Advanced protein structure engineering and analysis

• examine and criticize the quality of an already published protein structure
• access and download published data, for evaluation and re-refinement
• critically evaluate and compare protein structures from the literature or databases
• account for the building of crystalline materials in terms of symmetries and unit cells
• describe fundamental X-ray diffraction theory and define the reciprocal lattice and relate it to the direct lattice
• derive hypotheses for optimized protein design based on structural analysis
• perform structural comparisons and understand 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 alphafold models vs crystallographic experimental models
• understand how alphafold models have promoted structural biology
• Master refinement and validation of online crystallographic data

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.

protein chemistry, organic chemistry, physical chemistry

Lectures, computer exercises and practical exercises.

It is expected that the student bring their personal computer and have approx 2gb space to install the programs needed.

Minimum: 6.

Please be aware that this course will only be held if the required minimum number of participants is met. You will be informed 8 days before the start of the course, whether the course will be held.