Dynamics of Loop Formation in Active Chains

Sarkar, Debarati; Brahmanandan, Abhishekamole; Thakur, Snigdha

doi:10.1002/masy.201400203

Cited by 4 publications

(3 citation statements)

References 34 publications

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“…The above approximation has been derived in a more general setting [40,41] and confirmed in numerical simulation [41][42][43]. This model was quantitatively confirmed and in particular the diffusion coefficient equation [44] and the loop closure time equation [45] were found to be in close agreement.…”

Section: S8 Determining Termination Time In Crdme Simulationssupporting

confidence: 65%

The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions

Zhang

Clemens

Goyette

et al. 2018

Preprint

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Signalling by surface receptors often relies on tethered reactions whereby an enzyme bound to the cytoplasmic tail of a receptor catalyses reactions on substrates within reach. The overall length and stiffness of the receptor tail, the enzyme, and the substrate determine a biophysical parameter termed the molecular reach of the reaction. This parameter determines the probability that the receptor-tethered-enzyme will contact the substrate, in the volume proximal to the membrane, when separated by different distances within the membrane plane. In this work we develop particlebased stochastic reaction-diffusion models to study the interplay between molecular reach and diffusion. We find that increasing the molecular reach can increase reaction efficacy for slowly diffusing receptors, while for rapidly diffusing receptors increasing molecular reach reduces reaction efficacy. In contrast, if reactions are forced to take place within the 2D plasma membrane instead of the 3D volume proximal to it, or if molecules diffuse in 3D, increasing molecular reach increases reaction efficacy for all diffusivities. We show results in the context of immune checkpoint receptors (PD-1 dephosphorylating CD28), a standard opposing kinase-phosphatase reaction, and a minimal two-particle model. The work highlights the importance of the 3D nature of many 2D membraneconfined interactions, illustrating a role for molecular reach in controlling biochemical reactions.O.D. and S.A.I. contributed equally to this work.

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Section: S8 Determining Termination Time In Crdme Simulationssupporting

confidence: 65%

The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions

Zhang

Clemens

Goyette

et al. 2018

Preprint

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“…Motivated by these naturally occurring active polymers, there is a recent burst in theoretical − and experimental studies − of such polymers, wherein the usual route to synthesize this is by making a necklace of active colloidal particles. These active filaments exhibit fascinating phenomena like swelling, ,− coil–globule transitions, , loop formation, , spontaneous oscillations and spiral formations, , enhanced diffusion, , modification of dynamical properties by hydrodynamic interactions, and so on.…”

Section: Introductionmentioning

confidence: 99%

Collapse Dynamics of Chemically Active Flexible Polymer

Jain

Thakur

2022

Macromolecules

Self Cite

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We investigate the structural and dynamical properties of a chemically active flexible polymer chain immersed in a solvent bath by using hybrid molecular dynamics (MD) and multiparticle collision dynamics (MPCD) simulation techniques in a three-dimensional space. The source of activity on the polymer is the self-generating, nonequilibrium solvent gradient caused by the chemical reaction at different sites on the polymer. The chemical gradient then leads to the generation of the local tangential force along the filament. Here we present the effect of activity on the configurational dynamics of a flexible chain emphasizing globule-like transformation at the higher activity. Particular attention is paid to how the radius of gyration (R g) changes with the activity. We find that the polymer undergoes a coil-to-globule-like transition with increasing active force. Decreasing the Flory scaling exponent of R g, the correlation of the end-to-end vector C(t) and radial distribution g(r) of the monomers around the filament quantifies this transition. We also analyze the motion of a polymer and its center of mass in terms of time-averaged mean-squared displacement (MSD). The superdiffusive motion of the active flexible polymer reverts to random walk at a long time scale with an enhanced diffusion, where the scaling of the diffusion coefficient is the same as the Zimm model.

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“…References (47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61)(62)(63)(64) appear in the Supporting Material.…”

Section: Supporting Citationsmentioning

confidence: 99%

The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions

Zhang

Clemens

Goyette

et al. 2019

Biophysical Journal

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Signaling by surface receptors often relies on tethered reactions whereby an enzyme bound to the cytoplasmic tail of a receptor catalyzes reactions on substrates within reach. The overall length and stiffness of the receptor tail, the enzyme, and the substrate determine a biophysical parameter termed the molecular reach of the reaction. This parameter determines the probability that the receptor-tethered enzyme will contact the substrate in the volume proximal to the membrane when separated by different distances within the membrane plane. In this work, we develop particle-based stochastic reaction-diffusion models to study the interplay between molecular reach and diffusion. We find that increasing the molecular reach can increase reaction efficacy for slowly diffusing receptors, whereas for rapidly diffusing receptors, increasing molecular reach reduces reaction efficacy. In contrast, if reactions are forced to take place within the two-dimensional plasma membrane instead of the three-dimensional volume proximal to it or if molecules diffuse in three dimensions, increasing molecular reach increases reaction efficacy for all diffusivities. We show results in the context of immune checkpoint receptors (PD-1 dephosphorylating CD28), a standard opposing kinase-phosphatase reaction, and a minimal two-particle model. The work highlights the importance of the threedimensional nature of many two-dimensional membrane-confined interactions, illustrating a role for molecular reach in controlling biochemical reactions.

show abstract

Dynamics of Loop Formation in Active Chains

Cited by 4 publications

References 34 publications

The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions

The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions

Collapse Dynamics of Chemically Active Flexible Polymer

The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions

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