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RBM45 Preferential Binding to m6A: Simulations Suggest Synergy of RRM3 and Other Domains
Raeyeon Park1, Lydia M Contreras2, Phanourios Tamamis1,3
1Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.
RNA-binding motif protein 45 (RBM45) preferentially binds N6-methyladenosine (m6A) RNA motifs. Molecular dynamics simulations reveal synergistic interactions between RBM45 domains for this m6A preference, offering mechanistic insights.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- RNA-binding motif protein 45 (RBM45) is vital for brain development and RNA metabolism.
- RBM45's RNA recognition motif (RRM) domains bind GAC-containing RNA motifs, with or without N6-methyladenosine (m6A) modification.
- While individual RRMs don't show m6A preference, full-length RBM45 preferentially binds m6A-modified RNA.
Purpose of the Study:
- To investigate the biophysical mechanisms underlying RBM45's preferential binding to m6A-modified RNA.
- To elucidate the role of individual RRM domains and the full-length protein in RNA binding.
- To provide mechanistic insights into how RRM proteins recognize m6A.
Main Methods:
- Molecular dynamics (MD) simulations were employed to study RNA-protein interactions.
- Simulations analyzed the binding of various RNA motifs (GACG, GACU, GACA) with individual RRM domains and full-length RBM45.
- Focus on interactions with both unmodified and m6A-modified RNA.
Main Results:
- Individual RRM domains showed no strong preference for m6A.
- RBM45's RRM3 domain, in the context of the full-length protein, demonstrated favorable binding to GACA and GACU motifs.
- Synergistic cooperation among RRM, linker, and C-terminal domains enabled preferential m6A binding over adenine in GACA/GACU motifs.
- m6A modification enhanced RNA-protein stability and facilitated inter-domain interactions.
Conclusions:
- Full-length RBM45 exhibits preferential binding to m6A-modified RNA through domain cooperation.
- The study provides the first mechanistic insights into direct, preferential m6A recognition by an RRM domain in synergy with other protein regions.
- Non-RRM domains, including intrinsically disordered regions, play a crucial role in RBM45's m6A binding specificity.
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