1. How mechanical force regulates the function of proteins? Vesa Hytönen (veshyto@mat.ethz.ch) Research group of Professor Viola Vogel, Biologically Oriented Materials, Department of Materials, ETH- Hönggerberg, Zürich Beowulf Day January 30th, 2006

2. Folding of protein ● Protein folding is energetically favored reaction ● Components assisting folding could be needed (for example chaperones) www.press.uillinois.eduFerrera & Caflisch (2000), PNAS 97, 10780-

3. Conformation vs. function ● Different conformations of the protein can have different functions ● Native state vs. functional state ● Protein activation Prion Biology and Diseases. Cold Spring Harbor Laboratory Press, NY, 1999.

4. Conformation vs. function ● Different conformations of the protein can have different functions ● Native state vs. functional state ● Protein activation www.mad-cow.org Brain tissues showing amyloid plaques caused by aggregation of the particularly folded protein

5. Factors affecting protein conformation ● Physical parameters – temperature, pressure etc. ● Chemical parameters – pH, solvent electrophilicity etc. ● Mechanical force – force applied via interactions – force produced by the cell

6. Steered molecular dynamics ● Forced unfolding of protein ● NAMD molecular dynamics simulation ● 400 pN pulling force applied

7. Simulation methods ● Experimental protein structures used as a starting material ● Protein solvated in explicit water and ions added to neutralize the system ● Periodic water box used ● Typical system contains ~100 000 atoms (~70-80% water) ● CHARMM27 force field used (Newtonian mechanics) ● NAMD simulation package (Developed by research group of Professor Klaus Schulten, www.ks.uiuc.edu ) ● Visualization of simulations with VMD

8. Computation ● Simulation carried out in femtosecond resolution ● Typical simulation time is some nanoseconds ● To obtain 1 ns simulation of 100 000-atom system, ~24 hours simulation time is needed in Gonzales cluster using 64 processors ● Coordinates saved every ps -> 1 ns simulation produces about 2 GB of data. ● Atomic resolution of the protein and solvent behaviour

9. Conclusion ● Molecular dynamics simulations make it possible to study behaviour of proteins in equilibrium and non-equilibrium conditions ● We would like to study the role of mechanical signals in protein function regulation?

10. Computational research projects in the Professor Viola Vogel’s group ● Eileen Faucher – Functional properties of integrins ● John Saeger – Fluorescent proteins ● Lina Nilsson – Bacterial adhesion ● Vesa Hytönen – Dynamics of the focal contacts

11. Thank you!