Structural and dynamic properties of the YTH domain in complex with N⁶-methyladenosine RNA studied by accelerated molecular dynamics simulations

Abstract

Background: N⁶-methyl adenosine (m⁶A) modifications of mRNA and long non-coding RNA (lncRNAs) are known to play a significant role in regulation of gene expression and organismal development. Besides writer and eraser proteins of this dynamic modification, the YT521-B homology (YTH) domain can recognize the modification involved in numerous cellular processes. The function of proteins containing YTH domain and its binding mode with N⁶-Methyladenosine RNA has attracted considerable attention. However, the structural and dynamic characteristics of the YTH domain in complex with m⁶A RNA is still unknown.

Method: This work presents results of accelerated molecular dynamics (aMD) simulations at the timescale of microseconds. Principal component analysis (PCA), molecular mechanics generalized Born surface area (MM/GBSA) calculations, contact analysis and contact-based principal component analysis (conPCA) provide new insights into structure and dynamics of the YTH-RNA complex.

Results: The aMD simulations indicate that the recognition loop has a larger movement away from the binding pocket in the YTH-A3 RNA than that in the YTH-m⁶A3 RNA. In aMD trajectories of the apo YTH, there is a significant close-open transition of the recognition loop, that is to say, the apo YTH can take both the closed and open structure. We have found that the YTH domain binds more favorably to the methylated RNA than the non-methylated RNA. The per-residue free energy decomposition and conPCA suggest that hydrophobic residues including W380, L383-V385, W431-P434, M437, and M441-L442, may play important roles in favorable binding of the m⁶A RNA to the YTH domain, which is also supported by aMD simulations of a double mutated system (L383A/M437A).

Conclusion: The results are in good agreement with higher structural stability of the YTH-m⁶A RNA than that of the YTH-A3 RNA. The addition of a methylation group on A3 can enhance its binding to the hydrophobic pocket in the YTH domain. Our simulations support a ‘conformational selection’ mechanism between the YTH-RNA binding. This work may aid in our understanding of the structural and dynamic characteristics of the YTH protein in complex with the methylated RNA.

Author summary

N⁶-methyl adenosine (m⁶A) modifications play an important role in the regulation of RNA decay and gene expression at the post-transcriptional level. The YT521-B homology (YTH) domain-containing proteins can recognize m⁶A in numerous cellular processes. However, the binding mode of the YTH domain to m⁶A RNA is still unknown. In this work, we present an atomic description of the YTH-m6A RNA complex using computer simulations. The results have revealed the molecular mechanism of the RNA binding to the YTH domain. Our findings may be helpful for understanding the structural and dynamic characteristics of the YTH-m6A RNA complex.

Graphical abstract

Keywords

RNA methylation / YTH-m⁶A3 RNA / principal component analysis (PCA) / binding free energy / contact-based PCA

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.15302/ J-QB-022-0297.

ACKNOWLEDGEMENTS

This work is supported by the National Natural Science Foundation of China (No. 91953101), and the Strategic Priority Research Program of the Chinese Academy of Science (No. XDB37040202). The Supercomputing Center of USTC provides computer resources for this project, and we are grateful to Mr. Yundong Zhang for his technical supports.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Mingwei Li, Guanglin Chen and Zhiyong Zhang declare that they have no conflict of interests.

This article does not contain any studies with human or animal subjects performed by any of the authors.

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