Engineering Minimal Ribosomes to Test the Matter World Hypothesis: A Computational Simulation Framework(Estimated Calculation)
Fuente:
Zenodo
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Recurso digital |
| Veröffentlicht: |
Zenodo
2025
|
| Schlagworte: | |
| Online-Zugang: | |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| _version_ | 1866901331183140864 |
|---|---|
| author | Reza Hashemi |
| author_facet | Reza Hashemi |
| contents | <p>The Matter World Hypothesis (MWH) (Hashemi, 2025a) posits that life originated from co-evolutionary interactions among RNA, peptides, lipids, and metal ions in prebiotic microenvironments. This study uses computational simulations to engineer minimal ribosomes (~500 kDa) and estimate their peptide synthesis capability, testing MWH predictions without experimental validation. Through in silico comparative genomics, molecular dynamics (MD), Monte Carlo simulations, and simulated evolutionary selection, we estimate: (1) truncated rRNA (16S ~500 nt, 23S ~700 nt) with essential proteins (L2, L3, L4, S12, S17), poly-Lys, and polyphosphate (PPi) achieves >52% peptidyl transferase center (PTC) formation in simulated clay pores; (2) optimal conditions (pH 7.5, 90°C, 5 mM Mg²⁺/PPi) vastly outperform RNA-only systems (<1% activity); (3) 20 cycles of simulated evolution double catalytic efficiency (k<sub>cat</sub> +10×). These estimated outcomes suggest ribosomes could emerge from stochastic RNA-peptide-metal-PPi interactions, supporting MWH through computational modeling alone.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15161543 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Engineering Minimal Ribosomes to Test the Matter World Hypothesis: A Computational Simulation Framework(Estimated Calculation) Reza Hashemi RNA, peptides, Ribosome, Evolution, Simulation, Prebiotic, Catalysis, Clay, Polyphosphate, MWH <p>The Matter World Hypothesis (MWH) (Hashemi, 2025a) posits that life originated from co-evolutionary interactions among RNA, peptides, lipids, and metal ions in prebiotic microenvironments. This study uses computational simulations to engineer minimal ribosomes (~500 kDa) and estimate their peptide synthesis capability, testing MWH predictions without experimental validation. Through in silico comparative genomics, molecular dynamics (MD), Monte Carlo simulations, and simulated evolutionary selection, we estimate: (1) truncated rRNA (16S ~500 nt, 23S ~700 nt) with essential proteins (L2, L3, L4, S12, S17), poly-Lys, and polyphosphate (PPi) achieves >52% peptidyl transferase center (PTC) formation in simulated clay pores; (2) optimal conditions (pH 7.5, 90°C, 5 mM Mg²⁺/PPi) vastly outperform RNA-only systems (<1% activity); (3) 20 cycles of simulated evolution double catalytic efficiency (k<sub>cat</sub> +10×). These estimated outcomes suggest ribosomes could emerge from stochastic RNA-peptide-metal-PPi interactions, supporting MWH through computational modeling alone.</p> |
| title | Engineering Minimal Ribosomes to Test the Matter World Hypothesis: A Computational Simulation Framework(Estimated Calculation) |
| topic | RNA, peptides, Ribosome, Evolution, Simulation, Prebiotic, Catalysis, Clay, Polyphosphate, MWH |
| url | https://doi.org/10.5281/zenodo.15161543 |