Kaspar Locher: Catalogue data in Spring Semester 2022

Name Prof. Dr. Kaspar Locher
FieldMolecular Membrane Biology
Inst. f. Molekularbiol.u.Biophysik
ETH Zürich, HPK G 11
Otto-Stern-Weg 5
8093 Zürich
Telephone+41 44 633 39 91
RelationshipFull Professor

551-1324-00LBiochemistry5 credits4GK. Locher, N. Ban, R. Glockshuber, J. Piel, E. Weber-Ban
AbstractThe lecture teaches central reactions and metabolic pathways of biochemistry as well as molecular biology with emphasis on chemical and partly biophysical aspects.
ObjectiveUnderstanding of the most important metabolic processes involved in cellular energy production and storage as well as selected biosynthetic processes (incl. sugars, fats, steroids etc). Understanding of the molecular processes involved in replication, transcription and translation.
Prerequisites / NoticeSome lecture units are held in English.
551-1412-00LMolecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EM4 credits2VN. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers
AbstractThis course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.
ObjectiveStudents will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.
Content- History of Structural Molecular Biology

- X-ray diffraction from macromolecular crystals

- Data collection and statistics, phasing methods

- Crystal symmetry and space groups

- X-ray data processing

- Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)

- Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

- Tomography I, including basics and subtomogram averaging

- Tomography - recent techniques, including cryo-FIB
- EM specimen preparation (cryo, negative stain), initial EM data processing

- EM and X-ray structure building, refinement, validation and interpretation

- Model building and refinement
551-1556-00LStructure Determination by Cryo-EM: Data Processing and Analysis Restricted registration - show details
Does not take place this semester.
Number of participants limited to15

The block course will only take place with a minimum of 4 participants.

The enrolment is done by the D-BIOL study administration.
6 credits7PK. Locher
AbstractThis course will introduce the students to high-resolution structure determination using single particle cryo-electron microscopy, one of the key techniques for determining structures of biological macromolecules
ObjectiveThe goal of this course is to provide the students with the opportunity to pursue the processing of cryo-EM data and to gain experience in the building and refinement of an atomic model of a protein.
ContentThe students will receive a demonstration of sample vitrification and sample imaging using a cryo-electron microscope. The students will then use a pre-recorded data set to perform the calculations involved in determining the 3D structure of a model protein. Students will learn how to build an atomic model into their electron density maps, how to refine and analyze this model, and how to present their structural data. The following software packages will be used: Relion, Coot, Phenix, Pymol, Chimera.
Prerequisites / NoticeThe students will spend the majority of the time on data processing and are therefore expected to have some basic knowledge of bash terminal (Linux) commands. Basic physics, optics and linear algebra knowledge is also helpful. By the end of the course, the students will be expected to understand concepts such as the difference between Fourier and real space, image formation, the contrast transfer function (CTF), the fast Fourier transform (FFT), and Fourier shell correlation (FSC). During the course the students will be expected to complete homework assignments. At the end of the course, the students will give an oral presentation on what they learned. After the course, the students will submit a written report prepared individually.
551-1620-00LMolecular Biology, Biophysics1 credit1KR. Glockshuber, F. Allain, N. Ban, K. Locher, E. Weber-Ban, K. Wüthrich
AbstractThe course consists of a series of research seminars on Structural Biology and Biophysics, given by both scientists of the National Center of Competence in Research (NCCR) in Structural Biology and external speakers.
ObjectiveThe goal of this course is to provide doctoral and postdoctoral students with a broad overview on the most recent developments in biochemistry, structural biology and biophysics.
Prerequisites / NoticeInformation on the individual seminars is provided on the following websites: