Master’s studies

Syllabus for Experimental Methods in Structural Biology

Experimentella metoder i strukturbiologi

Syllabus

  • 10 credits
  • Course code: 1MB447
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Technology A1N
  • Grading system: Fail (U), 3, 4, 5.
  • Established: 2017-03-07
  • Established by: The Faculty Board of Science and Technology
  • Applies from: week 27, 2017
  • Entry requirements: 120 credits in the engineering programme in molecular biotechnology including Linear Algebra and Geometry I, Electromagnetism and Wave Physics, and Structural Bioinformatics.
  • Responsible department: Biology Education Centre

Learning outcomes

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

After passing 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).

Reading list

Applies from: week 27, 2017

  • Rupp, Bernhard. Biomolecular crystallography : principles, practice, and application to structural biology

    New York: Garland Science, c2010.

    Find in the library

    Mandatory

  • Goodman, Joseph W. Introduction to Fourier optics

    3. ed.: New York: McGraw-Hill, cop. 2005

    Find in the library

In addition, scientific articles will be used during the course.