SI2700 Protein Physics 7.5 credits

• Educational level

  Second cycle

• Academic level (A-D)

  D

• Subject area

  Physics
  

• Grade scale

  A, B, C, D, E, FX, F

• Link to homepage

• Course page on KTH Social

Learning outcomes

This is an advanced level course in collaboration between Stockholm University and KTH that covers structure, self-organization, and function of the biological macromolecules of life - primarily proteins.

Course main content

Biophysical chemistry: Amino acid conformations & properties, Ramachandran plots. Hydrogen bonds. Thermodynamics, entropy, free energy, and hydrophobic interactions. Electrostatics in biomolecules and solution, disulphide bonds. Properties of polypeptide chains. Alpha, 3-10, and Pi-helices. Parallel and anti-parallel beta sheets. Turns and loops. Conformational changes, helix-coil transitions, stability of secondary structure elements in water and other solvents. Non-polar, polar, and charged amino acid side chains.

Protein structure: Packing of helices and sheets, supersecondary structure. Collagen, keratin, silk, and other simple structures. Structure and function of water-soluble proteins, classification of protein folds. Protein aggregation/misfolding, prions (mad cow disease). Membranes and membrane proteins. Evolution and natural selection of structures.

Protein folding & structure prediction: Anfinsen's Hypothesis. Levinthal's paradox. Kinetics of protein folding. Two-state folding and intermediates. Molten globule or folding nuclei. Energy landscapes. Pathways. Prediction of structure from amino acid sequence. Threading.

Protein function: Docking and binding. Enzyme function. Active sites. Induced fit. Specificity and allostery. Membrane protein function. Protein engineering and design.

Eligibility

Recommended prerequisites: Differential equations, fourier transforms, thermodynamics, electrostatics, numerical methods and programming, elementary quantum mechanics and basic chemistry.

Literature

Finkelstein & Ptitsyn, Protein Physics, Academic Press (2002). ISBN 0-12-256781-1.

Examination

• TEN1 - Examination, 7.5 credits, grade scale: A, B, C, D, E, FX, F

Requirements for final grade

Exam (TEN1; 7,5 university credits).

Offered by

SCI/Theoretical Undergaduate Physics

Examiner

Erik Lindahl <erik@kth.se>

Version

Course plan valid from: Autumn 07.
Examination information valid from: Autumn 07.