Stochastic simulations of minimal cells: the Ribocell model
1Chemistry Department, University Aldo Moro, Bari, 70125, Italy. mavelli@chimica.uniba.it
BMC Bioinformatics
|April 28, 2012
Summary
Researchers developed the ENVIRONMENT computational platform to study stochastic dynamics in reacting lipid compartments. This tool aids in understanding minimal cell models, like the Ribocell, by simulating RNA and vesicle reproduction, revealing insights into randomness and system evolution.
Area of Science:
- Synthetic Biology
- Biophysics
- Computational Chemistry
Background:
- Lipid compartments (liposomes, droplets) serve as in vitro minimal cell models for biomolecular reactions.
- Progress has been made in synthesizing RNA and proteins within liposomes, but physical dynamics remain unclear.
- Understanding solute compartmentalization, reactivity, and stochastic effects is crucial for minimal cell research.
Purpose of the Study:
- To develop a computational platform for studying stochastic time evolution in reacting lipid compartments.
- To elucidate the role of randomness in the behavior of chemically reacting lipid compartments.
- To explore the feasibility of the Ribocell model, a hypothetical minimal cell.
Main Methods:
- Developed the ENVIRONMENT computational platform implementing the Gillespie Algorithm.
- Extended previous simulations to interacting and time-evolving systems.
- Utilized deterministic kinetic analysis and stochastic simulations.
Main Results:
- Identified optimal external conditions for synchronizing RNA and vesicle reproduction in the Ribocell model.
- Investigated the robustness of the Ribocell model to random fluctuations.
- Demonstrated the utility of the ENVIRONMENT platform for analyzing stochastic effects in compartmentalized systems.
Conclusions:
- The ENVIRONMENT platform provides a tool for understanding stochastic dynamics in minimal cell models.
- The Ribocell model's feasibility is explored, highlighting the interplay between genome replication and vesicle reproduction.
- Stochastic simulations are essential for revealing unexpected system behaviors driven by random fluctuations.
Related Concept Videos
01:16Non-equilibrium in the Cell
An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction. The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system...
02:15Replicative Cell Senescence
Replicative cell senescence is a property of cells that allows them to divide a finite number of times throughout the organism's lifespan while preventing excessive proliferation. Replicative senescence is associated with the gradual loss of the telomere — short, repetitive DNA sequences found at the end of the chromosomes. Telomeres are bound by a group of proteins to form a protective cap on the ends of chromosomes. Embryonic stem cells express telomerase — an enzyme that adds the telomeric...
02:15Replicative Cell Senescence
Replicative cell senescence is a property of cells that allows them to divide a finite number of times throughout the organism's lifespan while preventing excessive proliferation. Replicative senescence is associated with the gradual loss of the telomere — short, repetitive DNA sequences found at the end of the chromosomes. Telomeres are bound by a group of proteins to form a protective cap on the ends of chromosomes. Embryonic stem cells express telomerase — an enzyme that adds the telomeric...
02:53Ribosomal RNA Synthesis
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
02:53Ribosomal RNA Synthesis
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
01:19Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...