Protein and Enzyme Engineering

Uitgebreide vaknaam	Protein and enzyme engineering by mutagenesis and directed evolution
Leerdoelen	At the end of the course, the student is able to: 1) describe and explain the principles of modern methods for protein engineering and directed evolution aimed at enhancing stability, ligand binding and catalytic properties 2) perform basic computer modeling, visualization, design, and docking simulations, and to interpret the results with respect to applicability for a protein redesign task 3) carefully perform and analyze molecular biology experiments required for protein engineering (incl. primer design, oligonucleotide-directed mutagenesis, sequence analysis) on the basis of written protocols; 4) critically evaluate, present and discuss the work of other researchers or students, as included in presentations or published in the scientific literature
Omschrijving	This course aims to provide insight in the scientific basis and applications of protein engineering, especially of enzymes. Enzymes catalyze numerous biochemical reactions, and are highly important for bioprocessing, synthetic biology, biodegradation, as well as for diagnostics and therapeutics in medicine. They are attractive catalysts for the production of bioactive compounds because of their chemo-, regio- and stereoselectivity. Applications of enzymes often require protein engineering aimed at increasing catalytic activity, binding affinity or stability. For this, fundamental insight in structure-function relationships is of key importance. Furthermore, knowledge about methods in structure-based protein engineering and directed evolution contributes to solving many other problems in biomolecular sciences. The course trains students in the scientific background of protein engineering, including directed evolution, as well as the use of protein structures and computational methods. The course includes lectures, tutorials, computer practicals (computational protein design) and (for students lacking the experience) laboratory work to make students familiar with mutagenesis methods. Students are also trained in the ability to examine recent literature to critically present and discuss strategic options and experimental results. There are 2 schemes to follow this course: A) compact (full time), with all parts in three weeks (lectures, tutorials, computer practicals, lab practicals, assignments presentation, assignment report). Best for students full time Biomolecular Sciences or those who have exemption form the lab practicals. This may be too crowded for students who do not have an exemption for the laboratory practical and for students (chemistry, CB) who follow another course in parallel. B) stretched (for chemistry), with most parts (lectures, tutorials, computer practicals, lab practicals) in the first three weeks, but with the assignment presentation and reports scheduled in week 40.
Uren per week
Onderwijsvorm	Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC), Werkcollege (T) (Attending and active participation in all practicals is obligatory)
Toetsvorm	Opdracht (AST), Practisch werk (PR), Presentatie (P) (Assessment is by reviewing the assignment, computer practicals, and (if applicable) the laboratory practical. Both the practicals and the assignment require a pass (6 or higher) to obtain a final grade. Final grade: assignment text 50%, assignment presentation and discussion 50%. Computer practicals require a pass (>80% correctly completed) for the final grade.)
Vaksoort	master
Coördinator	Prof. Dr. G. Maglia, PhD.
Docent(en)	C.N. Pinto Teixeira, PhD. ,prof. dr. J.G. Roelfes ,dr. A.M.W.H. Thunnissen ,dr. H.J. Wijma
Verplichte literatuur	Titel Auteur ISBN Prijs FoldX, Yasara, Pymol etc. available on the PCs to be used during the computer practicals Assignments provided on Brightspace Course literature provided on Brightspace Course syllabus with detailed instructions provided on Brightspace Course slides provided on Brightspace
Entreevoorwaarden	For students admitted to Biomolecular Sciences and Chemistry track: Chemical Biology The course requires prior knowledge about biochemistry, molecular biology, organic chemistry, and catalysis, all studied in the first or second years of the BSc program Chemistry (tracks Life or Sustainability, both are fine) or Biology (Molecular Life Sciences). Basic experience with molecular biology is required. Note: students with hands-on skills in oligonucleotide-assisted mutagenesis (e.g. QuikChange, Gibson cloning) may request exemption from the laboratory practicals. Such a request should be carefully motivated and can be made to the coordinator.
Opmerkingen	Register for this course by sending an email to: academicadvisor.mscbio@rug.nl Obligatory: Filling out and handing in answers to any questions handed out during lectures, tutorials and computer practicals is mandatory (>80% correct). Mid-term review of the assignment and participation in the final presentation plus discussion are mandatory. Attending and active participation in laboratory practicals is obligatory (unless exemption). Participation in the GBB symposium is mandatory.
Opgenomen in	Opleiding Jaar Periode Type MSc Biomolecular Sciences  ( General programme) - semester I a verplicht MSc Chemistry  (Courses available for specializations) - semester I a verplicht