Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Paulina SzymańskaT Lipniacki

Abstract

We investigate the kinetics of the ubiquitous phosphorylation-dephosphorylation cycle on biological membranes by means of kinetic Monte Carlo simulations on the triangular lattice. We establish the dependence of effective macroscopic reaction rate coefficients as well as the steady-state phosphorylated substrate fraction on the diffusion coefficient and concentrations of opposing enzymes: kinases and phosphatases. In the limits of zero and infinite diffusion, the numerical results agree with analytical predictions; these two limits give the lower and the upper bound for the macroscopic rate coefficients, respectively. In the zero-diffusion limit, which is important in the analysis of dense systems, phosphorylation and dephosphorylation reactions can convert only these substrates which remain in contact with opposing enzymes. In the most studied regime of nonzero but small diffusion, a contribution linearly proportional to the diffusion coefficient appears in the reaction rate. In this regime, the presence of opposing enzymes creates inhomogeneities in the (de)phosphorylated substrate distributions: The spatial correlation function shows that enzymes are surrounded by clouds of converted substrates. This effect becomes important...Continue Reading

References

Jul 8, 1985·Physical Review Letters· van Beijeren H, R Kutner
Sep 3, 1999·FEBS Letters·G C Brown, B N Kholodenko
Feb 17, 2001·Current Opinion in Structural Biology·R J Ellis
Jul 25, 2003·Biochimica Et Biophysica Acta·Damien Hall, Allen P Minton
May 15, 2004·Progress in Biophysics and Molecular Biology·S Schnell, T E Turner
Feb 17, 2006·Nature Reviews. Molecular Cell Biology·Boris N Kholodenko
Oct 3, 2006·Biophysical Journal·Jeroen S van ZonPieter Rein ten Wolde
Oct 17, 2007·PLoS Computational Biology·Siebe B van Albada, Pieter Rein ten Wolde
Oct 20, 2007·Science·Edward C StitesKodi S Ravichandran
Jan 29, 2008·The Journal of Physical Chemistry. B·Soohyung Park, Noam Agmon
Sep 2, 2008·The Journal of Physical Chemistry. B·Soohyung Park, Noam Agmon
Feb 17, 2009·Biophysical Journal·Jun Soo Kim, Arun Yethiraj
Mar 25, 2009·Journal of Theoretical Biology·Bogdan Kazmierczak, Tomasz Lipniacki
Nov 17, 2009·Immunological Reviews·Pavel TolarSusan K Pierce
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Koichi TakahashiPieter Rein ten Wolde
Mar 3, 2010·Annual Review of Immunology·Naomi E Harwood, Facundo D Batista
Apr 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Christopher C GovernEric S Huseby
Nov 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·David FangeJohan Elf
Oct 15, 2011·PLoS Computational Biology·Beata HatTomasz Lipniacki
Mar 13, 2012·Biophysical Journal·Andrew MuglerPieter Rein ten Wolde
Jun 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Stefan HellanderLinda Petzold
Feb 19, 2013·Bulletin of the Korean Chemical Society·Attila Szabo, Huan-Xiang Zhou
Mar 27, 2013·Scientific Reports·Kazuhiro AokiMichiyuki Matsuda
May 3, 2013·Journal of the Royal Society, Interface·Marek KochanczykTomasz Lipniacki
Aug 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Matthias Weiss

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Citations

Dec 10, 2015·The Journal of Chemical Physics·Paweł Nałęcz-JaweckiTomasz Lipniacki
Sep 27, 2018·Physical Review. E·Pawel J ZukTomasz Lipniacki
May 29, 2021·Scientific Reports·Rosa D Hernansaiz-BallesterosAttila Csikász-Nagy

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