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Sergio Pantano spantano@pasteur.uy

A new CG model for water: WAT4?. Sergio Pantano spantano@pasteur.edu.uy. A new CG model for water: WAT4?. The WAT4 model. Coarse Graining Scheme. A new CG model for water: WAT4?. Comparison with Water Properties. The WAT4 model. RDF O-O (water). Comparison with Water Properties.

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Sergio Pantano spantano@pasteur.uy

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  1. A new CG model for water: WAT4? Sergio Pantano spantano@pasteur.edu.uy

  2. A new CG model for water: WAT4? The WAT4 model

  3. Coarse Graining Scheme A new CG model for water: WAT4?

  4. Comparison with Water Properties The WAT4 model RDF O-O (water)

  5. Comparison with Water Properties The WAT4 model RDF O-O (water) RDF WT4-WT4

  6. K+ Ionic Solvation at CG Level (second shell)

  7. CG-DNA + Na + WT4 Simulation Time [ns] WAT4? Solvation of Coarse Grain Systems The WAT4 model

  8. CG Solvent AA-Solute AA Solvent WAT4?Application to Hybrid systems!

  9. AA - CG Mixing of Bulk Water

  10. Folding “experiment” (EAAAK)3

  11. . . . . WT4 bead WT4 bead . . CG ION CG ION dWT4-ion SPC SPC dSPC-ion dSPC-ion = dSPC-ion dWT4-ion Hybrid AA/CG Ions (version 1.0) Parametrization Strategy: Add to the CG ions the difference in the radius between spc and wt4, only when they interact with spc, on order to reproduce the second solvation shell. dWT4-ion

  12. Hybrid AA/CG Ions (version 1.0) Bluish:AA Yellowish:CG

  13. WAT4? Solvation of Coarse Grain Systems Membrane-Ions Interactions

  14. Protein-Protein-Membrane:SNARE complex Blue: VAMP Red:Syntaxin Grey:SNAP25 Vesicle Plasma Membrane

  15. The Super SNARE Complex

  16. MD of single SNARE complex, AA and Hybrid Solvent atoms :241359 (AA) 105645 (Hybrid ~56 % reduction ) In collaboration with Marc Baaden

  17. MD of single SNARE complex, AA and Hybrid

  18. AA vs. Hybrid. Helicity per residue

  19. AA vs. Hybrid. Contact Map

  20. AA vs. Hybrid. Inter Protein Hydrogen Bonds

  21. AA vs. Hybrid. Membrane

  22. AA vs. Hybrid. Membrane thickness AA AA-CG

  23. AA vs. Hybrid. Intermembrane Space

  24. AA vs. Hybrid. Intermembrane Space

  25. Speed Up

  26. Institut Pasteur Montevideo Uruguay

  27. Astrid Bradner Pablo Dans Leonardo Darre Matias Machado Fernando Herrera Ari Zeida Sergio Pantano

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