NBIK10024U Advanced Protein Science 2 – Protein Structure Determination

Volume 2022/2023
Education

MSc Programme in Biochemistry
MSc Programme in Physics

Content

This course in integrative structural biology will introduce the student to a range of methods that can be used, often together, to study protein structures at various levels of resolution. A key thread through the course is the integration of computational and experimental methods. On the experimental side, the greatest focus is on X-ray crystallography, NMR spectroscopy and cryo-electron microscopy, but these can be supplemented by other biophysical techniques (small-angle X-ray and neutron scattering, fluorescence methods and electron paramagnetic resonance) and molecular simulations and modelling. The course will provide a broad background to how NMR, cryo-EM and X-ray crystallography can be used to derive the three-dimensional structures of proteins. Further examples, will include how other biophysical methods, sometimes integrated with computational tools, can be used to study structures when other methods fail or when the systems are highly dynamic. The students will also learn how to analyse and evaluate experimentally derived protein structures. Finally, the course will contain an overview of how computational methods in structural biology, e.g. molecular dynamics simulations, can be used to study the structure and dynamics of proteins, including of intrinsically disordered proteins. We will also discuss how homology modelling and deep-learning-based structure prediction methods can be used to predict the structures of proteins and be used together with experiments. The format for the course is a mixture of lectures, group discussions and journal clubs discussing examples of the how the different methods can be used. A substantial part of the reading material is primary research articles and review articles.

Learning Outcome

Knowledge:

  • Understand the fundamental principles in integrative structural biology
  • Understand how protein structures can be determined via X-ray crystallography
  • Understand how protein structures can be determined via NMR spectroscopy
  • Understand the key spectroscopic observables available in NMR
  • Understand how other biophysical techniques can be used to obtain lower resolution structural information
  • To understand the basic principles of simulation techniques and how they can be used together with experimental methods
  • Have an overview of methods for protein structure prediction and homology modelling
  • To have working knowledge on examples of how protein dynamics can affect protein function
     

Skills:

  • Have the ability to read and critically evaluate publications containing macromolecular X-ray crystallography or NMR structures/data
  • Be able to, at a rudimentary level, design strategies for structural studies of proteins
  • To compare the strengths, limitations and complementary potential of structural data obtained using techniques based on completely different physical phenomena
  • To be able to use simple methods for protein structure determination
  • To be able to visualize results from molecular simulations
     

Competencies:

The central competency is to be able to view and understand a broad range of biophysical methods, including those in computers, and to envisage how these methods can be integrated in structural studies of proteins.

See Absalon.

A bachelor degree either in Biochemistry, Chemistry or Nano-technology is required. Other applicants may be admitted on the basis of an evaluation of their individual qualifications. Basic knowledge of protein science, as obtained for example in dedicated protein science courses, is a requirement, as is a previous basic introduction to biophysical techniques.
Two weekly three-hour sessions for seven weeks.
Lectures, student presentations of research papers, group discussions and computer exercises.
  • Category
  • Hours
  • Lectures
  • 26
  • Preparation
  • 160
  • Theory exercises
  • 7
  • Seminar
  • 12
  • Exam
  • 1
  • Total
  • 206
Oral
Continuous feedback during the course of the semester
Feedback by final exam (In addition to the grade)
Credit
7,5 ECTS
Type of assessment
Oral examination, 20 minutes (20 minutes preparation time)
Exam registration requirements

To be allowed to the final exam, the student has to have participated in minimum 80% of the sessions, to present at least a single paper and have to hand in answers to all questions. The latter must be accepted by the lecturer.

Aid
Without aids
Marking scale
7-point grading scale
Censorship form
No external censorship
One internal examiner
Re-exam

The same as ordinary exam.

Students who have fulfilled the 80% presence rule but have not had their hand-ins accepted, have to hand in new answers no later than three weeks before the reexamination.

If the requirement of 80% participation in the sessions is not fulfilled, the student must take the course again the next year.

Criteria for exam assesment

In order to achieve the grade 12 the student should be able to demonstrate a substantial amount of the knowledge, skills and competencies described under "Learning outcome".
The student should also have participated actively in the lectures, contributed actively in the student presentations, in both cases as outlined above.