Dynamical simulations of virus wrapping and budding T. Ruiz-Herrero 1, M. F. Hagan 2, E. Velasco 1...
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Transcript of Dynamical simulations of virus wrapping and budding T. Ruiz-Herrero 1, M. F. Hagan 2, E. Velasco 1...
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
INTRODUCTION
Budding
exiting the cell
acquiring membrane coating
Attachment to the cell membraneWrappingFusion of the final neck
Budding steps
T. RUIZ-HERRERO 1/13
COARSE GRAINING
polar head Hydrophilic tail
T. RUIZ-HERRERO 2/13
MEMBRANE MODEL:cooke model
Vrep
Vbond
Vbend
Vatrr
[Cooke et al, Phys. Rev. E, 72 (2205)]
T. RUIZ-HERRERO 3/13
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
T. RUIZ-HERRERO 4/13
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
T. RUIZ-HERRERO 5/13
SIMULATIONS RESULTS: MAIN BEHAVIORS
WRAPPING NON-WRAPPING
T. RUIZ-HERRERO 6/13
MEMBRANE BREAKING
SYSTEM BEHAVIOR 1: NON-WRAPPING
/0=1e3 /0=5e3
/0=1e4/0=3e4
T. RUIZ-HERRERO 7/13
SYSTEM BEHAVIOR 2: WRAPPING
/0=5e2 /0=5e3 /0=1.5e4
/0=1.55e4 /0=1.6e4 /0=1.65e4
T. RUIZ-HERRERO 8/13
SYSTEM BEHAVIOR 3: MEMBRANE BREAKING
/0=5.5e3 /0=6e3 /0=7e3
/=7.5e3 /0=9.5e3 /0=1e4
T. RUIZ-HERRERO 9/13
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
T. RUIZ-HERRERO 10/13
ELASTIC THEORY
T. RUIZ-HERRERO 11/13
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
T. RUIZ-HERRERO 12/13
BUDDING DYNAMICS: TIME SCALES AND PENETRATION
Penetration vs time
• steepness of the budding pathway ---> process speed • strenght adhesion energy ---> maximum penetration
T. RUIZ-HERRERO 13/13