NBIK22004U Integrative Structural Biology
MSc Programme in Biochemistry
MSc Programme in Biology
MSc Programme in Nanoscience
The course introduces students to the many advanced techniques researchers use to capture biological structure including various X-ray and neutron techniques, single molecule fluorescence methods, cryo-electron microscopy, nuclear magnetic resonance spectroscopy and hydrogen deuterium exchange mass spectrometry. This will involve hands on experimental exercises during which students learn how to use these methods in order to derive the three-dimensional structures of proteins. To become properly familiar with the different techniques, students will visit and conduct exercises at the large-scale infrastructure facilities in the region, such as ESS and MAX-IV in Lund, as well as the state-of-the-art facilities at UCPH such as the Core Facility for Integrated Microscopy, the cOpenNMR facility for nuclear magnetic resonance spectroscopy and the facility for biological small-angle X-ray scattering, CPHSAXS. Building on this, the course will provide an overview of how computational methods in structural biology, e.g. molecular dynamics simulations and Monte Carlo methods, can be used to study the structure and dynamics of proteins. The course will also teach students to integrate data obtained from various structural biology techniques using state-of-the-art computational modelling and machine learning methods. This will involve hands-on experience in computational experiments.
The course is highly interdisciplinary and relevant to students from biology, physics, chemistry and health science backgrounds. As such, after the initial introduction, students receive a crash course in either Protein Science (specifically for students with a physics, chemistry or computer science background) or Computer Science (for students with a background in the bio- and health sciences), depending on their background. The format will be a mixture of lectures, journal clubs, practical exercises, group discussions, facility visits and hands-on introductions to e.g. software used in protein structure determination and molecular simulations. A substantial part of the reading material is expected to be primary research articles and review articles.
This course is part of a network of four advanced, experimental and interdisciplinary courses being offered at the University of Copenhagen, Aarhus University, the Technical University of Denmark and SydDansk University. The network is called the Interdisciplinary Teaching in Natural & Technical Science network is funded by the Novo Nordisk Foundation. Students enrolled in this course will have the opportunity to participate in networking activities such as a seminar series, research facility visits and summer camps.
Knowledge:
- Knowledge on advanced structural biology techniques and instrumentation including X-ray crystallography, NMR spectroscopy, cryo-EM, mass-spectrometry, single molecule methods and small angle scattering.
- Understand how protein structures are determined via X-ray crystallography, NMR or cryo-EM.
- Understand how different methods may be integrated to study complex and dynamic macromolecules and their assemblies.
- Understand the time and length scales that different methods can access.
- Understand the basic principles of computer simulation techniques and how they can be used together with experimental methods.
- Have an overview of methods for protein structure prediction.
Skills:
- Ability to read and critically evaluate publications containing structural biology data including X-ray crystallography, cryo-EM, NMR spectroscopy and small angle scattering.
- Be able to, at a basic level, design strategies for structural studies of proteins.
- Can differentiate between methods according to resolution in both time and length scales.
- To compare the strengths, limitations and complementary potential of structural data obtained using different techniques.
- Be able to use simple methods for protein structure determination.
- Be able to perform and visualize results from structure prediction methods and molecular simulations.
- Can read and extract key scientific findings from primary literature on integrative structural biology.
- Can perform experiments within structural biology and use computational tools to evaluate structural biology data.
Competences:
- Critically evaluate data obtained in structural biology research.
- Combine a broad range of biophysical methods, including those based on computational methods to envisage how these methods can be integrated in structural studies of proteins.
- Ability to combine methods to study the structure, dynamics and functions of proteins for use in both pharmaceutical sciences (for example as drug targets or protein pharmaceuticals) or biotechnology (for example enzymes)
See Absalon for a list of course literature
This course will involve trips to large-scale infrastructure at Lund and several excursions around Copenhagen. All travel costs are provided. In addition, students will be invited to participate in networking activities with students in similar advanced, experimental and interdisciplinary courses based at SDU, AU, and DTU. These will include a seminar series, research facility visits and summer camps. Again, all travel costs will be provided.
- Category
- Hours
- Lectures
- 67
- Preparation
- 301
- Practical exercises
- 23
- Excursions
- 15
- Exam Preparation
- 6
- Exam
- 0,5
- Total
- 412,5
- Credit
- 15 ECTS
- Type of assessment
- Oral examination, 30 minutes
- Type of assessment details
- Students will have 48 hours to prepare with an assigned journal article which will then be discussed in a 30-minute exam.
- Exam registration requirements
To be allowed to the final exam, the student has to have participated in minimum 60% of the practical exercises assigned to them. In addition, the student must have submitted a poster. If the student has not completed at least 60% of the practical exercises assigned to them, the student is permitted to submit 2-page written reports on the topic of the missed practical exercises.
- Aid
- Without aids
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
Two internal examiners
- Re-exam
The same as the ordinary exam.
Criteria for exam assesment
See Learning Outcome
Course information
- Language
- English
- Course code
- NBIK22004U
- Credit
- 15 ECTS
- Level
- Full Degree Master
- Duration
- 2 blocks
- Placement
- Block 3 And Block 4
- Schedule
- A
- Course capacity
- 40
The number of places might be reduced if you register in the late-registration period (BSc and MSc) or as a credit or single subject student.
Study board
- Study Board for the Biological Area
Contracting departments
- Department of Biology
- Department of Computer Science
- Department of Pharmacy
- Department of Drug Design and Pharmacology
- Department of Chemistry
- The Niels Bohr Institute
Contracting faculty
- Faculty of Science
Course Coordinators
- Kresten Lindorff-Larsen (lindorff@bio.ku.dk)
Lecturers
Annette E. Langkilde, Department of Drug Design and Pharmacology
Birthe B. Kragelund, Department of Biology
Heloisa N. Bordallo, Niels Bohr Institute
Henriette E. Autzen, Department of Biology
Karen L. Martinez, Department of Chemistry
Karen Skriver, Department of Biology
Kasper D. Rand, Department of Pharmacy
Kresten Lindorff-Larsen, Department of Biology
Kristoffer E. Johansson, Department of Biology
Leila Lo Leggio, Department of Chemistry
Nikos Hatzakis, Department of Chemistry
Poul Martin Bendix, Niels Bohr Institute
Wouter Boomsma, Department of Computer Science