1. Modelling of Protein-Lipid Interactions Lea Thøgersen PUMPKIN Opfølgningsmøde February 24, 2009

2. Outline A PUMPKIN Postdoc Work in Progress Future Work

3. A PUMPKIN Postdoc Bachelor in Chemistry and Molecular Biology PhD in Theoretical Chemistry (2005)  Method development  Software development  Small molecules 2Y Postdoc from LundbeckFonden (2005-8)  Bioinformatics Research Center (BiRC)  Membrane Proteins – new insight via MD simulations  Antimicrobial peptides – interaction with lipid bilayer. Collaboration with NMR (inSPIN) PUMPKIN Postdoc since August 2008  Pumps are fascinating systems, with all kinds of interesting modelling aspects, which have not yet been touched  Fantastic setup of extraordinary insights and years of experience

4. Membrane Proteins

5. Protein-Lipid Interactions Lipid is the new water Annular shell (like solvation shell)  Generally not structure specific Non-annular lipids  Acting as co-factors  Affect function  Potentially structure specific

6. SERCA – Lipid Interaction Sarcoplasmic reticulum Ca 2+ ATPase  Membrane position  First time annular lipids observed in high-res X-ray  Thapsigargin – lipid mimicking? SR membrane  Low concentrations of sterols and sphingolipids X-ray membrane  Native  Detergent C12E8, lipid:detergent 7:16

7. All-Atom MD Study POPC E2 form (Thapsigargin-like inhibitor removed from the structure). No Ca 2+ ions, 0.2M K + +Cl - DOPC DMPC +2 SAPC -2 MPPC O O O O O O O O O O

8. MDX-ray POPC – TRP shown X-ray lipids in orange

9. SERCA Position in Bilayer DMPC MPPC POPC DOPC SAPC A.G. Lee, Biochimica et Biophysica Acta 1612 (2003) 1-40

10. Lys972 and Arg63 POPC SAPC

11. How to Adapt PCd/Å dev TM5/° dev TM9/° dev TM6/° dev di(C14:0)27 4.3 41.8 0.9 31.4 1.2 41.4 0.9 C14:0,C16:127 5.4 36.1 0.8 33.6 1.7 43.6 1.1 C16:0,C18:129 5.2 37.6 0.8 28.6 1.2 40.2 1.0 di(C18:1)29 5.1 36.5 1.0 22.3 1.2 35.9 1.0 C18:0,C20:133 5.2 35.1 1.2 28.0 1.1 36.6 1.0 Within 8 Å α

12. Thapsigargin Pocket TM3 TM5 TM7

13. Future Plans Model lipid-protein setup with detergent Develop “shape” model to describe ms dynamics of ATPase – lipid system

14. Acknowledging… Birgit Schiøtt Biomodelling Group Department of Chemistry Maria Musgaard Biomodelling Group Department of Chemistry Carsten Wiuf BiRC Bioinformatics Research Center Christian Storm BiRC Bioinformatics Research Center Yonathan Sonntag Poul Nissen group Department of Molecular Biology Poul Nissen Department of Molecular Biology Anne-Marie Lund Winther Poul Nissen group Department of Molecular Biology Claus Olesen Jesper Møller group Institute of Physiology and Biophysics Jesper Vuust Møller Institute of Physiology and Biophysics

15. Activity Depend on Bilayer DOPC A.G. Lee, Biochimica et Biophysica Acta 1376 (1998) 381-390