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Dynamical simulations of virus wrapping and budding

Dynamical simulations of virus wrapping and budding. T. Ruiz-Herrero 1 , M. F. Hagan 2 , E. Velasco 1. Universidad Autónoma de Madrid, Madrid, Spain Brandeis University, Waltham, MA, USA. INTRODUCTION. exiting the cell. Budding. acquiring membrane coating. Attachment to the cell membrane

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Dynamical simulations of virus wrapping and budding

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  1. Dynamical simulations of virus wrapping and budding T. Ruiz-Herrero1, M. F. Hagan2, E. Velasco1 • Universidad Autónoma de Madrid, Madrid, Spain • Brandeis University, Waltham, MA, USA

  2. INTRODUCTION exiting the cell Budding acquiring membrane coating Attachment to the cell membrane Wrapping Fusion of the final neck Budding steps 1/13 T. RUIZ-HERRERO

  3. polar head Hydrophilic tail COARSE GRAINING 2/13 T. RUIZ-HERRERO

  4. Vrep Vbond Vbend Vatrr MEMBRANE MODEL:cooke model [Cooke et al, Phys. Rev. E, 72 (2205)] 3/13 T. RUIZ-HERRERO

  5. A/σ2 κ/ε0 ωC ωC MEMBRANE MODEL CHARACTERISTICS ● Broad range of fluidity ● Easily tunable ● Good agreement with measurements: rigidity, diffusion, density kBT/ε0=1.1 [from Cooke et al,Phys Rev E, 72 (2205)] Area per molecule Bending rigidity 4/13 T. RUIZ-HERRERO

  6. MEMBRANE PARTICLE INTERACTION AND SIMULATION CHARACTERISTICS Membrane-particle interaction s s=R-σ/2 • Simulation characteristics: Important parameters: • Molecular dynamics simulation R • NPT ensamble ε • Langevin thermostat kBT/ε=1.1 ωc κ,ρ • Andersen barostat P=0 • Verlet algorithm 5/13 T. RUIZ-HERRERO

  7. SIMULATIONS RESULTS: MAIN BEHAVIORS WRAPPING NON-WRAPPING MEMBRANE BREAKING 6/13 T. RUIZ-HERRERO

  8. /0=1e3 /0=5e3 /0=3e4 /0=1e4 SYSTEM BEHAVIOR 1: NON-WRAPPING 7/13 T. RUIZ-HERRERO

  9. /0=5e3 /0=5e2 /0=1.5e4 /0=1.55e4 /0=1.6e4 /0=1.65e4 SYSTEM BEHAVIOR 2: WRAPPING 8/13 T. RUIZ-HERRERO

  10. /0=6e3 /0=7e3 /0=5.5e3 /=7.5e3 /0=9.5e3 /0=1e4 SYSTEM BEHAVIOR 3: MEMBRANE BREAKING 9/13 T. RUIZ-HERRERO

  11. /kBT=12.5 R/σ=10 ε/ε0 R/σ /ε0 PHASE DIAGRAMS ε/ε0 In general, good agreement between simulations and theory Subtle dependence on bending coefficient For small epsilons deviation from theory 10/13 T. RUIZ-HERRERO

  12. ELASTIC THEORY 11/13 T. RUIZ-HERRERO

  13. ENERGY MAPS AND BUDDING PATHWAYS ε/ε0=0.9 ε/ε0=0.7 θ[rad] θ[rad] Penetration[σ] ε/ε0=1.1 Penetration[σ] θ[rad] Penetration[σ] 12/13 T. RUIZ-HERRERO

  14. BUDDING DYNAMICS: TIME SCALES AND PENETRATION Penetration vs time • steepness of the budding pathway ---> process speed • strenght adhesion energy ---> maximum penetration 13/13 T. RUIZ-HERRERO

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