ArticleBiophysical journal2007
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Improvements to the APBS biomolecular solvation software suite.Protein science : a publication of the Protein Society · 2018Article
- SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.The journal of physical chemistry. B · 2017Article
- Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion.The journal of physical chemistry. B · 2016Article
- Hybrid finite element and Brownian dynamics method for charged particles.The Journal of chemical physics · 2016Article
- Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.BMC biophysics · 2015Article
- Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.The Journal of chemical physics · 2014Article
- Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.Computational science & discovery · 2012Article
- 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
- Differential geometry based solvation model II: Lagrangian formulation.Journal of mathematical biology · 2011Article
- Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules.IEEE transactions on bio-medical engineering · 2011Article
- Differential geometry based solvation model I: Eulerian formulation.Journal of computational physics · 2010Article
- Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum.PLoS computational biology · 2010Article
- From Split to Sibenik: the tortuous pathway in the cholinesterase field.Chemico-biological interactions · 2010Article
- Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer.Biophysical journal · 2009Article
- Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.Biophysical journal · 2008Article
- PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystems.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2008Article
- Dynamics of the acetylcholinesterase tetramer.Biophysical journal · 2008Article
- Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models.Biophysical chemistry · 2007Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This article describes the numerical solution of the time-dependent Smoluchowski equation to study diffusion in biomolecular systems. Specifically, finite element methods have been developed to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to the mouse acetylcholinesterase (mAChE) monomer and several tetramers. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different time steps. Calculated rates show very good agreement with experimental and theoretical steady-state studies. Furthermore, these finite element methods require significantly fewer computational resources than existing particle-based Brownian dynamics methods and are robust for complicated geometries. The key finding of biological importance is that the rate accelerations of the monomeric and tetrameric mAChE that result from electrostatic steering are preserved under the non-steady-state conditions that are expected to occur in physiological circumstances.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.