Bimolecular annihilation reactions with immobile reactants

Schnörer, H.; Kuzovkov, V. N.; Blumen, A.

doi:10.1063/1.457972

Cited by 34 publications

(17 citation statements)

References 28 publications

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“…The low copy number of substrates within reach of tethered enzymes means that stochastic effects are prevalent. To capture these effects, we used the MPD formalism previously used in the study of solid state physics ( 22 , 23 ). …”

Section: Methodsmentioning

confidence: 99%

Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1

et al. 2017

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Section: Methodsmentioning

confidence: 99%

Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1

et al. 2017

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“…Models based on standard partialdifferential-equations (PDEs) fail to fit the experimental data because they do not account for stochastic fluctuations (not shown). We therefore used the multi-particle density (MPD) formalism, previously used to study defects in solid state physics (21)(22)(23), to develop a hybrid integral MPDPDE model that includes the reactions specified for the stochastic simulation (see Materials & Methods). We found good agreement between the stochastic simulation and the computationally efficient MPDPDE model ( Fig.…”

Section: A Mathematical Model Quantifies the Tethered Enzymatic Spr Amentioning

confidence: 99%

“…The low copy number of substrates within reach of tethered enzymes means that stochastic effects are prevalent. To capture these effects, we use the multi-centre particle density formalism previously used in the study of solid state physics (21,22).…”

Section: Deterministic Mpdpde Calculationsmentioning

confidence: 99%

Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1

Goyette

Salas

Gordon

et al. 2016

Preprint

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Tethered enzymatic reactions are ubiquitous in signalling networks but are poorly understood. Here, a novel mathematical analysis is established for tethered signalling reactions in surface plasmon resonance (SPR). Applying the method to the phosphatase SHP-1 interacting with a phosphorylated tether corresponding to an immune receptor cytoplasmic tail provides 5 biophysical/biochemical constants from a single SPR experiment: two binding rates, two catalytic rates, and a reach parameter. Tether binding increased the activity of SHP-1 by 900-fold through a binding-induced allosteric activation (20-fold) and a more significant increase in local substrate concentration (45-fold). The reach parameter indicates that this local substrate concentration is exquisitely sensitive to receptor clustering. We further show that truncation of the tether leads not only to a lower reach but also to lower binding and catalysis. The work establishes a new framework for studying tethered signalling processes and highlights the tether as a control parameter in clustered signalling.

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“…The reason is that unless longer-range reactions are allowed for [15][16], the time dependence involves exponential relaxation to an absorbing state rather than power-law behavior typical of the fast-diffusion reactions. Thus there are no universal fluctuation effects involved.…”

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confidence: 99%