PřF:FA602 Biophys. asp. of struct, biol. - Course Information

FA602 Biophysical aspects of structural biology

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

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

• Applied Physics (programme PřF, B-AF, specialization Medical Physics)
• Biophysics (programme PřF, B-FY) (2)
• Biophysics (programme PřF, N-FY, specialization Aplikovaná biofyzika) (2)
• Biophysics (programme PřF, N-FY, specialization Molekulární biofyzika) (2)

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.

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)

The course is taught annually.
The course is taught: every week.

• Enrolment Statistics (Spring 2013, recent)
  
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