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Advanced protein structure engineering and analysis


Technical University of Denmark


General course objectives:
This is a PhD course parallel to the course 27325, which will give the participants the same deep insight into how proteins are determined and described in 3 dimensions and how the technique is used for rational structural engineering. The difference is that the course participants must be able to understand the material at a level where they can teach it themselves. The exam format reflects this higher level of learning. As in course 27325, it is expected that the participants will gain knowledge and experience with crystallization and X-ray structure determination, as well as an understanding of which statistical methods are used to validate protein structures. You will learn how to independently process and optimize the model with the latest structure processing programs, such as Coot and the refinement programs Phenix, and you will be expected to train it on models that present special challenges, such as models with post-translational modifications, such as glycosylations or complex structures with multiple polypeptide chains present in the asymmetric unit. The course will provide an introduction to basic structural chemical concepts and how X-ray and synchrotron radiation is used to determine the structure of proteins. After the course, the participants will be able to interpret and use structural chemical results and databases and will have received a thorough task-based introduction to rational protein redesign, protein-protein complexes, and an understanding of enzymatic active sites. You will gain insight into how to write your own script for pymol. As well as insight into how the protein structure database can be used as a biochemical tool to direct biochemical experiments or form the basis for new structure-based hypotheses. The course will also describe the new possibilities that the model prediction program alphafold2 has given structural biology. How alphafold can optimize the yield of already existing x-ray data.

Learning objectives:
A student who has met the objectives of the course will be able to:
  • Use the insight from the course to lecture on a specific topic beyond the scope of the course
  • select and sort published data, for evaluation and re-refinement
  • critically evaluate and compare protein structures from the literature or databases, with structural data from own project
  • account and understand the underlying principles for the building of crystalline materials in terms of symmetries and unit cells
  • describe and understand fundamental X-ray diffraction theory and define the reciprocal lattice and relate it to the direct lattice
  • derive and develop hypotheses for optimized protein design based on structural analysis
  • perform structural comparisons and evaluate the consequences of differences in data quality
  • set up a crystallization experiment and evaluate future experimental setups
  • explain how to solve a protein structure by the use of X-ray diffraction
  • evaluate alphafold2 models vs crystallographic experimental models
  • understand how alphafold2 models have promoted structural biology
  • examine, evaluate and criticize the quality of an already published protein structure

Contents:
Primary, secundary, tertiary and quaternary structure of proteins and other macromolecules. Analysis of molecular binding motifs, such as how to distinguish water, chloride or metals by using published diffraction data, examples of small molecule binding and catalytic active sites. Symmetry operations, crystal systems and space group notation. Experimental work with crystallization and test of crystal quality. Solving protein structures using X-ray diffraction, cryo electron microscopy and small angle scattering. Structure validation and article reading. Theory of X-ray scattering from crystals, including scripting for pymol.

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Course organizer
Jens Preben
Place/Venue
Anker Engelunds Vej 1
City
2800 Kgs. Lyngby
Country
Denmark
Workload
5
Link
http://kurser.dtu.dk/course/27845