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Modelling of Protein-Lipid Interactions. Lea Thøgersen PUMPKIN Opfølgningsmøde February 24, 2009. Outline. A PUMPKIN Postdoc Work in Progress Future Work. A PUMPKIN Postdoc. Bachelor in Chemistry and Molecular Biology PhD in Theoretical Chemistry (2005) Method development

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modelling of protein lipid interactions

Modelling of Protein-Lipid Interactions

Lea Thøgersen

PUMPKIN Opfølgningsmøde

February 24, 2009

outline
Outline
  • A PUMPKIN Postdoc
  • Work in Progress
  • Future Work
a pumpkin postdoc
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
protein lipid interactions
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
serca lipid interaction
SERCA – Lipid Interaction
  • Sarcoplasmic reticulum Ca2+ 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
all atom md study
All-Atom MD Study
  • E2 form (Thapsigargin-like inhibitor removed from the structure).
  • No Ca2+ ions, 0.2M K++Cl-

O

O

+2 SAPC

DOPC

DOPC

O

O

O

POPC

O

O

O

O

DMPC

-2 MPPC

O

slide8

MD

X-ray

X-ray lipids in orange

POPC – TRP shown

serca position in bilayer
SERCA Position in Bilayer

DMPC MPPC POPC DOPC SAPC

A.G. Lee, Biochimica et Biophysica Acta 1612 (2003) 1-40

how to adapt
How to Adapt

α

Within 8 Å

future plans
Future Plans
  • Model lipid-protein setup with detergent
  • Develop “shape” model to describe ms dynamics of ATPase – lipid system
acknowledging
Acknowledging…

Maria Musgaard

Biomodelling Group

Department of Chemistry

Birgit Schiøtt

Biomodelling Group

Department of Chemistry

Anne-Marie Lund Winther

Poul Nissen group

Department of Molecular Biology

Yonathan Sonntag

Poul Nissen group

Department of Molecular Biology

Poul Nissen

Department of Molecular Biology

Claus Olesen

Jesper Møller group

Institute of Physiology and Biophysics

Jesper Vuust Møller

Institute of Physiology and Biophysics

Carsten Wiuf

BiRC

Bioinformatics Research Center

Christian Storm

BiRC

Bioinformatics Research Center

activity depend on bilayer
Activity Depend on Bilayer

DOPC

A.G. Lee, Biochimica et Biophysica Acta 1376 (1998) 381-390

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