Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size

We perform Monte Carlo simulations in three-dimensional (3D) lattice in order to study diffusion-controlled and mixed activation-diffusion reactions following Michaelis-Menten scheme in crowded media. The simulation data reveal the rate coefficient dependence on time for diffusion-controlled bimolec...

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Autores: Pitulice, Laura, Vilaseca i Font, Eudald, Pastor, Isabel, Madurga Díez, Sergio, Garcés, Josep Lluís, Isvoran, Adriana, Mas i Pujadas, Francesc
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2014
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/104306
Acceso en línea:https://hdl.handle.net/2445/104306
Access Level:acceso abierto
Palabra clave:Algorismes
Simulació per ordinador
Fractals
Cinètica enzimàtica
Algorithms
Computer simulation
Enzyme kinetics
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spelling Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative sizePitulice, LauraVilaseca i Font, EudaldPastor, IsabelMadurga Díez, SergioGarcés, Josep LluísIsvoran, AdrianaMas i Pujadas, FrancescAlgorismesSimulació per ordinadorFractalsCinètica enzimàticaAlgorithmsComputer simulationFractalsEnzyme kineticsWe perform Monte Carlo simulations in three-dimensional (3D) lattice in order to study diffusion-controlled and mixed activation-diffusion reactions following Michaelis-Menten scheme in crowded media. The simulation data reveal the rate coefficient dependence on time for diffusion-controlled bimolecular reactions developing in three- dimensional media with obstacles, as predicted by fractal kinetics approach. For the cases of mixed activation-diffusion reactions, the fractality of the reaction decreases as the activation control increases. We propose a modified form of the Zipf-Mandelbrot equation to describe the time dependence of the rate coefficient, k (t ) = k0 (1 + t /τ )− h . This equation provides a good description of the fractal regime and it may be split into two terms: one that corresponds to the initial rate constant (k0) and the other one correlated with the kinetics fractality. Additionally, the proposed equation contains and links two limit expressions corresponding to short and large periods of time: k1 =k0 (for t<<τ) that relates to classical kinetics and the well-known Kopelman' s equation k ~ t − h (for t>>τ) associated to fractal kinetics. The τ parameter has the meaning of a crossover time between these two limiting behaviours. The value of k is mainly dependent on the excluded volume and the enzyme-obstacle relative size. This dependence can be explained in terms of the radius of an average confined volume that every enzyme molecule feels, and correlates very well with the crossover length obtained in previous studies of enzyme diffusion in crowding media.Elsevier B.V.2014info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfhttps://hdl.handle.net/2445/104306Articles publicats en revistes (Ciència dels Materials i Química Física)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésVersió postprint del document publicat a: https://doi.org/10.1016/j.mbs.2014.03.012Mathematical Biosciences, 2014, vol. 251, p. 72-82https://doi.org/10.1016/j.mbs.2014.03.012(c) Elsevier B.V., 2014info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1043062026-05-27T06:46:51Z
dc.title.none.fl_str_mv Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
title Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
spellingShingle Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
Pitulice, Laura
Algorismes
Simulació per ordinador
Fractals
Cinètica enzimàtica
Algorithms
Computer simulation
Fractals
Enzyme kinetics
title_short Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
title_full Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
title_fullStr Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
title_full_unstemmed Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
title_sort Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
dc.creator.none.fl_str_mv Pitulice, Laura
Vilaseca i Font, Eudald
Pastor, Isabel
Madurga Díez, Sergio
Garcés, Josep Lluís
Isvoran, Adriana
Mas i Pujadas, Francesc
author Pitulice, Laura
author_facet Pitulice, Laura
Vilaseca i Font, Eudald
Pastor, Isabel
Madurga Díez, Sergio
Garcés, Josep Lluís
Isvoran, Adriana
Mas i Pujadas, Francesc
author_role author
author2 Vilaseca i Font, Eudald
Pastor, Isabel
Madurga Díez, Sergio
Garcés, Josep Lluís
Isvoran, Adriana
Mas i Pujadas, Francesc
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Algorismes
Simulació per ordinador
Fractals
Cinètica enzimàtica
Algorithms
Computer simulation
Fractals
Enzyme kinetics
topic Algorismes
Simulació per ordinador
Fractals
Cinètica enzimàtica
Algorithms
Computer simulation
Fractals
Enzyme kinetics
description We perform Monte Carlo simulations in three-dimensional (3D) lattice in order to study diffusion-controlled and mixed activation-diffusion reactions following Michaelis-Menten scheme in crowded media. The simulation data reveal the rate coefficient dependence on time for diffusion-controlled bimolecular reactions developing in three- dimensional media with obstacles, as predicted by fractal kinetics approach. For the cases of mixed activation-diffusion reactions, the fractality of the reaction decreases as the activation control increases. We propose a modified form of the Zipf-Mandelbrot equation to describe the time dependence of the rate coefficient, k (t ) = k0 (1 + t /τ )− h . This equation provides a good description of the fractal regime and it may be split into two terms: one that corresponds to the initial rate constant (k0) and the other one correlated with the kinetics fractality. Additionally, the proposed equation contains and links two limit expressions corresponding to short and large periods of time: k1 =k0 (for t<<τ) that relates to classical kinetics and the well-known Kopelman' s equation k ~ t − h (for t>>τ) associated to fractal kinetics. The τ parameter has the meaning of a crossover time between these two limiting behaviours. The value of k is mainly dependent on the excluded volume and the enzyme-obstacle relative size. This dependence can be explained in terms of the radius of an average confined volume that every enzyme molecule feels, and correlates very well with the crossover length obtained in previous studies of enzyme diffusion in crowding media.
publishDate 2014
dc.date.none.fl_str_mv 2014
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/104306
url https://hdl.handle.net/2445/104306
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Versió postprint del document publicat a: https://doi.org/10.1016/j.mbs.2014.03.012
Mathematical Biosciences, 2014, vol. 251, p. 72-82
https://doi.org/10.1016/j.mbs.2014.03.012
dc.rights.none.fl_str_mv (c) Elsevier B.V., 2014
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Elsevier B.V., 2014
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier B.V.
publisher.none.fl_str_mv Elsevier B.V.
dc.source.none.fl_str_mv Articles publicats en revistes (Ciència dels Materials i Química Física)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300719

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