Experimental Methods in Structural Biology

10 credits

Syllabus, Master's level, 1MB447

A revised version of the syllabus is available.
Code
1MB447
Education cycle
Second cycle
Main field(s) of study and in-depth level
Technology A1N
Grading system
Pass with distinction, Pass with credit, Pass, Fail
Finalised by
The Faculty Board of Science and Technology, 21 October 2019
Responsible department
Biology Education Centre

Entry requirements

120 credits in the engineering programme in molecular biotechnology including Linear Algebra and Geometry I, Structural Bioinformatics, and one of the courses Electromagnetism and Wave Physics or Applied Physics for Molecular Biotechnology. Proficiency in English equivalent to the Swedish upper secondary course English 6.

Learning outcomes

The course gives an introduction to methods for structure determination of biological macromolecules with special focus on diffraction based methods.

On completion of the course, the student should be able to:

  • account for basic Fourier optics theory and its applications in structure determination of biological macromolecules
  • account for basic concepts in X-ray crystallographic theory
  • account for basic methods that are used in macromolecular crystallography
  • build models of macromolecules by means of electron density maps and analyse the possible errors of such models by means of different validation methods
  • critically review and evaluate structures solved with X-ray crystallography
  • account for requirements, possibilities and limitations of different structure determination methods and for the information provided by the different methods.

Content

Basics This course module covers basic concepts and theory of diffraction (both X-ray and electron diffraction) and Fourier optics and gives a basis to understand several of the most important methods for biomacromolecular structure determination (X-ray diffraction, cryo-EM). The concepts and the theory are developed, and are applied in later parts of the course.

X-Ray Crystallography Here, the theory for X-ray crystallography and its application in modern methods for structure determination of biological macromolecules is further developed. Topics covered include collection and processing of data from synchrotron radiation sources, experimental phasing, interpretation of electron density maps and modelling, refinement and validation of structural models. Students will also get practical experience of all essential stages in a structure determination. The course module gives the students the knowledge and experience needed to critically review and evaluate structures solved with X-ray crystallography.

Other methods: Cryo-EM, XFEL single particle imaging, SAXS Focus will be on cryo electron microscopy, that in recent years has progressed greatly and is rapidly becoming an attractive alternative to X-ray crystallography for structure determination of larger (>250 the kDa) biological macromolecules, but XFEL single particle imaging, SAXS, and NMR will also be introduced.

Instruction

Lectures, literature seminars, laboratory sessions and computer exercises. Participation in seminars, laboratory sessions and computer exercises are compulsory.

Assessment

Written examination (6 credits). Seminars, exercises and laboratory sessions (4 credits).

If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.

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