Teaching

Related links: PhD program of the Faculty of Biosciences | Studying Biophysics at Heidelberg University | Streifzug durch die Energielandschaft der Proteine

Our group offers a variety of teaching for physicists, chemists and biochemists interested in understanding the structure and dynamics of molecular systems. As a member of the Biosciences faculty at Heidelberg University Prof. Smith organizes the Biophysics/Structural Biology component of the Biology Diploma of Heidelberg University, together with Dr. Fischer and a number of other lecturers from other groups. These courses are for students of the Biology Diploma who have chosen to follow the Biochemistry/Biophysics option. The Biophysics/Structural Biology part of this comprises two lecture courses (both in the Summer semester), practical courses and seminars. Any physics, chemistry or biology student wishing to find out more about molecular modelling and simulation, biophysics, or structural biology is invited to contact Prof. Smith or another member of our group.

Courses will be offered in the Biology Diploma (Hauptfach Biophysik/Biochemie) and the Physics Diploma (Hauptfach Biophysik). For more information on the Physics Diploma courses please contact Prof. C. Cremer (Physics Department).

Below is the Kommentiertes Vorlesungsverzeichnis for the Structural Biology Option of the Biochemie/Biophysik Hauptfach/Nebenfach of the Biology Diploma:

Lehrveranstaltungen im Winter Semester

Lehrveranstaltungen im Sommer Semester

Studenten des Diplom-Studiengangs Biologie an der Universität Heidelberg können das Hauptfach Biochemie/ Strukturbiologie wählen. Innerhalb dieses Hauptfaches kann eine Vertiefung in Strukturbiologie gewählt werden - dies ist eine neue Lehrinitiative in Heidelberg. Die meisten Lehrveranstaltungen werden auf Deutsch, einige auf Englisch angeboten.

We now describe this field and the teaching at Heidelberg.

Structural Biology

Structural biology is the story of how the information present in the genetic code is translated into function - it is therefore the biology of the 21^st century. Genes are translated into amino-acid sequences that contain the chemical information required for proteins to fold into functional three-dimensional structures. Structural biology is largely concerned with finding out these three-dimensional structures at atomic detail, understanding how they fold and how these structures lead to biological function.
Specifically, students will receive a training in:

1. the major experimental techniques in structure determination (X-ray crystallography/NMR spectroscopy).
2. modelling and computer simulation of biological structures
3. molecular biophysics and associated biochemistry in solution. Motions in biomolecules.
4. in-depth study of structure:dynamics:function relationships in specific biological systems e.g. chromatin, muscle.

Specific Structural Biology courses:

Vorlesungen Strukturbiologie (SS)

SS: Biochemie II: Introduction to structure and dynamics of biomolecules.
This lecture course gives a grounding in methods and principles of protein and nucleic acid folding and structure, interactions between macro-molecules, X-ray crystallography, NMR spectroscopy, biomolecular modelling and simulation, solution biophysics and associated biochemistry.

SS: Biochemie IV: Structure and dynamics of biomolecules II.
Advanced topics in structural biology including: How does a protein fold? Macromolecular complexes. Ligand-protein interactions. Dynamics of proteins and DNA. DNA structure-sequence relationships. Methods in biomolecular simulation. Sequence-structure relationships. Chromatin structure and function. How does muscle work? And much more...

SS: Einführung in Molekulare Modellierung und Simulation. (Prof. Dr. Jeremy C. Smith, Dr. Stefan Fischer, Prof. Dr. Jörg Langowski). Mi 11.15-12.45 INF 368, R.220.
An introduction to the basic techniques useful for examining molecules on the computer: Principles of Protein and Nucleic Acid Structure, Protein Folding, Emprical Potential Energy Functions, Energy minimization, Molecular Dynamics Simulation, Vibrational Analysis of Proteins, Conformational Pathways, Brownian Dynamics, Ligand Binding calculations. Molecular Graphics.

WS: Protein Folding (Prof. Dr. Jennifer Reed (DKFZ) and Prof. Dr. Jeremy Smith)
N.B. Prof. Reed has submitted a full description of this course to the Kommentiertes Vorlesungsverzeichnis of the Biosciences faculty. Principles of the folding of proteins into their three dimensional active structures will be discussed from the biochemical and biophysical points of view. The biochemistry of protein folding will include in vivo folding with chaperone proteins. The principles of in vitro folding of small proteins will also be examined.

WS and SS: Mitarbeiterseminar Computational Molecular Biophysics. Mo 11.15-12.45 INF 368 R. 220.
All Biology Diploma students are welcome to the Computational Molecular Biophysics Lehrstuhl research seminars. For a detailed programme, see http://www.iwr.uni-heidelberg.de/groups/biocomp/seminars.html

SS: Strukturbiologie Wochenendseminar. (Prof. J.C. Smith)
We will spend a weekend together in the Schwarzwald or the Odenwald. On the Saturday and Sunday mornings and the Saturday evening, seminars will be given by participating students. Saturday afternoon will be devoted to a Strukturbiologie Wanderung. Student places strictly limited to 15. First-come first-served. For more information please contact Frau Ellen Vogel in the Lehrstuhl für Computational Molecular Biophysics, Tel. 548858.

F-Praktikum Strukturbiologie (HP-F, WS, 4. Quintal, 3 Wochen):
Dieses Praktikum soll an Hand interessanter Beispiele aus der aktuellen Forschung in die wichtigsten Techniken und Arbeitsweisen der modernen Strukturbiologie einführen. Dieses Praktikum ist Vorbedingung zur Teilnahme an dem Strukturbiologie L-Praktikum.

1. Computational Molecular Biophysics (Prof. Smith or Dr. Fischer):
   This practical introduces students to modern-day molecular modelling, simulation and graphics techniques. Starting from the Protein Data Bank of structures, the three-dimensional structure of a protein will be examined and computer simulations of protein flexibility and interaction undertaken.
2. Biophysik von Makromolekülen in Lösung (Langowski, Rippe)
   In diesem Praktikumsteil werden Methoden vorgestellt, die die Struktur und Dynamik großer Biomoleküle in freier Lösung untersuchen. Insbesondere werden an Beispielen aus der aktuellen Forschung Protein-DNA-Wechselwirkungen, die Assoziation von Multiproteinkomplexen und die Dynamik großer DNA-Moleküle mit Hilfe der analytischen Ultrazentrifugation, dynamischen Lichtstreuung und Fluoreszenzkorrelationsspektroskopie untersucht.

Structural Biology L-practical (HP-L).
L-practicals can be undertaken in any of the laboratories of the Dozenten. They are designed to be full 6 week research projects that allow students to perform in-depth research. A prerequisite for participation is the prior attendance to the Strukturbiologie F-Praktikum and the course Einführung in Molekulare Modellierung und Simulation. Examples of possible L-practicals are:

1. L-Praktikum: Computational Molecular Biophysics.
   The Student performs a protein modelling task which is part of an ongoing research project in the group of Computational Molecular Biophysics or the group of Computational Biochemistry, with the aim of understanding the function of a particular protein or of describing the properties of proteins in general. This can include running Molecular Dynamics, computing vibrational flexibility, mapping the electrostatic properties, simulating an enzymatic reaction or a conformational transition, computing ligand binding properties, etc. This L-Practikum is a prerequisite for students who wish to do a diploma-thesis in the group. Please contact Prof. Smith or Dr. Fischer.
2. L-Praktikum: Biophysik der Makromoleküle.
   Im Rahmen der aktuellen Forschungsarbeiten sollen die Studenten die Anwendung einer biophysikalischen Technik zur Untersuchung molekularbiologischer Systeme erlernen und möglichst selbständig Experimente durchführen. Der Schwerpunkt der Forschung in der Abteilung liegt in der Untersuchung der Struktur und Dynamik großer DNA-Moleküle und DNA-Protein-Komplexe (superhelikale DNA, Promoter-Enhancer-Systeme, Chromatin), des intrazellulären Transports von Makromolekülen sowie der Modellierung großer biomolekularer Systeme (von superhelikaler DNA bis zum kompletten Genom) mit modernen Computersimulationsverfahren. Die zur Verfügung stehenden Techniken umfassen zur Zeit Absorptions- und Fluoreszenzspektroskopie, Lichtstreuung, Fluoreszenzkorrelationsspektroskopie, analytische Ultrazentrifugation, Rasterkraftmikroskopie sowie Messungen der schnellen Kinetik mit stopped-flow-Methoden. Bitte Prof. Langowski kontaktieren.