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Dynamic Virus Wrapping and Budding Simulations: Insights and Mechanisms

Explore the process of virus wrapping and budding through dynamical simulations, from attachment to cell membrane fusion. Study membrane models, interactions, simulation results, system behaviors, phase diagrams, elastic theory, energy maps, and budding dynamics.

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Dynamic Virus Wrapping and Budding Simulations: Insights and Mechanisms

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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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