Studying protein assembly with reversible Brownian dynamics of patchy particles

Klein, Heinrich C. R.; Schwarz, Ulrich S.

doi:10.1063/1.4873708

Cited by 27 publications

(44 citation statements)

References 90 publications

(155 reference statements)

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“…For non-interacting PBRD, a detailed balance scheme was first introduced in [47]. Other schemes have been developed more recently [48,49]. In Sec.…”

Section: Introductionmentioning

confidence: 99%

Reversible Interacting-Particle Reaction Dynamics

Fröhner

Noé

2018

J. Phys. Chem. B

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Interacting-particle reaction dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enables a wide range of complex reactive systems in biology and chemistry to be simulated, but gives rise to new questions such as how to evolve the dynamical equations in a computationally efficient and statistically correct manner. Here we consider reversible reactions such as A + B ⇄ C with interacting particles and derive expressions for the microscopic iPRD simulation parameters such that desired values for the equilibrium constant and the dissociation rate are obtained in the dilute limit. We then introduce a Monte Carlo algorithm that ensures detailed balance in the iPRD time-evolution (iPRD-DB). iPRD-DB guarantees the correct thermodynamics at all concentrations and maintains the desired kinetics in the dilute limit, where chemical rates are well-defined and kinetic measurement experiments usually operate. We show that in dense particle systems, the incorporation of detailed balance is essential to obtain physically realistic solutions. iPRD-DB is implemented in ReaDDy 2.

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“…For non-interacting PBRD, a detailed balance scheme was first introduced in [47]. Other schemes have been developed more recently [48,49]. In Sec.…”

Section: Introductionmentioning

confidence: 99%

Reversible Interacting-Particle Reaction Dynamics

Fröhner

Noé

2018

J. Phys. Chem. B

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“…In order to study reversible dynamics, every existing bond can also dissociate with the probability P dissoc = k d ∆t ≪ 1. If bond dissociation results in two unconnected clusters, they are positioned relative to each other according to a computational scheme which ensures detailed balance in order to prevent additional, non-physical driving forces for the selfassembly [53].…”

Section: Methodsmentioning

confidence: 99%

Role of dynamic capsomere supply for viral capsid self-assembly

2015

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Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to persistent infections, capsomeres are continuously produced in the cytoplasm of the host cell while completed capsids exit the cell for a new round of infection. Here we use coarse-grained Brownian dynamics simulations of a generic patchy particle model to elucidate the role of the dynamic supply of capsomeres for the reversible self-assembly of empty T1 icosahedral virus capsids. We find that for high rates of capsomere influx only a narrow range of bond strengths exists for which a steady state of continuous capsid production is possible. For bond strengths smaller and larger than this optimal value, the reaction volume becomes crowded by small and large intermediates, respectively. For lower rates of capsomere influx a broader range of bond strengths exists for which a steady state of continuous capsid production is established, although now the production rate of capsids is smaller. Thus our simulations suggest that the importance of an optimal bond strength for viral capsid assembly typical for in vitro conditions can be reduced by the dynamic influx of capsomeres in a cellular environment.

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“…To fill this computational gap, and gain insights into cellular processes, the development and application of coarse-grained models is an important aspect of computer simulation. A particularly promising framework to model cellular signaling processes at membranes, involving space exclusions and specific geometries found at membrane scaffolds, is particlebased reaction-diffusion (PBRD) simulation [21][22][23][24] , especially the so-called interacting-particle reaction-diffusion (iPRD) models that include interaction forces between particles [25][26][27][28][29] . The particles in such models typically represent entire proteins, protein domains or metabolites, and thus represent a spatial resolution of a few nanometers.…”

Section: Introductionmentioning

confidence: 99%

Particle-based membrane model for mesoscopic simulation of cellular dynamics

Sadeghi

Weikl

Noé

2018

The Journal of Chemical Physics

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We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending, and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model, and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.

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Studying protein assembly with reversible Brownian dynamics of patchy particles

Cited by 27 publications

References 90 publications

Reversible Interacting-Particle Reaction Dynamics

Reversible Interacting-Particle Reaction Dynamics

Role of dynamic capsomere supply for viral capsid self-assembly

Particle-based membrane model for mesoscopic simulation of cellular dynamics

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