Protein Physics

Welcome to the spring 2014 Round Of The Protein physics course!

Important: The first lecture will be held on Monday January 20, 4-6pm, in room FE21 (floor 2) at Albanova University Center. See the schedule below for additional lecture dates.

This is an advanced/research level course that combines physics, chemistry, and biology approaches to understand structure and function of biological macromolecules, in particular proteins. The course runs in period 3, is open to students both from KTH and Stockholm University, and gives 7.5 ECTS credits.

Teacher Contact:

Magnus Andersson, researcher at Theoretical & Computational Biophysics KTH/Scilifelab.

E-mail (easiest way to reach me):

Phone: +46769469872

Office: Science for Life Laboratory, 6th floor

The course examination consists of two parts:

Handin tasks

Last submission dates: Hand-in task 1: Feb 8, 2014. Hand-in task 2: March 7, 2014. Hand-in task 3: March 7, 2014.

Course Literature

There is a very nice course literature directly based on a series of lectures given by Alexei Finkelstein in Moscow (pretty unusual at this level), which we highly recommend:

Alexei V. Finkelstein and Oleg B. Ptitsyn, Protein physics, Academic press 2002.

Despite raving reviews and a recent release, the book can be a bit hard to find since the second printing is presently a bit uncertain due to lots of color figures (high cost to the editor). You can still find it from several internet book stores (start with Amazon); please contact the teacher if this proves difficult, and we'll try to help!

Extra Material

We have a separate page with extra non-public reading material available at You can e-mail Magnus Andersson to get the password if you are registered on the course, or ask during class. The rest of that site is currently under production...

  • Lecture 1: Monday Jan 20, 4-6pm, Room FE21
    Introduction, proteins, amino acids. Chapters 1 & 2 of the book. slides
    The review by David Eisenberg - it's a good read - and will facilitate your understanding of protein secondary structure - optional though. 2003_Review

  • Lecture 2: Tuesday Jan 21, 4-6pm, Room FE21
    Molecular interactions (chapters 3-4). slides
    Cyrus Levinthals paper in Scientific American on protein structure & folding - good introduction - but optional for this course. Levinthal

  • Lecture 3: Monday Jan 27, 3-5pm, Room FE21
    Thermodynamics, defining hydrophobic effect from free energies, electrostatics (chapter 5-6). slides

  • Lecture 4: Thursday Jan 30, 3-5pm, Room FB41
    Secondary structure (chapters 7,10). Note that we cover chapters 8 & 9 later! slides

  • Lecture 5: Monday Feb 3, 3-5pm, Room FE21
    Statistical mechanics, the partition function, phase transitions & a-helix formation (chapter 8 & 9 (to p. 109)). slides

  • Lecture 6: Thursday February 6, 3-5pm, Room FE21
    Protein secondary structure formation and free energy (rest of chapter 9). slides

  • Lecture 7: Wednesday February 12, 1-3pm, Room FA31
    Fibrous proteins and globular proteins with alpha-helix and beta-sheet structure (chapter 11, 13 & 14). slides

  • Lecture 8: Thursday February 13, 8-10am, Room FE21
    Membranes & membrane proteins (chapter 12, but we will deviate a lot from the book). slides

  • Lecture 9: Friday February 21, 3-5pm, Room FE21
    Protein folds (chapter 15-16). slides

  • Lecture 10:Monday February 24, 3-5pm, Room FE21
    Denaturation & the character of transitions - cooperativity or not (chapter 17-18). slides

  • Lecture 11:Wednesday Feb 26, 3-5pm, Room FE21
    Kinetics of protein foldning (chapters 19-21). slides

  • Lecture 12:Friday Feb 28, 3-5pm, Room FE21
    Prediction and design of protein structure, bioinformatics (chapters 22-23). slides

  • Lecture 13:Monday March 3, 3-5pm, Room FE21
    GPCRs, docking and drug design (chapters 24-25, deviate a lot from the book). slides

  • Lecture 14:Friday March 11, 3-5pm, Room FB51
    Course repetition. slides
  • Examination:

    3 hand-in tasks, and a written examination, which will take place 1 pm to 5 pm in Room Fb51 on March 17.

    The re-examination will take place 8 am to 1 pm in Room FD41 on May 22.

    Example questions for the written examination.

    Voluntary visit at Scilifelab:

    I have asked one of our PhD students Iman Pouya to show some of our work on ligand-gated ion channels. Also, Goran Klement will present our electrophysiology lab.

    Date: March 5, Time: 11-12 am. Place: Scilifelab, Tomtebodavagen 23A, Ask for me at the reception. Please, be on time as the building is locked!