Computational Simulation of RNA-Based Protocell Competition: mRNA Sequence Selection and Prebiotic Genetic Code Evolution
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2025
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| author | Reza Hashemi |
| author_facet | Reza Hashemi |
| contents | <p>The RNA World hypothesis posits that RNA-based protocells, coupled with proto-ribosomes, were pivotal in the emergence of early genetic codes through competitive interactions. This study employs advanced computational modeling to simulate competition among RNA-based protocells in a prebiotic montmorillonite-rich environment, featuring a 200-nucleotide rRNA-based proto-ribosome stabilized by L16/RPL10 (peptide bond catalysis, RMSD ~2.1 Å) and S12/RPS23 (translation accuracy). Using quantum mechanics/molecular mechanics (QM/MM), reactive force fields (ReaxFF), constant-pH molecular dynamics (CpHMD), graph neural networks (GNNs), and 3D stochastic modeling, we modeled two protocell types: viral-like (gp10 protein envelope) and prokaryotic-like (phospholipid vesicles), each encapsulating RNA, one of 12 distinct 4-6mer mRNA sequences (e.g., GGCC, AUUA), and the proto-ribosome. Under prebiotic conditions (pH 5.5–8.5, 40–70°C, 5–15% oxidative stress), simulations revealed that 30% nucleotide depletion drove viral-like protocells to parasitize vesicles, facilitating RNA transfer and mRNA translation. The proto-ribosome catalyzed peptide bond formation (e.g., HWWH peptide), with mRNA binding energies ranging from -8.5 to -15.2 kcal/mol, favoring G/C-rich sequences (e.g., GGCC, 42% higher affinity than AUUA). Chi-square analysis confirmed the statistical significance of G/C-rich sequence preference (χ² = 12.45, p = 0.0004). These findings, aligned with the Matter World Hypothesis (MWH) and prior studies, underscore mRNA sequence selection as a driver of genetic code evolution, with implications for synthetic biology pending experimental validation.All findings in this study are derived from advanced simulations and thus require empirical validation before drawing definitive conclusions.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15282697 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
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| spellingShingle | Computational Simulation of RNA-Based Protocell Competition: mRNA Sequence Selection and Prebiotic Genetic Code Evolution Reza Hashemi RNA World, proto-ribosome, prebiotic competition, mRNA sequence selection, genetic code evolution, L16/RPL10, S12/RPS23, computational modeling, chi-square analysis <p>The RNA World hypothesis posits that RNA-based protocells, coupled with proto-ribosomes, were pivotal in the emergence of early genetic codes through competitive interactions. This study employs advanced computational modeling to simulate competition among RNA-based protocells in a prebiotic montmorillonite-rich environment, featuring a 200-nucleotide rRNA-based proto-ribosome stabilized by L16/RPL10 (peptide bond catalysis, RMSD ~2.1 Å) and S12/RPS23 (translation accuracy). Using quantum mechanics/molecular mechanics (QM/MM), reactive force fields (ReaxFF), constant-pH molecular dynamics (CpHMD), graph neural networks (GNNs), and 3D stochastic modeling, we modeled two protocell types: viral-like (gp10 protein envelope) and prokaryotic-like (phospholipid vesicles), each encapsulating RNA, one of 12 distinct 4-6mer mRNA sequences (e.g., GGCC, AUUA), and the proto-ribosome. Under prebiotic conditions (pH 5.5–8.5, 40–70°C, 5–15% oxidative stress), simulations revealed that 30% nucleotide depletion drove viral-like protocells to parasitize vesicles, facilitating RNA transfer and mRNA translation. The proto-ribosome catalyzed peptide bond formation (e.g., HWWH peptide), with mRNA binding energies ranging from -8.5 to -15.2 kcal/mol, favoring G/C-rich sequences (e.g., GGCC, 42% higher affinity than AUUA). Chi-square analysis confirmed the statistical significance of G/C-rich sequence preference (χ² = 12.45, p = 0.0004). These findings, aligned with the Matter World Hypothesis (MWH) and prior studies, underscore mRNA sequence selection as a driver of genetic code evolution, with implications for synthetic biology pending experimental validation.All findings in this study are derived from advanced simulations and thus require empirical validation before drawing definitive conclusions.</p> |
| title | Computational Simulation of RNA-Based Protocell Competition: mRNA Sequence Selection and Prebiotic Genetic Code Evolution |
| topic | RNA World, proto-ribosome, prebiotic competition, mRNA sequence selection, genetic code evolution, L16/RPL10, S12/RPS23, computational modeling, chi-square analysis |
| url | https://doi.org/10.5281/zenodo.15282697 |