Effect of Protein Environment on the Shape Resonances of RNA Nucleobases: Insights From a Model System
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arXiv
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| Format: | Preprint |
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2025
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| author | Arora, Sneha J, Jishnu Narayanan S Haritan, Idan Adhikary, Amitava Dutta, Achintya Kumar |
| author_facet | Arora, Sneha J, Jishnu Narayanan S Haritan, Idan Adhikary, Amitava Dutta, Achintya Kumar |
| contents | In this work, the effect of amino acid environment on the nucleobase-centered anion radical shape resonances is investigated by employing uracil as a model system for pyrimidine base in RNA. Anionic uracil-glycine complexes have been used to model the RNA-protein interactions. The resonance positions and widths of these complexes have been simulated using the equation of motion coupled cluster method coupled with resonance via Padé approach. Our work shows that in the transient negative ion (TNI, or, the anion radical of glycine:uracil complex), glycine stabilizes the nucleobase-centered resonances through hydrogen bonding, increasing the lifetime of TNI. At the same time, a glycine-centered resonance shows the ability of amino acids to capture the electron density and move it away from the uracil nucleobase. At the micro-solvation level, this modeling indicates that amino acids would have more influence on nucleobase-centered resonances in the TNI than that displayed by the corresponding aqueous environment. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_01020 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Effect of Protein Environment on the Shape Resonances of RNA Nucleobases: Insights From a Model System Arora, Sneha J, Jishnu Narayanan S Haritan, Idan Adhikary, Amitava Dutta, Achintya Kumar Chemical Physics In this work, the effect of amino acid environment on the nucleobase-centered anion radical shape resonances is investigated by employing uracil as a model system for pyrimidine base in RNA. Anionic uracil-glycine complexes have been used to model the RNA-protein interactions. The resonance positions and widths of these complexes have been simulated using the equation of motion coupled cluster method coupled with resonance via Padé approach. Our work shows that in the transient negative ion (TNI, or, the anion radical of glycine:uracil complex), glycine stabilizes the nucleobase-centered resonances through hydrogen bonding, increasing the lifetime of TNI. At the same time, a glycine-centered resonance shows the ability of amino acids to capture the electron density and move it away from the uracil nucleobase. At the micro-solvation level, this modeling indicates that amino acids would have more influence on nucleobase-centered resonances in the TNI than that displayed by the corresponding aqueous environment. |
| title | Effect of Protein Environment on the Shape Resonances of RNA Nucleobases: Insights From a Model System |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2505.01020 |