Abstract
We have used the Smoldyn software to create spatially detailed models of the Escherichia coli chemotaxis pathway. With it we can follow signalling reactions at high spatio-temporal resolution, observe the formation of gradients of phospho-proteins as well as total protein and analyse the effects of macromolecular crowding on signalling. It has enabled us to propose new regulatory elements of the signalling pathway, which are mediated through the dynamic localisation and activity of the CheZ phosphatase. We used the Smoldyn software to model quantitative fluorescent microscopy data and to determine diffusion coefficients and binding affinities. We can reliably gain information obtained under conditions with high levels of experimental noise. Smoldyn can accommodate various cellular architectures, and we show that cell shape becomes an integral part of the signalling process.
Keywords: Bacterial chemotaxis, cellular signalling, particle based simulation, protein gradients, review, smoldyn.
Current Chemical Biology
Title:Simulating the Bacterial Chemotaxis Pathway at High Spatio-temporal Detail
Volume: 7 Issue: 3
Author(s): Sven Sewitz and Karen Lipkow
Affiliation:
Keywords: Bacterial chemotaxis, cellular signalling, particle based simulation, protein gradients, review, smoldyn.
Abstract: We have used the Smoldyn software to create spatially detailed models of the Escherichia coli chemotaxis pathway. With it we can follow signalling reactions at high spatio-temporal resolution, observe the formation of gradients of phospho-proteins as well as total protein and analyse the effects of macromolecular crowding on signalling. It has enabled us to propose new regulatory elements of the signalling pathway, which are mediated through the dynamic localisation and activity of the CheZ phosphatase. We used the Smoldyn software to model quantitative fluorescent microscopy data and to determine diffusion coefficients and binding affinities. We can reliably gain information obtained under conditions with high levels of experimental noise. Smoldyn can accommodate various cellular architectures, and we show that cell shape becomes an integral part of the signalling process.
Export Options
About this article
Cite this article as:
Sewitz Sven and Lipkow Karen, Simulating the Bacterial Chemotaxis Pathway at High Spatio-temporal Detail, Current Chemical Biology 2013; 7 (3) . https://dx.doi.org/10.2174/221279680703140508101810
DOI https://dx.doi.org/10.2174/221279680703140508101810 |
Print ISSN 2212-7968 |
Publisher Name Bentham Science Publisher |
Online ISSN 1872-3136 |
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
Perception or Reality of Body Weight: Which Matters the Most to Adolescents’ Emotional Well-being?
Current Psychiatry Reviews Comparative Proteomics and Bioinformatics Analysis of Tissue from Non-Small Cell Lung Cancer Patients
Current Proteomics Subjective Spatial Navigation Complaints - A Frequent Symptom Reported by Patients with Subjective Cognitive Decline, Mild Cognitive Impairment and Alzheimer's Disease
Current Alzheimer Research Are Some Drinkers Resistant to Hangover? A Literature Review
Current Drug Abuse Reviews Anti-Alzheimer’s Materials Isolated from Marine Bio-resources: A Review
Current Alzheimer Research The Role of Cytokine Network in the Pathophysiology of Schizophrenia
Current Psychiatry Reviews Tribute to Prof. Gerald Farin: Remembering A Geometric Modeling Researcher and Educator
Neuroscience and Biomedical Engineering (Discontinued) Cellular Receptors of Extracellular Matrix Molecules
Current Pharmaceutical Design Mouse Models of Autoimmune Diseases: Immune Thrombocytopenia
Current Pharmaceutical Design Gut Mycobiota and Fungal Metabolites in Human Homeostasis
Current Drug Targets Mitochondria Sentencing About Cellular Life and Death: A Matter of Oxidative Stress
Current Pharmaceutical Design Green Tea from the Far East to the Drug Store: Focus on the Beneficial Cardiovascular Effects
Current Pharmaceutical Design Alcoholic Hepatitis: Pathogenesis, Diagnosis and Treatment
Reviews on Recent Clinical Trials Cytochrome P450-Activated Prodrugs: Targeted Drug Delivery
Current Medicinal Chemistry Meet Our Editorial Board Member
Recent Patents on Inflammation & Allergy Drug Discovery Construction of a Neuro-Immune-Cognitive Pathway-Phenotype Underpinning the Phenome of Deficit Schizophrenia
Current Topics in Medicinal Chemistry Meet Our Associate Editor:
Current Alzheimer Research Common Genetic Variants of the Mitochondrial Trafficking System and Mitochondrial Uncoupling Proteins Affect the Development of Two Slowly Developing Demyelinating Disorders, Leukoaraiosis and Multiple Sclerosis
Current Medicinal Chemistry Piper sarmentosum Roxb. Root Extracts Confer Neuroprotection by Attenuating Beta Amyloid-Induced Pro-Inflammatory Cytokines Released from Microglial Cells
Current Alzheimer Research Effect of Antihypertensive Drugs on Cognition and Behavioral Symptoms of Patients with Alzheimer’s Disease: A Meta-analysis
Current Pharmaceutical Biotechnology