FSI3430 Protein Physics 7.5 credits


This covers structure, self-organization, and function of the biological macromolecules of life - primarily proteins.

Offering and execution

Course offering missing for current semester as well as for previous and coming semesters

Course information

Content and learning outcomes

Course contents *

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.

Intended 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 Disposition

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Literature and preparations

Specific prerequisites *

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

Recommended prerequisites

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

Examination and completion

Grading scale *

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Examination *

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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.

Other requirements for final grade *


Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination

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Erik Lindahl

Further information

Course web

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Offered by

SCI/Applied Physics

Main field of study *

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Education cycle *

Third cycle

Add-on studies

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Erik Lindahl

Ethical approach *

  • 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.

Postgraduate course

Postgraduate courses at SCI/Applied Physics