Background:N^(6)-methyladenosine(m^(6)A)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 ...Background:N^(6)-methyladenosine(m^(6)A)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 N^(6)-methyladenosine RNA has attracted considerable attention.However,the structural and dynamic characteristics of the YTH domain in complex with m^(6)A 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-m^(6)A3 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 nonmethylated 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 m^(6)A 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-m^(6)A 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.展开更多
基金the National Natural Science Foundation of China(No.91953101)the Strategic Priority Research Program of the Chinese Academy of Science(No.XDB37040202).
文摘Background:N^(6)-methyladenosine(m^(6)A)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 N^(6)-methyladenosine RNA has attracted considerable attention.However,the structural and dynamic characteristics of the YTH domain in complex with m^(6)A 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-m^(6)A3 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 nonmethylated 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 m^(6)A 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-m^(6)A 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.
