TY - JOUR KW - molecular dynamics KW - RNA KW - RNA-Binding Proteins KW - X-ray crystallography KW - epitranscriptomics KW - m6A KW - m6A reader AU - Y. Li AU - R. K. Bedi AU - L. Wiedmer AU - D. Huang AU - P. Śledź AU - A. Caflisch AB -

-Methyladenosine (m6A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m6A-containing RNAs to their readers are still elusive due to the unclear roles of m6A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-GG(mA)CU-3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m6A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Notably, simulations of unbound RNA motifs reveal that the methyl group of m6A and the 5' terminus shift the conformational preferences of the oligoribonucleotide to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m6A reader proteins.

BT - Journal of Chemical Theory and Computation C1 - 0250 DA - 2019 Dec 10 DO - 10.1021/acs.jctc.9b00987 IS - 12 J2 - J. Chem. Theory Comput. LA - eng M3 - Research Article N2 -

-Methyladenosine (m6A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m6A-containing RNAs to their readers are still elusive due to the unclear roles of m6A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-GG(mA)CU-3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m6A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Notably, simulations of unbound RNA motifs reveal that the methyl group of m6A and the 5' terminus shift the conformational preferences of the oligoribonucleotide to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m6A reader proteins.

PY - 2019 SP - 7004 EP - 7014 T2 - Journal of Chemical Theory and Computation TI - Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif VL - 15 SN - 1549-9626 ER -