Daniel J. Müller: Catalogue data in Spring Semester 2021

Name Prof. Dr. Daniel J. Müller
FieldBiophysics
Address
Professur für Biophysik
ETH Zürich, BSS F 43.2
Klingelbergstrasse 48
4056 Basel
SWITZERLAND
Telephone+41 61 387 33 07
Fax+41 61 387 39 94
E-maildaniel.mueller@bsse.ethz.ch
URLhttp://www.bsse.ethz.ch/biophysics
DepartmentBiosystems Science and Engineering
RelationshipFull Professor

NumberTitleECTSHoursLecturers
636-0116-00LNanomachines of the Cell
Attention: This course was offered in previous semesters with the number: 636-0008-00L "Nanomachines of the Cell II". Students that already passed course 636-0008-00 cannot receive credits for course 636-0116-00.
Prerequisites: Students should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering.
4 credits3GD. J. Müller
AbstractThe lecture "Nanomachines of the Cell" introduces the concept of using functional biomolecular units of the cell as nanoscopic machines and to assemble them to nanoscopic factories. The specific aim is to be able to use these machines and factories in more complex biotechnological processes as nanoscale functional elements or to control cellular systems and health
ObjectiveGain of an interdisciplinary research and development competence which qualifies for scientific work (master`s or doctoral thesis) as well as for work in the research and development department of a biotechnological company. The module is of general use in nano- and biotechnological courses of study focusing modern biomolecular technologies.
Content- What are nanomachines of the cell? Understanding the cell as a complex factory. Are there engineering principles of the cell and if so what can we learn? New ways to understand and to apply engineering principles of cellular nanomachines in biotechnology and nanotechnology.
- Introduction into factors and mechanisms that determine protein folding and stability. Inter- and intramolecular interactions. Energy landscape concept to describe protein folding, stabilization, destabilization, and unfolding. Mechanisms of protein stabilization, destabilization and aggregation in health and disease. Mechanisms of protein (de-)stabilization in biomaterials science, bioengineering, and in biotechnological and pharmacological applications. Methods to prevent protein destabilization in biotechnological applications. Ways to adjust and manipulate the protein stability in biotechnology and medicine. Designing molecular compounds that stabilize specific proteins. Molecular compounds that lead to protein destabilization, misfolding and denaturation.
- Biological and artificial membranes. Principles of membrane assembly, properties, stability and durability. Vesicles as containers for cargo. Engineering vesicles from native and synthetic components. Engineering ultrastable synthetic vesicles. Applying vesicles in biotechnology and medicine. Functionalizing vesicular membranes with proteins.
- Principles of membrane proteins. Structure and function relationship of membrane proteins. Importance of membrane proteins in pharmacology and biotechnology. Structural and functional characterization of membrane proteins. Bionanotechnological tools to handle and manipulate single membrane proteins.
- Membrane proteins as a toolbox to assemble nanoscopic functional vesicles. Multifunctional synthetic vesicles: Vesicles for drug delivery, vesicles for active transport, vesicles converting energy, vesicles switching their affinity, function, stability, and other properties.
- Energy currencies of the cell. Energy conversion. Storable and transient forms of energy. Nature created a variety of light-driven ion pumps. How to use the pumps and to modify them to our purpose? Employing light-driven ion pumps in biotechnology. Employing light-driven proton pumps adsorbing different wavelengths to boost the membrane gradient. Tuning the adsorption spectra of a light-driven ion pump.
- Structure, function, engineering and application of F-ATP synthases. Engineering artificial vesicular systems to convert light into ion gradients to synthesize ATP. Engineering ATP synthases as nanopropellers to move vesicles. Engineering a light-frequency tuned proton pumps to control the speed of nanopropelled vesicles. Engineering light-driven ion pumps to power the synthetic ATP propellers and to steer vesicles. Engineering and employing ATP synthases as molecular mixing devices.
Principles of signal transduction. The family of G-protein coupled receptors (GPCRs). Structure and function of GPCRs. Engineering (and other) possibilities to manipulate the functional state of GPCRs.
- Engineering light-activated channels for cellular control: Optogenetics.
- Assembly and employing fibrillar structures.
- DNA origami. Using DNA to build artificial three-dimensional structures at nanometer precision.
- Microtubuli. Occurrence, structure, function, and properties. Designing supports as circuits for molecular shuttles. Biofunctionalization of the circuits. Transporting molecular cargo along circuits. Engineering molecular devices to switch the transport 'on' and 'off'.
- Motor proteins. Translational motors, rotary motors, chemical driven motors, light-driven motors, unidirectional and bidirectional motors, reversibility, molecular ratchets, future visions. Common and different engineering principles of the F-ATP synthase and the flagella motor. Structure, function, energy source, and rotational modes. Controlled assembly of a complex machinery such as the flagella motor.
Lecture notesWill be provided as needed.
LiteratureAlberts et al: Molecular Biology of the cell

Biochemistry (5th edition), Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN 0-7167-4684-0, Freeman

Principles of Biochemistry, Nelson & Cox; ISBN: 1-57259-153-6, Worth Publishers, New York

Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania
Intermolecular & Surface Forces, Israelachvili; ISBN: 0-12-375181-0, Academic Press, London

Proteins: Biochemistry and Biotechnolgy, Walsh; ISBN: 0-471-899070, Wiley & Sons, New York

Textbook of Biochemistry with Clinical Correlations, Devlin; ISBN: 0-471-411361, Wiley & Sons, New York

Molecular Virology, Modrow et al.; ISBN: 3-8274-1086-X, Spektrum Verlag, Heidelberg
Prerequisites / NoticeStudents should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering.

The module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher.
636-0301-00LCurrent Topics in Biosystems Science and Engineering2 credits1SR. Platt, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, A. Moor, D. J. Müller, S. Panke, S. Reddy, T. Schroeder, T. Stadler, J. Stelling, B. Treutlein
AbstractThis seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
ObjectiveTo provide an overview of current systems biology research.
ContentThe final list of topics will be available at http://www.bsse.ethz.ch/education/.
636-1001-AALBio I: General Biology
Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement.

Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit.
5 credits7RD. J. Müller
Abstract
Objective
LiteratureCampbell “Biology“, chapters: 1 – 28, 40, 42, 43, 45
636-1003-AALBio III: Cellular Biology
Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement.

Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit.
5 credits7RD. J. Müller
Abstract
Objective
LiteratureAlberts “Molecular biology of the cell”, chapters: 7-13, 15-17