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Protein-membrane association. Theoretical model, Lekner summation. A.H. Juffer The University of Oulu Finland-Suomi. A.H.Juffer The University of Oulu Finland-Suomi. A.H.Juffer The University of Oulu Finland-Suomi. A.H.Juffer The University of Oulu Finland-Suomi. A.H.Juffer

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protein membrane association

Protein-membrane association.

Theoretical model, Lekner summation

A.H. Juffer

The University of Oulu

Finland-Suomi

A.H.Juffer

The University of Oulu

Finland-Suomi

A.H.Juffer

The University of Oulu

Finland-Suomi

A.H.Juffer

The University of Oulu

Finland-Suomi

A.H.Juffer

The University of Oulu

Finland-Suomi

A.H.Juffer

The University of Oulu

Finland-Suomi

slide2

Previous work

  • W. Xin and A.H. Juffer, Polarization and dehydration effects in protein-membrane association, To Be Submitted, 2004
  • W.Xin and A.H. Juffer, A BEM formulation of biomolecular interaction, To Be Submitted, 2004
  • C.M. Shepherd, H.J. Vogel and A.H. Juffer, Monte Carlo and molecular dynamics studies of peptide-bilayer binding, in: High Performance Computing Systems and Applications 2000 (Nikitas J. Dimpoulos and Kin F. Li, Eds.), Kluwer Academic Publishers (Dordrechts, The Netherlands), Chapter 29, 447-464, 2002.
  • C.M. Shepherd, K.A. Schaus, H.J. Vogel and A.H. Juffer, A Molecular Dynamics Study of Peptide-Bilayer Adsorption. Biophys. J. 80, 579-596, 2001.
  • A.H. Juffer, C.M. Shepherd and H.J. Vogel, Protein-membrane electrostatic interactions: Application of the Lekner summation technique. J. Chem. Phys. 114, 1892-1905, 2001.
  • A.H. Juffer, J. de Vlieg and P. Argos, Adsorption of Proteins onto Charged Surfaces: A Monte Carlo Approach with Explicit Ions. J. Comput. Chem., 17, 1783-1803, 1996.
background
Background
  • Interactions between lipid molecules and proteins crucial role in regulation biological function.
  • Membrane proteins:
    • Integral proteins: e.g. photosynthetic reaction center:
      • Fully embedded into membrane
    • Peripheral proteins: e.g. phospholipase C-1:
      • Only weakly bound to surface, separable by change in pH or ionic strength
background1
Background
  • Understanding the physics of protein-lipid interactions leads to deeper insight

Equilibrium constant

Standard free energy

THERMODYNAMICS, NOT MECHANISM

modeling protein membrane binding
Modeling protein-membrane binding

lipid bilayers

sandostatin

slide6

Free energy of binding

Conformational

Change.

Non-polar hydrophobic effect (expulsion of non-polar compounds from water

Changes in motional

degrees of freedom.

Difference in dielectric

properties between water

and hydrocarbon region (mutual polarization effects).

Direct electrostatic interaction

between basic residues and

anionic lipids.

Changes inside

membrane.

slide7

Coulomb interaction

rij

+

+

Long-ranged:

beyond dimension of protein

how to calculate it
How to calculate it?

Assume periodicity along x, y-direction

Lx

Ly

q

Image

Ly

the lekner summation
The Lekner Summation

Conditionally

converging sum

Fast absolutely

converging sum

slide12

Ions next to flat surface

  • carrying a negative surface
  • charge density.
  • Accumulation of Na+.
  • Depletion of Cl-.
  • Electric moment pointing
  • towards flat surface.
  • Symmetry along x- and y-axis
  • but not along z-axis.

z-axis

free energy of adsorption
Free energy of adsorption

Change in free energy in moving protein from bulk solution at z=- to

A point z=z0 near the surface:

Thermodynamic integration

slide18

Movie

The first 2 ns of a 6 ns MD simulation.

Biophys. J. 80, 579-596, 2001.

future improvements
Future improvements
  • Inclusion of internal (`essential’) degrees of freedom.
  • Dynamical simulations
  • Stochastic modeling of proteins
  • Effects of pH.
acknowledgements
Weidong Xin

Craig Shepherd

Heritage Foundation

Human frontiers

MRC

Biocenter

Academy of Finland.

Acknowledgements
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