C8801 Biomolecular crystallography

Faculty of Science
Spring 2004
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)
Mgr. Jitka Vévodová, Ph.D. (lecturer)
Guaranteed by
Mgr. Jitka Vévodová, Ph.D.
Chemistry Section – Faculty of Science
Contact Person: Mgr. Jitka Vévodová, Ph.D.
Prerequisites
C9530 Structure of biomacromolecules
Basic work with operation system UNIX (for ex. C2110 course) is suitable for practical exercise of knowledges obtained in this course.
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 course is focused on 3D structure of biomacromolecules (proteins and nucleic acids) and its study by methods of X-ray crystallography. The first part of the course is focused on description of symmetry and preparation of the crystals. Next part refers to explanation of the principles of X-ray diffraction and data collection and processing. The final part includes the solution and refinement of 3D structure of biomacromolecules. In the end, there will be shown practical examples of protein crystallization and of the work with crystallographic software.
Syllabus
  • 1. Crystals Symmetry of crystals, point and space groups, assymetric unit 2. Expression and purification of the proteins, crystallization experiment, judging of the quality of crystals 3. Geometric principles of diffraction I. Braggs law, reciprocal space, Ewald construction. 4. Geometric principles of diffraction II. B-factors, unit cell symmetry, intensity of diffraction. 5. Diffraction data collection I. X-ray sources, detectors. 6. Diffraction data collection II. Diffraction experiment, data processing. 7. From diffraction data to electron density maps Atomic scattering factor, structure factors and their 2D representaion, amplitude and phase of the structure factor, Fourier transformation of the structure factors to electron density. 8. Phase problem solution I. Molecular replacement method (rotational and translational function), isomorphous replacement method, preparation of the heavy atom derivatives, Patterson maps. 9. Phase problem solution II. Anomalous scattering method, phase improvement (solvent flattening, molecular averaging, histogram matching),. 10. Refinement of the model structure I. Rigid body refinement, the method of least squares (restraints). 11. Refinement of the model structure II. Temperature factors, molecular dynamics and simulated annealing. 12. Model building, difference electron density maps, OMIT maps. 13. Checking of the accuracy of the structural model R-factors, Ramachandran plot, B-factors, Luzzati diagram. 14. Practical examples.
Literature
  • RHODES, Gale. Crystallography made crystal clear : a guide for users of macromolecular models. San Diego: Academic Press, 1993, xiii, 202. ISBN 0125870752. info
  • MCPHERSON, Alexander. Preparation and analysis of protein crystals. Malabar: Krieger Publishing Company, 1989, 371 s. ISBN 0-89464-355-X. info
  • DRENTH, Jan. Principles of protein X-ray crystallography. New York: Springer-Verlag, 1994, xiii, 311. ISBN 0-387-94091-X. info
Assessment methods (in Czech)
2h přednáška. Podle možností praktické ukázky krystalizace biomolekul, krystalografického software, Internetových zdrojů. Podmínkou pro vykonání zkoušky je teoretická znalost metod krystalizace, získání a zpracování difrakčních snímků a metod určení 3D struktury biomolekul.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2000, Spring 2003, Spring 2005, spring 2012 - acreditation, Spring 2015, Spring 2016, Spring 2017.
  • Enrolment Statistics (Spring 2004, recent)
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