dynamical simulations of virus wrapping and budding t. ruiz-herrero 1, m. f. hagan 2, e. velasco 1...
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Dynamical simulations of virus wrapping and budding
T. Ruiz-Herrero1, M. F. Hagan2, E. Velasco1
1. Universidad Autónoma de Madrid, Madrid, Spain2. Brandeis University, Waltham, MA, USA
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INTRODUCTION
Budding
exiting the cell
acquiring membrane coating
Attachment to the cell membraneWrappingFusion of the final neck
Budding steps
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COARSE GRAINING
polar head Hydrophilic tail
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MEMBRANE MODEL:cooke model
Vrep
Vbond
Vbend
Vatrr
[Cooke et al, Phys. Rev. E, 72 (2205)]
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MEMBRANE MODEL CHARACTERISTICS
● Broad range of fluidity● Easily tunable● Good agreement with measurements: rigidity, diffusion, density
ωC
κ/ε0
ωC
A/σ2
kBT/ε0=1.1 [from Cooke et al,Phys Rev E, 72 (2205)]
Area per molecule Bending rigidity
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MEMBRANE PARTICLE INTERACTION AND SIMULATION CHARACTERISTICS
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
s
Membrane-particle interaction
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SIMULATIONS RESULTS: MAIN BEHAVIORS
WRAPPING NON-WRAPPING
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MEMBRANE BREAKING
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SYSTEM BEHAVIOR 1: NON-WRAPPING
/0=1e3 /0=5e3
/0=1e4/0=3e4
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SYSTEM BEHAVIOR 2: WRAPPING
/0=5e2 /0=5e3 /0=1.5e4
/0=1.55e4 /0=1.6e4 /0=1.65e4
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SYSTEM BEHAVIOR 3: MEMBRANE BREAKING
/0=5.5e3 /0=6e3 /0=7e3
/=7.5e3 /0=9.5e3 /0=1e4
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PHASE DIAGRAMS
ε/ε0
In general, good agreement between simulations and theorySubtle dependence on bending coefficientFor small epsilons deviation from theory
/ε0
R/σ=10
R/σ
ε/ε0
/kBT=12.5
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ELASTIC THEORY
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ENERGY MAPS AND BUDDING PATHWAYS
Penetration[σ]Penetration[σ]
Penetration[σ]
θ[rad] θ[rad]
θ[rad]
ε/ε0=0.7 ε/ε0=0.9
ε/ε0=1.1
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BUDDING DYNAMICS: TIME SCALES AND PENETRATION
Penetration vs time
• steepness of the budding pathway ---> process speed • strenght adhesion energy ---> maximum penetration
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