NBIK10024U Advanced Protein Science 2 – Protein Structure Determination

Volume 2019/2020
Education

MSc Programme in Biochemistry

Content

The course gives an introduction to the range of methods that can be used to study protein structures at various levels of resolution. Most central are X-ray crystallography and NMR spectroscopy, but these can be supplemented by other biophysical techniques (Cryo electron microscopy, FRET, EPR, etc) and molecular simulations. The course will provide a broad background to how NMR 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 e.g. X-ray or NMR fails. 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 and Monte Carlo methods, can be used to study the structure and dynamics of proteins, including of intrinsically disordered proteins. The format for the course is a mixture of lectures, group discussions 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.

Learning Outcome

Knowledge:

  • 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.

Literature

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 is a requirement, as is a 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
  • Exam
  • 1
  • Lectures
  • 21
  • Practical exercises
  • 20
  • Preparation
  • 143
  • Theory exercises
  • 21
  • 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.