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Molecular Dynamics Simulations Modeling Domain Movements of P-type ATPases Pumpkin Annual Meeting September 19, 2008.

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Presentation on theme: "Molecular Dynamics Simulations Modeling Domain Movements of P-type ATPases Pumpkin Annual Meeting September 19, 2008."— Presentation transcript:

1 Molecular Dynamics Simulations Modeling Domain Movements of P-type ATPases Pumpkin Annual Meeting September 19, 2008

2 Outline Setup  Model of the Molecular System  Energy Potential and Force Field Choosing the Right Setup Project Teasers

3 Model of the Molecular System Define the basic building blocks (The units) Implicit or explicit water and lipid description ε = 80 ε = 2 water bilayer

4 Energy Potential Non-bonding interactions Describing the physics and chemistry of the interactions of the units Bonding interactions r or θ E E VDW r mn

5 Moving in Time Collisions should occur smoothly!  Time step ~ 1/10 T fast motion period  T C-H vib ~ 10 fs => Time step = 1 fs Good ? Bad Input: r i (0) v i (0) Output: trace of r i (t) Bonding interactions Non-bonding interactions

6 The Cost Dependence on Unit Size Small units Large units Small mass/unitLarge mass/unit Fast motionsSlower motions Many unitsFew units Small time stepsLarge time steps Evaluation of force contribution - for every unit in every time step Long simulations with few details Short simulations with many details handled in parallel on many computers time steps cannot be handled in parallel on many computers

7 All-atom MD Lipid Study P P P To compare with: Single lipids observed with X-ray Lipid headgroups seen in the electron density map POPC

8 Three Levels of MD All atoms represented Partial charges assigned to each atom. Different types of each atom dependent on the surroundings. Possible to describe specific chemistry. Atoms collected in groups of app. 4 heavy atoms Units have integral charges and descriptors for hydrophobicity, hydrogen- bond donor/acceptor and charge. Atoms collected in domains and linkers Surface chemistry described in equidistant points. Charge and hydrophobicity represented. Time scale: 100 nsTime scale: several μs Time scale: ms Well established Under development Not developed

9 Development of Shape Model Benefits Keeps focus on large scale movements. ms time scale for describing mechanism. Explicit lipid bilayer. Disadvantages Only makes sense if surface chemistry and shape of domains are preserved throughout mechanism. Detailed chemistry not described. Implicit water. Potentially difficult to describe single water, ATP, ions, ligands....

10 Are the Domains Preserved? A M1M2 M3M4 P N M5M6 M7M10 6.66Å 5.33Å 4.00Å 2.66Å 1.33Å 0.00Å

11 The People 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 me BiRC Bioinformatics Research Center

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