Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration

Krepl, Miroslav; Damberger, Fred F.; Schroetter, Christine von; Theler, Dominik; Pokorná, Pavlína; Allain, Frédéric H.‐T.; Šponer, Jiřı́

doi:10.1021/acs.jpcb.1c03541

Cited by 20 publications

(24 citation statements)

References 72 publications

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“…As expected the binding enthalpy with the hairpin RNA is slightly reduced compared to the single-stranded m 6 A RNA due to the local unfolding of the closing base pair. Interestingly, recognition of m 6 A in the context of both the single-stranded or the hairpin RNA ligand by the YTH domain shows slightly unfavorable binding entropy (consistent with previous reports), although the release of solvent molecules from the pocket of the protein that accommodates the N 6 methyl is expected to show favorable entropic contributions for binding ( 60 , 61 ).…”

Section: Discussionsupporting

confidence: 88%

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1

Jones

Tikhaia

Mourão

et al. 2022

Nucleic Acids Research

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The A-repeat region of the lncRNA Xist is critical for X inactivation and harbors several N6-methyladenosine (m6A) modifications. How the m6A modification affects the conformation of the conserved AUCG tetraloop hairpin of the A-repeats and how it can be recognized by the YTHDC1 reader protein is unknown. Here, we report the NMR solution structure of the (m6A)UCG hairpin, which reveals that the m6A base extends 5′ stacking of the A-form helical stem, resembling the unmethylated AUCG tetraloop. A crystal structure of YTHDC1 bound to the (m6A)UCG tetraloop shows that the (m6A)UC nucleotides are recognized by the YTH domain of YTHDC1 in a single-stranded conformation. The m6A base inserts into the aromatic cage and the U and C bases interact with a flanking charged surface region, resembling the recognition of single-stranded m6A RNA ligands. Notably, NMR and fluorescence quenching experiments show that the binding requires local unfolding of the upper stem region of the (m6A)UCG hairpin. Our data show that m6A can be readily accommodated in hairpin loop regions, but recognition by YTH readers requires local unfolding of flanking stem regions. This suggests how m6A modifications may regulate lncRNA function by modulating RNA structure.

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Section: Discussionsupporting

confidence: 88%

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1

Jones

Tikhaia

Mourão

et al. 2022

Nucleic Acids Research

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“…Others have shown that ignoring the size-dependent artifact can still give results that give a good correlation with the experimental data. 47 Similarly, there are studies that have shown that the Rocklin correction has very little effect on the RBFE calculations. 48 This is likely best explained by the fact that the Rocklin correction mainly corrects for the long-range effects of the electrostatic interactions.…”

Section: Discussionmentioning

confidence: 99%

Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers

Biggin

2022

J. Chem. Theory Comput.

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Absolute binding free-energy (ABFE) calculations are playing an increasing role in drug design, especially as they can be performed on a range of disparate compounds and direct comparisons between them can be made. It is, however, especially important to ensure that they are as accurate as possible, as unlike relative binding free-energy (RBFE) calculations, one does not benefit as much from a cancellation of errors during the calculations. In most modern implementations of ABFE calculations, a particle mesh Ewald scheme is typically used to treat the electrostatic contribution to the free energy. A central requirement of such schemes is that the box preserves neutrality throughout the calculation. There are many ways to deal with this problem that have been discussed over the years ranging from a neutralizing plasma with a post hoc correction term through to a simple co-alchemical ion within the same box. The post hoc correction approach is the most widespread. However, the vast majority of these studies have been applied to a soluble protein in a homogeneous solvent (water or salt solution). In this work, we explore which of the more common approaches would be the most suitable for a simulation box with a lipid bilayer within it. We further develop the idea of the so-called Rocklin correction for lipid-bilayer systems and show how such a correction could work. However, we also show that it will be difficult to make this generalizable in a practical way and thus we conclude that the use of a “co-alchemical ion” is the most useful approach for simulations involving lipid membrane systems.

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“…So far, this has been only sparsely noted in the literature. (55)(56)(57)(58) The problem is now defined and documented in this work, by comparing the performance of the ff12SB, ff14SB, and ff19SB ffs for the isolated HuR RRM3 protein.…”

Section: System Building and Simulation Protocolmentioning

confidence: 99%

Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field

Krepl

Pokorná

Mlýnský

et al. 2022

Preprint

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Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using NMR and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics (MD) simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using millisecond-scale aggregate ensemble of unbiased simulations we were able to observe a few dozens of binding events. The HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. The SRFS1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force-field modification scaling down the intramolecular vdW interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes and future perspectives of such research are discussed.

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Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration

Cited by 20 publications

References 72 publications

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1

Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers

Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field

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