Courses

The training involves a series of practical courses which will allow the fellows to have a deep understanding of the possibilities (and limitations) of the various techniques of SBMP. They will acquire the necessary interdisciplinarity and scientific culture which is required in modern science.

The goal is to provide our fellow with state of the art theoretical and experimental insight in more than one field of structural biology (usually the one at the heart of their PhD project). Each PhD student will be given the opportunity, every year, to follow a 4 days experimental course in one of the following fields (the groups in charge of the organisation are given In parenthesis; it should be noted that each group in charge is a highly renowned expert in the corresponding field):

1. Liquid state NMR spectroscopy of membrane proteins

Organisation: V. Dötsch, University of Frankfurt, Germany; 2 days
Location: Institute of Biophysical Chemistry, University of Frankfurt, Germany.
Participants: 4-6 students
Objectives: Training in setting up liquid state NMR experiments, optimization of NMR parameters and pulse sequences, discussion of specific problems and solutions for membrane proteins
Content: Practical training in optimizing pulse length, delays, power levels and other parameters, measurement of 2D- and 3D NMR experiments

2. Solid state NMR of membrane proteins

Organisation: M. Baldus, H. Oschkinat, 3 days
Location: MPI Göttingen, Germany.
Participants: 4-6 students
Objectives: The objective of this course will be to familiarize scientists with state-of-the-art solid state NMR spectroscopy for biological systems. In particular, the theoretical principles and practical implementation of ssNMR approaches ranging from spectral assignment to 3D structure determination will be given in lectures covering 1-2 hours. Ample time will be allocated for questions after each presentation. In addition, aspects regarding sample labelling and membrane preparation and reconstitution will be discussed. Hands-on examples on how to analyze ssNMR data obtained on membrane proteins will be given and analyzed during the session. Ongoing research to enhance ssNMR signal intensities using DNP will be introduced by lectures given by RG Griffin (visiting scientist). In addition, ssNMR-based ligand binding studies will be conducted in close context to industrial partner ZoBio.

3. X-Ray crystallography

Organisation: E. Pebay-Peyroula, M. Archer, J.L. Popot, 3 days
Location: IBS Grenoble, France.
Participants: 4-6 students
Objective and contents:
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Characterization of protein-detergent solutions by analytical ultracentrifugation (oligomerization, aggregation,…), by IR spectroscopy for proper folding and/or endogenous lipid association (this part will be taken into account by J. Baenziger, visiting scientist from Ottawa Univ.),…
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Crystallization with classical approaches and with lipidic cubic phases
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Behavior of lipids and amphiphiles as function of different parameters
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Handling and characterization of crystals, data collection using synchrotron radiation sources, data treatment
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New designed compounds for heavy atom derivatives.
All these aspects will be approached by courses followed by practicals, not only with model systems but also with proteins from the participants.

4. Electron microscopy

Organisation: A. Engel; 5 days
Location: Center for cellular imaging and nanoanalytics, Biozentrum, University of Basel, Switzerland.
Participants: 6 students
Objectives: This course introduces the students to the use of the EM for (i) checking the quality of purifed proteins, and screening 2D crystallization condition, (ii) producing high resolution projections of single complexes by cryo-EM, (iii) producing high resolution projections of crystals by cryo- EM, and (iv) electron diffraction. Students are asked to bring their own samples. The course will mainly be practical, although the basics of EM will be presented in few theoretical lectures.

5. Atomic force microscopy and single-molecule force spectroscopy

Organisation: D. Müller and A. Engel, 4 days
Location: Center of Biotechnology, Dresden, Germany
Participants: 4-6 students
Objectives and content: The students will be trained towards becoming theoretical knowledge and practical skills of AFM and SMFS to characterize the structure and function of native membrane proteins. On the basis of standard samples (e.g., purple membrane, bovine rhodopsin, OmpF, …) the students will learn sample preparation procedures and how to conduct highresolution AFM to observe the native membrane protein assembly and oligomeric state. In a next step SMFS will be applied to characterize molecular interactions stabilizing the membrane protein and switching its functional state. Procedures to analyze experimental AFM and SMFS data will be teached and applied. Industrial partners (JPK Instruments) will support the practicals closely to understand the necessary tasks to further improve their methods to characterize native membrane proteins. As a consequence the companies will develop the next generation of AFM and SMFS instrumentation being improved technically and made much more user friendly to membrane protein biophysics.

6. Numerical simulations

Organisation: S. Filipek and H. Grubmüller, 3 days
Location: IIMCB, University of Warsaw, Poland.
Participants: 6-8 students
Objectives and content: The modelling course will focus main aspects associated with membrane proteins: homology modelling techniques (Modeller program), ab-initio loop predictions, creating the periodic box with the membrane (VMD program), immersing the protein and optimizing the system, molecular dynamics simulations (Namd2 and Gromacs programs), steered molecular dynamics for protein unfolding and domain movement (Namd2). The course will start with lectures explaining theory of modelling and simulations, then hands-on classes will be carried on including practical learning of usage of particular programs. The more difficult tasks like building complexes of membrane proteins and elucidation of mechanisms of action of these proteins will be discussed during the seminars. They will be multipurpose devoted to proteins of interests to particular PhD students. Ligand docking classes will start with manual docking using software equipped with 3D glasses (VMD, Yasara), then programs for automated docking Autodock and FlexX will be presented and used, and results compared.

7. Expression-purification-biophysical characterization

Organisation: F. Bernhard, H. Vogel, J.L. Popot, University of Frankfurt, Germany; 3 days
Location: J.W. Goethe University, Frankfurt, Germany.
Participants: 4-6 students
Objectives: In this course students will cover the entire procedure from construction of a DNA of a certain membrane protein, the expression of this gene in a particular cell line, the characterization of the protein in a living cell to the solubilization and purification and the final biophysical characterization (functional tests by different spectroscopic procedures). Alternatively, in vitro, cell-free expression procedures will also be employed.

8. Complementary skill training and contacts with the private sector

Course Title: Biotechnology, the interface between science and the market place.
Course Organizer: Gregg Siegal, Chief Scientific Officer, ZoBio, NL
Location: ZoBio Inc., Leiden, The netherlands.
Participants: 8-10 students
Objectives: The students may have to be organised twice in the course of the ITN action, according to student’s need. Each student will follow this course or a similar one available in his University. While the biotechnology world depends on science, life in a biotechnology company involves far more than simply performing experiments. This course will aim to provide academic students with their first encounter with the demands of a small biotechnology company. Students will be introduced to a number of areas specific to the commercial sphere including: organization and quality assurance of a commercial research projects, protecting an invention – an introduction to the patent system and managing scientists. Special emphasis will be placed on the requirements for starting a small company such as market analysis, funding and general entrepreneurialism. Teaching will be in the form of lectures, short projects and presentation such as practicing “pitching”.