Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays
RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experim...
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| Format: | Article |
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MDPI AG
2023-03-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/13/3/796 |
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| author | Felix Jenne Ivan Berezkin Frank Tempel Dimitry Schmidt Roman Popov Alexander Nesterov-Mueller |
| author_facet | Felix Jenne Ivan Berezkin Frank Tempel Dimitry Schmidt Roman Popov Alexander Nesterov-Mueller |
| author_sort | Felix Jenne |
| collection | DOAJ |
| description | RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work. |
| first_indexed | 2024-03-11T06:17:26Z |
| format | Article |
| id | doaj.art-98ccb8a957e94b5ea3cb7a801935d4f8 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-11T06:17:26Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-98ccb8a957e94b5ea3cb7a801935d4f82023-11-17T12:12:29ZengMDPI AGLife2075-17292023-03-0113379610.3390/life13030796Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide ArraysFelix Jenne0Ivan Berezkin1Frank Tempel2Dimitry Schmidt3Roman Popov4Alexander Nesterov-Mueller5Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, GermanyInstitute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, GermanyInstitute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, GermanyInstitute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, GermanyAxxelera UG, DE-76189 Karlsruhe, GermanyInstitute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, GermanyRNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work.https://www.mdpi.com/2075-1729/13/3/796RNA peptide interactionshigh-density peptide arraysthe origin of the genetic code |
| spellingShingle | Felix Jenne Ivan Berezkin Frank Tempel Dimitry Schmidt Roman Popov Alexander Nesterov-Mueller Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays Life RNA peptide interactions high-density peptide arrays the origin of the genetic code |
| title | Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays |
| title_full | Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays |
| title_fullStr | Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays |
| title_full_unstemmed | Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays |
| title_short | Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays |
| title_sort | screening for primordial rna peptide interactions using high density peptide arrays |
| topic | RNA peptide interactions high-density peptide arrays the origin of the genetic code |
| url | https://www.mdpi.com/2075-1729/13/3/796 |
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