Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations
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The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding interactions between these two molecules. The simulations show that: (i) 16S rRNA remains in a highly folded structure when it is bound to S15; (ii) in the absence of S15, 16S rRNA significantly alters its conformation and transiently forms conformations that are similar to the bound structure that make it available for binding with S15; (iii) the unbound rRNA spends the majority of its time in extended conformations. The formation of the extended conformations is a result of the molecule reaching a lower electrostatic energy and the formation of the highly folded, crystal-like conformation is a result of achieving a lower solvation energy. In addition, our MD simulations show that 16S rRNA and S15 bind across the major groove of helix 22 (H22) via electrostatic interactions. The negatively charged phosphate groups of G658, U740, G741 and G742 bind to the positively charged S15 residues Lys7, Arg34 and Arg37. The current study provides a dynamic view of the binding of 16S rRNA with S15.
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The changes added by human players tend to agree with the 16S structural model, especially in regions linked to important functional sites, such as S8 and S15 binding sites, and a region that undergoes conformational readjustment during 30S assembly.
“In Fig. 4, we show that the changes added by human players tend to agree with the 16S structural model, especially in regions linked to important functional sites, such as S8 and S15 binding sites, and a region that undergoes conformational readjustment during 30S assembly44–49.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [46]
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- Structure of H22 and its in¯uence on its binding with S15. (A) The structure of H22 is taken from the snapshot showing a crystal-like conformation (left). The orange arrow on the left represent the width of the major groove. G658 is located close to residue Lys7 of S15 (red ribbon at right) and U740±G742 are located close to Arg34 and Arg37. (B) The structure of H22 taken from the snapshot showing an extended conformation (left). In this structure, the binding nucleotides U740±G742 are too distant to interact with Arg34 and Arg37 (dashed arrow). Nucleic Acids Research, 2003, Vol. 31, No. 2 637
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- Authors
- Li, W.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Li, W.
- ORCID
- Li, W.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-01-15
- Volume
- 31
- Issue
- 2
- Pages
- 629-638
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC140513
- OpenAlex
- W2148044701
- Cited by
- 31
- References
- 38
- Citations by year
- 2026: 1 · 2024: 2 · 2020: 1 · 2019: 1 · 2016: 2 · 2014: 1 · 2012: 5
- FWCI
- 1.15
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- 16S rRNA, ribosomal protein S15, major groove, electrostatic interactions, solvation energy, rRNA folding
- MeSH terms
- Base Sequence, Binding Sites, Computer Simulation, Hydrogen Bonding, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Protein Binding, Protein Conformation, Ribosomal Proteins, RNA, Ribosomal, 16S, Thermodynamics, Thermus thermophilus, Protein Structure, Tertiary
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