Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

The Journal of Chemical Physics
Osman N Yogurtcu, Margaret E Johnson

Abstract

The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from o...Continue Reading

References

Nov 1, 1977·Biophysical Journal·H C Berg, E M Purcell
Nov 21, 1988·Physical Review Letters·M Bramson, J L Lebowitz
Feb 15, 2001·Physical Review Letters·I V GopichA Szabo
Jan 6, 2006·The Journal of Chemical Physics·Jeroen S van Zon, Pieter Rein ten Wolde
Feb 7, 2009·Chemical Reviews·G SchreiberH-X Zhou
Mar 12, 2009·The Journal of Chemical Physics·Sotiria LampoudiLinda R Petzold
Apr 4, 2009·Science·Michael Schmidt, Hod Lipson
Jun 3, 2010·The Journal of Chemical Physics·Alexander B DoktorovAlexey A Kipriyanov
Oct 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Tadashi Ando, Jeffrey Skolnick
Nov 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·David FangeJohan Elf
Jun 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Stefan HellanderLinda Petzold
Aug 17, 2012·The Journal of Chemical Physics·Thorsten Prüstel, Martin Meier-Schellersheim
Mar 1, 1992·Journal of Fluorescence·B Medhage, M Almgren
Dec 22, 2014·The Journal of Chemical Physics·Daniel T GillespieCarol A Gillespie

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Citations

Mar 6, 2018·PLoS Computational Biology·Osman N Yogurtcu, Margaret E Johnson
Oct 18, 2019·PLoS Biology·Nicholas T HendersonDaniel J Lew
May 22, 2019·Physical Review. E·Wei-Xiang ChewSatya N V Arjunan
Nov 30, 2019·BMC Bioinformatics·Till KösterAdelinde M Uhrmacher
May 30, 2020·Biophysical Journal·Matthew J VargaMargaret E Johnson
Jul 10, 2021·The Journal of Chemical Physics·Bhavya Mishra, Margaret E Johnson
Jul 16, 2021·PLoS Computational Biology·Samuel A RamirezTimothy C Elston
Sep 18, 2021·Science Advances·Veneta GerganovaSophie G Martin

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