ArticleBiophysical journal2008
Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi-enzyme colocalization and environment.Protein science : a publication of the Protein Society · 2024Article
- Markov State Study of Electrostatic Channeling within the Tricarboxylic Acid Cycle Supercomplex.ACS nanoscience Au · 2022Article
- Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions.PLoS computational biology · 2020Article
- Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling.The Journal of chemical physics · 2015Article
- Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling.Biophysical journal · 2014Article
- Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.The Journal of chemical physics · 2014Article
- A model study of sequential enzyme reactions and electrostatic channeling.The Journal of chemical physics · 2014Article
- Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.Molecular based mathematical biology · 2013Article
- Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.The Journal of chemical physics · 2012Article
- Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction.Computational science & discovery · 2012Article
- Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries.Frontiers in physiology · 2012Article
- Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum.PLoS computational biology · 2010Article
- Multiple Scales in the Simulation of Ion Channels and Proteins.The journal of physical chemistry. C, Nanomaterials and interfaces · 2010Article
- Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics.The journal of physical chemistry letters · 2010Article
- The structural dynamics of macromolecular processes.Current opinion in cell biology · 2009Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Enzymes required for sulfur metabolism have been suggested to gain efficiency by restricted diffusion (i.e., channeling) of an intermediate APS(2-) between active sites. This article describes modeling of the whole channeling process by numerical solution of the Smoluchowski diffusion equation, as well as by coarse-grained Brownian dynamics. The results suggest that electrostatics plays an essential role in the APS(2-) channeling. Furthermore, with coarse-grained Brownian dynamics, the substrate channeling process has been studied with reactions in multiple active sites. Our simulations provide a bridge for numerical modeling with Brownian dynamics to simulate the complicated reaction and diffusion and raise important questions relating to the electrostatically mediated substrate channeling in vitro, in situ, and in vivo.
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Registered trials
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