NBIK10024U Advanced Protein Science 2 – Protein Structure Determination

Volume 2013/2014
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 (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
  • 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.
Two weekly three-hour sessions for seven weeks and one week of 20 hours laboratory/computer course.
Lectures, student presentations, group discussions and computer and laboratory exercises, written reports for evaluation.
  • Category
  • Hours
  • Lectures
  • 21
  • Practical exercises
  • 20
  • Preparation
  • 144
  • Theory exercises
  • 21
  • Total
  • 206
Credit
7,5 ECTS
Type of assessment
Continuous assessment
It is a requirement to pass the course to have been present at 80% of the sessions and 80% of the laboratory/computer course; to have presented papers for at least two topics in the course; to have written and handed in a report for each of the sessions of the course; and to have these reports accepted.
Marking scale
passed/not passed
Censorship form
No external censorship
Re-exam
Students who have fulfilled the 80% presence rule but not have all the reports accepted may pass the course if the reports are accepted no later than two months after the end of the course.
Criteria for exam assesment
In order to pass 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. The student should also have participated actively in the laboratory/computer course.