Effective reaction rates for diffusion-limited reaction cycles
PBN-AR
Instytucja
Wydział Matematyki, Informatyki i Mechaniki (Uniwersytet Warszawski)
Informacje podstawowe
Główny język publikacji
en
Czasopismo
JOURNAL OF CHEMICAL PHYSICS
ISSN
0021-9606
EISSN
1089-7690
Wydawca
AMER INST PHYSICS
DOI
URL
Rok publikacji
2015
Numer zeszytu
Strony od-do
215102-1-215102-12
Numer tomu
143
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Streszczenia
Język
en
Treść
Biological signals in cells are transmitted with the use of reaction cycles, such as the phosphorylation-dephosphorylation cycle, in which substrate is modified by antagonistic enzymes. An appreciable share of such reactions takes place in crowded environments of two-dimensional structures, such as plasma membrane or intracellular membranes, and is expected to be diffusion-controlled. In this work, starting from the microscopic bimolecular reaction rate constants and using estimates of the mean first-passage time for an enzyme–substrate encounter, we derive diffusion-dependent effective macroscopic reaction rate coefficients (EMRRC) for a generic reaction cycle. Each EMRRC was found to be half of the harmonic average of the microscopic rate constant (phosphorylation c or dephosphorylation d), and the effective (crowding-dependent) motility divided by a slowly decreasing logarithmic function of the sum of the enzyme concentrations. This implies that when c and d differ, the two EMRRCs scale differently with the motility, rendering the steady-state fraction of phosphorylated substrate molecules diff usion-dependent. Analytical predictions are verified using kinetic Monte Carlo simulations on the two-dimensional triangular lattice at the single-molecule resolution. It is demonstrated that the proposed formulas estimate the steady-state concentrations and effective reaction rates for different sets of microscopic reaction rates and concentrations of reactants, including a non-trivial example where with increasing diffusivity the fraction of phosphorylated substrate molecules changes from 10% to 90%.
Cechy publikacji
ORIGINAL_ARTICLE
Inne
System-identifier
681628
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