THIS MODULE IS NOT ANYMORE AVAILABLE

Module Title

Concepts of protein (un)folding (74408S, 1,5 ov, advanced course, 14h)

Degree Programme: Protein science and Biotechnology

Remarks:

• This lecture module is offered in cooperation with the Biocenter Graduate School.
• This course was originally termed: Thermodynamics of protein (un)folding.

Lecturer(s):

André Juffer, PhD

Pre-requisites:

• Students should have completed the Bachelor degree program
• General knowledge of proteins and protein structures
• Some feeling for physical chemistry, in particular thermodynamics

Co-requisites:

• Registration is mandatory

Aims:

• To teach thermodynamical aspects of the protein folding process
• To teach some of the modern theories about the protein folding process

Learning outcomes:

Students should be able to:

• understand and discuss the various physical forces that interplay to (de)stabilize (membrane) protein structures
• understand and discuss the various views about protein folding
• understand and discuss the difference between chemical reactions and the protein folding process

Online syllabus:

This course introduces certain concepts which are of relevance for a better understanding of protein folding process. Main topics include a discussion about the structural stability of protein structures (thermodynamics of protein folding, cooperatively in protein folding, membrane protein folding and stability), kinetics of protein folding (reaction dynamics of small molecules, reaction rate theory and folding, implications of the Levinthal's paradox) and folding pathways and energy landscapes (classical mechanisms for folding, theory of protein folding: The folding funnel, Levinthal's paradox revisited). The ideas put forward in this module are based upon both experimental and theoretical (computer simulation) data, but the underlying experimental and theoretical methods are not explained in so many details.

Related modules:

• Protein structure
• Enzymology
• Introduction to Biocomputing

Lecture schedule:

Day	Date	Time	Room
Tuesday	22.03-12.04.2005	10.00-12.00h	BK130
Wednesday	23.03-06.04.2005	10.00-12.00h	BK130

Recommended text books:

• Creighton, T.E. Proteins. Structures and Molecular Properties, Second edition, Freeman and Company, New York, 1993. (somewhat outdated, but still very useful)
• Atkins, P. Physical Chemistry, 7th ed., Oxford University Press, 2001.

Assessment methods:

• Participants are required to present an article related to the subject of the course. The lecturer will handout these articles.
• Participants should also prepare questions for a second article which are to be discussed with the group and especially with the presenter (another participant) of that second article.
• You should not miss more than 2 lectures (one lecture is 2x45 minutes).

Lecture notes:

If you trouble in downloading, opening these Powerpoint files or printing them, please contact me.

• Introduction
• Brief introduction to Thermodynamics^*:
  • Older notes ( Notice: this link refers to a postscript file, not to a powerpoint file.
  • From"Introduction to Biocomputing".
• Thermodynamics of protein folding:
  • Part 1
  • Part 2
  • Part 3
• Membrane protein folding and stability:
  • Part 1
  • Part 2
• Folding pathways, Energy landscapes, folding funnel:
  • Part 1.
  • Part 2.
• Protein dynamics:
  • Protein dynamics