752347 Practical course in protein engineering and technology

Type
Practical course
Semester hours
5
Lecturer (assistant)
Furtmüller, Paul Georg , Hofbauer, Stefan , Schaffner, Irene , Altmann, Friedrich , Ludwig, Roland , Poliak, Peter , Petrov, Drazen , Wozniak-Knopp, Gordana
Organisation
Offered in
Wintersemester 2024/25
Languages of instruction
Englisch
Content

The Practical Course in Protein Engineering and Technology is meant to conclude your studies within the specialization "Protein Engineering and Technology" of the Biotechnology Master (H418). Therefore, we encourage the application of students who have already successfully mastered all or most of the courses of this specialization. These will have preferred access to this course.

The participants of this course will work in a team to achieve their goals, which are different in the summer semester and winter semester. In the summer semester, you will be part of a (fictional) biosensor start-up that develops biosensors for medical applications, whereas in the winter semester you will join a (fictional) company research team to develop bispecific antibodies. You are encouraged to choose the topic of your interest.

Summer semester:
A (fictional) start-up wants to develop its first prototype of a blood glucose biosensor. The timeline is killing and the budget is tight. You are part of the research team that gathers information from all available sources and you plan, perform and analyze laboratory experiments. The prototype you want to develop is based on the currently most advanced biosensor platform. For your third-generation biosensor, you want to apply cellobiose dehydrogenase (CDH), a two-domain enzyme capable of direct electron transfer. Because of new FDA regulations, you will not only have to prove that your prototype can detect glucose in the blood, but also that it is not affected by maltose, which could cause patient fatalities. In the beginning, you have to select the best available CDH for this task. Based on homology modelling and docking experiments to the active-site of CDH you determine your candidate CDHs. After you obtained results from in silico methods you have to verify the quality of the available CDHs by methods of protein analytics. Which CDH is the most stable (differential scanning calorimetry (DSC)), has a high cofactor loading and a native conformation (circular dichroism (CD) spectroscopy), is least glycosylated (mass spectrometry, MS), or most active (steady-state and pre-steady-state kinetics)? Finally, you will prepare biosensors with the selected CDHs and test their performance in different buffers and for different substrates. At the end you will present your research and the prototype to a "consortium of investors".

Winter semester:
A small team of scientists in the research division of a big (fictional) pharma company has developed a new cool bispecific antibody format and wishes to forward it for manufacturing, so they have to defend their invention and show its advantages among over 30 different formats available. You will determine heterodimer purity with analytical methods (size exclusion chromatography, mass spectrometry) and its thermostability with differential scanning calorimetry. You will examine if the binding to two cognate antigens is retained with affinity measurements via Octet, and perform a cell surface titration to verify that this still holds for a cell-bound antigen. Finally, the result of a biological cell-based assay will demonstrate the activity of the bispecific antibody. With this, you will wrap-up a data package to be presented to the senior management to support their decision on the future of your favorite project.
Previous knowledge expected

Applicants are expected to have participated and finished most of the courses in the specialization of "Protein Engineering and Technology". Especially VU 772328 “Methods in Protein Characterization”, VU 894308 “Modelling and Simulation of Biomolecules” and VO 752345 “Enzyme Reactions: Mechanisms and Kinetics”.
Please also study the available information on BOKUlearn (Moodle) carefully before our first, introductory meeting.

You should:
- be able to download, edit and save protein sequences
- to perform basic homology modelling and use PyMol as a structure viewing program
- have understood the principles of molecular docking
- know how to use methods for protein analysis like DSC, CD, MS, SEC, Octet (biolayer interferometry)
- be trained to measure enzyme kinetics (summer semester) or binding affinity (winter semester)
- be highly motivated to collaborate with your colleagues
- participate in the management of your research team
Objective (expected results of study and acquired competences)

After successfully finishing the practical course in Protein Engineering and Technology you will fulfill the following criteria:

1. Knowledge: Identify amino acids in protein structures and their contribution to protein properties; Know methods to analyze protein structures and methods to analyze proteins

2. Comprehension: Explain the principles of molecular docking and the rationale for choosing different protein analysis methods

3. Application: Select the most appropriate method/approach to investigate and characterize proteins in silico and in vitro; Apply enzymes in biosensor production or antibodies in medical diagnostics

4. Analysis: Define relevant research tasks in a project; Break-down the research into manageable tasks and evaluate the performance of team members within a sub-task; Analyze obtained data and their significance for the project.

5. Synthesis: Recognize important results; Combine results to select the most suitable protein; Organize the most efficient production of the prototype

6. Evaluation: Assess the success of your project; Predict the chances of your prototype to be commercialized
You can find more details like the schedule or information about exams on the course-page in BOKUonline.