Takashi Ishikawa: Catalogue data in Spring Semester 2019

Name Prof. Dr. Takashi Ishikawa
Inst. f. Molekularbiol.u.Biophysik
ETH Zürich, HPK F 18
Otto-Stern-Weg 5
8093 Zürich
RelationshipAdjunct Professor

551-1402-00LMolecular and Structural Biology VI: Biophysical Analysis of Macromolecular Mechanisms
This course is strongly recommended for the Masters Major "Biology and Biophysics".
4 credits2VR. Glockshuber, T. Ishikawa, S. Jonas, B. Schuler, D. Veprintsev, E. Weber-Ban
AbstractThe course is focussed on biophysical methods for characterising conformational transitions and reaction mechanisms of proteins and biological mecromolecules, with focus on methods that have not been covered in the Biology Bachelor Curriculum.
ObjectiveThe goal of the course is to give the students a broad overview on biopyhsical techniques available for studying conformational transitions and complex reaction mechanisms of biological macromolecules. The course is particularly suited for students enrolled in the Majors "Structural Biology and Biophysics", "Biochemistry" and "Chemical Biology" of the Biology MSc curriculum, as well as for MSc students of Chemistry and Interdisciplinary Natural Sciences".
ContentThe biophysical methods covered in the course include advanced reaction kinetics, methods for the thermodynamic and kinetic analysis of protein-ligand interactions, static and dynamic light scattering, analytical ultracentrifugation, spectroscopic techniques such as fluorescence anisotropy, fluorescence resonance energy transfer (FRET) and single molecule fluorescence spectrosopy, modern electron microscopy techniques, atomic force microscopy, and isothermal and differential scanning calorimetry.
Lecture notesCourse material from the individual lecturers wil be made available at the sharepoint website

Prerequisites / NoticeFinished BSc curriculum in Biology, Chemistry or Interdisciplinary Natural Sciences. The course is also adequate for doctoral students with research projects in structural biology, biophysics, biochemistry and chemical biology.
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.
ContentFebruary 22 Lecture 1 Prof. Dr. Kurt Wüthrich
History of Structural Molecular Biology

March 1 Lecture 2 Prof. Dr. Kaspar Locher
X-ray diffraction from macromolecular crystals

March 8 Lecture 3 Prof. Dr. Kaspar Locher
Data collection and statistics, phasing methods

March 15 Lecture 4 Prof. Dr. Nenad Ban
Crystal symmetry and space groups

March 22 Lecture 5 Ban Lab
Practical session with X-ray data processing

March 29 Lecture 6 Prof. Dr. Takashi Ishikawa
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)

April 5 Lecture 7 Dr. Daniel Boehringer
Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

April 12 Lecture 8 Ban Lab
Practical session including specimen preparation (cryo, negative stain, visit to ScopeM

May 3 Lecture 9
Prof. Dr. M. Pilhofer
Tomography I, including basics and subtomogram averaging

May 10 Lecture 10 Ban Lab
Practical session with example initial EM data processing

May 17 Lecture 11 Prof. Dr. Martin Pilhofer
Practical session (including recent techniques, including cryo-FIB)

May 24 Lecture 12 Prof. Dr. Nenad Ban
EM and X-ray structure building, refinement, validation and interpretation

May 31 Lecture 13 Ban Lab
Practical session with model building and refinemen