Integrative Structural Biology

Course content

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.

Learning outcome

Knowledge:

  • Knowledge on advanced structural biology techniques and instrumentation including for 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 from 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)

Lectures, journal clubs, practical exercises, facility visits, group discussions

See Absalon for a list of course literature

The course is an advanced interdisciplinary course and students interested in biological structure are encouraged to apply from a wide variety of disciplines, including chemistry, biology, physics, computer sciences, human biology, neuroscience, and the pharmaceutical sciences. It will be beneficial to have some basic knowledge of protein science and students who do not should expect to supplement their knowledge on this topic during the course. To make it possible for students from a variety of disciplines to participate, students will receive a brief six-hour introductory crash course to either protein science or computer science, depending on their background.

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.

ECTS
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.
Aid
Only certain aids allowed

All aids are allowed during the preparation (48 hours).  

During the exam, the student may only bring the assigned article.  

 

 

Marking scale
7-point grading scale
Censorship form
No external censorship
Two internal examiners
Criteria for exam assessment

See intended learning outcomes

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 67
  • Preparation
  • 301
  • Practical exercises
  • 23
  • Excursions
  • 15
  • Exam Preparation
  • 6
  • Exam
  • 0,5
  • English
  • 412,5

Kursusinformation

Language
English
Course number
NBIK22004U
ECTS
15 ECTS
Programme level
Full Degree Master
Duration

2 blocks

Placement
Block 3 And Block 4
Schedulegroup
A
Capacity
40
Studyboard
Study Board for the Biological Area
Contracting department
  • 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 Coordinator
  • Kresten Lindorff-Larsen   (8-807d827883867a7a54767d83427f8942787f)
Course Secretary: Lucy Holt (lucy.holt@bio.ku.dk)
Teacher

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

Saved on the 14-07-2022

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