basics of biomolecular structural analysis (X-ray, NMR and CD spectroscopy, FRET, electron microscopy) and molecular biophysics.
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
there are 7 fields of study the course is directly associated with, display
Course objectives
Students will be provided with overview of fundamental biophysical principles that used by cells to modulate biomolecular function. Particular attention is devoted to highlighting of:
i) relationships between biomolecular function and structure and environment,
ii) principles of intra- and intermolecular signalization and its modulation by environmental factors.
After successful passing the course the students should be able to design complex structural biological experiment based on set of biological, in vivo functional data.
Learning outcomes
After passing the course, students should be abel to
- describe relationships between biomolecular function and structure and environment,
- explain principles of intra- and intermolecular signalization and its modulation by environmental factors.
- design a structural biological experiment based on set of biological, in vivo functional data.
Syllabus
  • (1) Introduction into structural biology; (2) Causal relationships between biomolecular structure/function and environment; (3) Functional role of structural symmetry, rhythm, and repetition; (4) Molecular crowding; (5) Biophysical aspects of cellular signalization; (6) Structural investigations of unstructured biopolymers; (7) Principles of biomolecular structural analysis in vivo; (8) Principles of rational drug design – relationships between in vivo function and in vitro structure; (9) Biomimetic systems in structural analysis.
Literature
    recommended literature
  • WILEN, Samuel H. and Lewis N. MANDER. Stereochemistry of organic compounds. Edited by Ernest Ludwig Eliel. New York: John Wiley & Sons, 1993, xv, 1267. ISBN 0471016705. info
  • Exner, O. Statistic factors and symmetry numbers. Chemicke listy, 87, 473-483, 1993.
  • Dubois JM, Ouanounou G, Rouzaire-Dubois B. The Boltzmann equation in molecular biology. Prog Biophys Mol Biol. 2009 99(2-3):87-93.
  • Protein intrinsic disorder and oligomericity in cell signaling. Sigalov AB. Mol Biosyst. 2010 Mar;6(3):451-61. Epub 2009 Nov 3. Review
  • Chebotareva NA, Kurganov BI, Livanova NB. Biochemical effects of molecular crowding. Biochemistry (Mosc). 2004 69(11):1239-51.
  • Uversky VN. Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein J. 2009 28(7-8):305-25.
  • 3D QSAR in drug design. Edited by Hugo Kubinyi - Gerd Folkers - Yvonne Connolly Martin. Dordrecht: Kluwer Academic Publishers, 1998, vi, 416. ISBN 0792347927. info
  • 3D QSAR in drug design. Vol. 2, Ligand-protein interactions and molecular similarity. Edited by Hugo Kubinyi - Gerd Folkers - Yvonne C. Martin. Dordrecht: Kluwer Academic Publishers, 1998, vi, 416 s. ISBN 0-7923-4790-0. info
Teaching methods
lectures, class discussion
Assessment methods
Final oral exam – dissection of scientific publication
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught once in two years.
General note: S.
The course is also listed under the following terms Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2017, Spring 2019, Spring 2022, Spring 2024.
  • Enrolment Statistics (Spring 2020, recent)
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