PUMPKIN Ideas. Objectives Development and application of methods to:  Model the dynamics of domain motion in large proteins  Incorporate experimental.

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Presentation transcript:

PUMPKIN Ideas

Objectives Development and application of methods to:  Model the dynamics of domain motion in large proteins  Incorporate experimental data such as point mutation results in a protein domain model Improved understanding of the structure and function of P-type ATPases

The Time Scale Obstacle Pump reaction cycle => ms time scale CG MD => only μs time scale Even coarser formalism needed!

Implicit Solvent Nature Letter 2007 Reynwar et al. Max Planck Institute, Mainz

Protein Domain Model Sarcoplasmic reticulum Ca 2+ -ATPase (SERCA)

Chemical Grid Rigid but soft – use knowledge from SERCA Flexible Lipid model3456 Resolution /Å

Chemical Grid Every amino acid or functional group has a degree of hydrophobicity assigned e.g. from 0 – 1 The overall hydrophobicity of the grid-point-area is found => hydrophilic grid point => both hydrophobic and hydrophilic => hydrophobic grid point Electrostatics: The overall charge of the grid-point-area is used?

Special Challenges Sometimes single waters are relevant... Typically ions are involved.... Bonds are broken and formed... Point mutations.... Points / amino acids of known importance...

Build Protocol AA struct. known? e.g. X-ray pdb e.g. pdb with coors for Cα Remove everything but the protein. Prep protein. Known domains? Protocol that tests and suggests how domains could be defined. Define domains from resids like e.g. D1 8-20, 40-52,..... D , 60-84, Generate surface grid for every domain and linkers. Assign every grid point a chemical class. Make sure that important spots have the right chemistry and modify manually if necessary. Add lipid bilayer and other molecules such as ions, ATP, water... Model ready for simulation Yes No

Work Plan Recruit - physicist, computer scientist, mathematician? Develop a protein domain model and make it work with the lipid model in a MD framework. Refine the protein domain model  improve accuracy  allow for description of various detailed chemistry Generalize model to other proteins with domain motion Modelling studies with AA, CG and the current version of the protein domain model. * To increase the understanding of the system * To collect data at a higher resolution levels for testing and forming the protein domain model * Together with Birgit’s group

Input Comments to these ideas? Other ideas for projects? Expectations?