SI2700 Protein Physics 7.5 credits

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.

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.

English B / English 6

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

If the course is discontinued, students may request to be examined during the following two academic years.

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

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Exam (TEN1; 7,5 university credits).

Erik Lindahl

• All members of a group are responsible for the group's work.
• In any assessment, every student shall honestly disclose any help received and sources used.
• In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.