P11-08
Analysis of interactions between fatty acid membranes with pH-dependent phase structures and nucleic acid monomers using Molecular Dynamics simulation
Ryoji ABE *1, Taren GINTER1, Kosuke FUJISHIMA1, 2
1Department of Life Science and Technology, Institute of Science Tokyo
2Earth-Life Science Institute, Institute of Science Tokyo
( * E-mail: fujiki.r.aa@m.titech.ac.jp )
Fatty acids are amphipathic molecules with simple structures and have attracted attention as prebiotic membrane compartments. Furthermore, nucleic acids are molecules that serve as the basis for replication, and their synthesis in prebiotic environments and experiments has been confirmed. Recent experimental verification suggests the possibility of coevolution between fatty acids and nucleic acids. Fatty acid vesicles have also been shown to form at a different pH range in the presence of nucleic acid monomers, suggesting that nucleic acids reduce the pH sensitivity of fatty acids. Moreover, two different diffusion rates were observed for nucleic acid monomers in the presence of fatty acid vesicles, suggesting that nucleic acid monomers are adsorbed to the fatty acids.
Despite these experimental results, the detailed mechanism of fatty acid-nucleic acid interaction has yet to be elucidated. However, a thorough understanding of this interaction is essential in clarifying the prebiotic coevolution of fatty acid membranes and nucleic acids. Therefore, to understand this detailed mechanism, we conducted all-atom molecular dynamics simulations using GROMACS and the CHARMM36 force field to analyse the interaction.
We conducted simulations for 200 ns on a system comprising a fatty acid membrane and nucleic acid monomers in an aqueous solution. The fatty acid membranes were 1:1 to 2:1 mix of protonated and deprotonated oleic acid (18 carbons, 1 degree of unsaturation, cis) based on the conditions necessary for vesicle formation. We also calculated the radial distribution functions of heteroatoms in nucleic acids for each oxygen atom of oleic acid to interpret the results.
Our analysis demonstrated the formation of hydrogen bonds between oleic acid and the nucleobases and sugars. We observed differences in the formation of hydrogen bonds based on the positions of the hydrogen donors and acceptors of the nucleobases. We also found that the probability of forming hydrogen bonds varies depending on the position of the hydroxyl group in the sugar moiety. Furthermore, we noted differences in forming hydrogen bonds with nucleic acids for fatty acid membranes with different protonation composition ratios.
This study partially reproduced the experimental results of previous studies and clarified the contribution of hydrogen bonds in the interaction between the fatty acid membrane and nucleic acid monomers. In addition, the hydrogen bonds formed between the nucleic acid and the fatty acid membrane differ depending on the type of nucleobase and the protonation composition ratio of the fatty acid, suggesting coevolutionary selectivity between fatty acids and nucleic acids. Further simulations are being performed to systematically understand the interactions between fatty acids and nucleic acids and clarify the coevolution of fatty acids and nucleic acids related to the origin of life.