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Protein Folding, Bridging Lattice Models and Reality

Protein Folding, Bridging Lattice Models and Reality. Skorobogatiy Maksim, Ned Wingreen, Chao Tang NEC, Princeton, NJ. The Protein Folding Problem. A Reductionist’s Approach. Real Problem. Simple Model. General Features From Simple Models. Physical Interactions.

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Protein Folding, Bridging Lattice Models and Reality

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  1. Protein Folding, Bridging Lattice Models and Reality Skorobogatiy Maksim, Ned Wingreen, Chao Tang NEC, Princeton, NJ

  2. The Protein Folding Problem

  3. A Reductionist’s Approach Real Problem Simple Model General Features From Simple Models

  4. Physical Interactions Van der Waals interaction Electrostatic interaction Hydrogen bonding Hydrophobic interaction

  5. Essentials for a “Minimal” Model of Protein Folding • Self-avoiding polymer • At least two different types of monomers • Short range contact interaction

  6. HP Model on a Lattice (Lau, Chan, Dill) Sequence {s}: Structure {r}: 2D 3D

  7. Designability of Structures A structure S is designable by a sequence {s} if S is the unique ground state of {s}

  8. Designability Histogram Number of structures Number of sequences designing a structure

  9. Most Designable Structures a Helix b Strand

  10. Characterizing Highly Designable Structures What are the geometric properties which make These structures special ? 112222221101221122101122110122112210

  11. Real Proteins

  12. Implementation of Realistic Geometries

  13. Thermodynamics F=E-TS= NbbEbb+NwwEww+NwrEwr+NwbEwb- -TSchain-TSsolution Schain is simulated by MD or MC Ssolution=NwwSww+NwrSwr+NwbSwb Nww≈N0-Nwr-Nwb F-N0(Eww-T Sww) ≈ NbbEbb+ Nwr((Ewr- Eww)-T(Swr-Sww)) + Nwb((Ewb- Eww)-T(Swb-Sww))-TSchain F-F0= NbbEbb+ NwrEwr+ NwbEwb- TSchain

  14. Compact Structures Space F-F0= -Nbb|Ebb|+ Nwr|Ewr|- Nwb|E|wb- TSchain |Ebb| Ebb < 0 Ewr > 0 Ewb < 0 |Ewb| |Ewr|

  15. Spanning the Phase-Space Globular a Helical b Strand Globular “Real” protein like

  16. Coarse-Graining the Structures 110010111110000010100... Surface to Bulk Transition Rate Surface to Core Ratio

  17. Rate of Surface to Bulk Transitions

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