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PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.

Esmaeili A, Davison T, Wu A, Alcantara J, Jacob C - BMC Bioinformatics (2015)

Bottom Line: Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes.Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, T2N 1N4, Canada. afshin@invistaware.com.

ABSTRACT

Background: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon. Prokaryo, our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes.

Results: The dynamics of cellular 'agents' are defined by their rules of interaction, implemented as finite state machines. The agents are embedded within a 3-dimensional virtual environment with simulated physical and electrochemical properties. The hybrid model is driven by a combination of (1) mathematical equations (DEQs) to capture higher-scale phenomena and (2) agent-based rules to implement localized interactions among a small number of molecular elements. Consequently, our model is able to capture phenomena across multiple spatial scales, from changing concentration gradients to one-on-one molecular interactions. We use the classic gene regulatory mechanism of the lactose operon to demonstrate our model's resolution, visual presentation, and real-time interactivity. Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.

Conclusion: We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes. Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

No MeSH data available.


Related in: MedlinePlus

Transcription and Translation. a Polymerase initiates transcription and generates mRNA; (b and c) Ribosomes initiate translation on each mRNA; (d) Translation of mRNA generates peptide chains, which (e) fold and get converted to a protein structure (compare Fig. 8); (f) Multiple ribosomes translate mRNA at the same time
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Fig7: Transcription and Translation. a Polymerase initiates transcription and generates mRNA; (b and c) Ribosomes initiate translation on each mRNA; (d) Translation of mRNA generates peptide chains, which (e) fold and get converted to a protein structure (compare Fig. 8); (f) Multiple ribosomes translate mRNA at the same time

Mentions: Repressor Inactivation. a and b RNA polymerase and CAP are blocked by the repressor. Allolactose approaches repressor. c Allolactose has docked onto repressor, causing its conformational change (visualized by a colour change of the repressor protein). Subsequently, repressor will undock from DNA, initiating transcription (Fig. 7)


PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.

Esmaeili A, Davison T, Wu A, Alcantara J, Jacob C - BMC Bioinformatics (2015)

Transcription and Translation. a Polymerase initiates transcription and generates mRNA; (b and c) Ribosomes initiate translation on each mRNA; (d) Translation of mRNA generates peptide chains, which (e) fold and get converted to a protein structure (compare Fig. 8); (f) Multiple ribosomes translate mRNA at the same time
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587781&req=5

Fig7: Transcription and Translation. a Polymerase initiates transcription and generates mRNA; (b and c) Ribosomes initiate translation on each mRNA; (d) Translation of mRNA generates peptide chains, which (e) fold and get converted to a protein structure (compare Fig. 8); (f) Multiple ribosomes translate mRNA at the same time
Mentions: Repressor Inactivation. a and b RNA polymerase and CAP are blocked by the repressor. Allolactose approaches repressor. c Allolactose has docked onto repressor, causing its conformational change (visualized by a colour change of the repressor protein). Subsequently, repressor will undock from DNA, initiating transcription (Fig. 7)

Bottom Line: Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes.Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, T2N 1N4, Canada. afshin@invistaware.com.

ABSTRACT

Background: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon. Prokaryo, our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes.

Results: The dynamics of cellular 'agents' are defined by their rules of interaction, implemented as finite state machines. The agents are embedded within a 3-dimensional virtual environment with simulated physical and electrochemical properties. The hybrid model is driven by a combination of (1) mathematical equations (DEQs) to capture higher-scale phenomena and (2) agent-based rules to implement localized interactions among a small number of molecular elements. Consequently, our model is able to capture phenomena across multiple spatial scales, from changing concentration gradients to one-on-one molecular interactions. We use the classic gene regulatory mechanism of the lactose operon to demonstrate our model's resolution, visual presentation, and real-time interactivity. Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.

Conclusion: We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes. Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

No MeSH data available.


Related in: MedlinePlus