Structural effects of modified ribonucleotides and magnesium in transfer RNAs

Abstract

Modified nucleotides are ubiquitous and important to tRNA structure and function. To understand their effect on tRNA conformation, we performed a series of molecular dynamics simulations on yeast tRNAPhe and tRNAinit, E. coli tRNAinit and HIV tRNALys. Simulations were performed with the wild type modified nucleotides, using the recently developed CHARMM compatible force field parameter set for modified nucleotides [Xu, Y., Vanommeslaeghe, K., Aleksandrov, A., Mackerell AD, Nilsson, L., J. Comp. Chem., 2016], or with the corresponding unmodified nucleotides, and in the presence or absence of Mg2+. Results showed a stabilizing effect associated with the presence of the modifications and Mg2+ for some important positions, such as modified guanosine in position 37 and dihydrouridines in 16/17 including both structural properties and base interactions. Some other modifications were also found to make subtle contributions to the structural properties of local domains. While we were not able to investigate the effect of Adenosine 37 in tRNAinit and limitations were observed in the conformation of E. coli tRNAinit, the presence of the modified nucleotides and of Mg2+ better maintained the structural features and base interactions of the tRNA systems than in their absence indicating the utility of incorporating the modified nucleotides in simulations of tRNA and other RNAs.

Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m6A) Recognition by the Reader Domain of YTHDC1

“…However, the detailed mechanism of the molecular recognition is still vague because most previous studies drew conclusions based either on static structural models or macroscopic observations, thus missing the dynamic feature of the interactions or atomic resolution, respectively. Moreover, as newly discovered functions of epitranscriptomic proteins, the field has gradually turned its focus into unlocking new therapeutic targets, editing tools of RNA methylation and demethylation, − medicinal chemistry, ,− and molecular mechanics. , This transition requires a thorough elucidation of how the proteins recognize their natural and artificial binders.…”

“…Moreover, as newly discovered functions of epitranscriptomic proteins, the field has gradually turned its focus into unlocking new therapeutic targets, 24 editing tools of RNA methylation and demethylation, 25−27 medicinal chemistry, 22,28−30 and molecular mechanics. 31,32 This transition requires a thorough elucidation of how the proteins recognize their natural and artificial binders.…”

Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif

“…For this purpose, different methodologies have been explored, for example, refining bonded and nonbonded potentials ,, and adding external hydrogen terms . The improved force fields have led to successful implementations of MD simulations on some RNA-containing systems, including conformational dynamics of folded RNAs − and biological catalysis. − Concerning the second issue, naturally occurring modified ribonucleotides’ parameters have now been developed and are consistent with commonly used force fields. , The last issue may be most critical for the successful simulation of a protein–RNA complex. For balancing protein–RNA interactions, one strategy is to modify pair-specific corrections to nonbonded interactions by targeting related osmotic pressure. − Besides, polarizable force fields may capture essential physical effects for protein–RNA interactions, but their developments are not fully mature yet. − …”

Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

“…Unfortunately, the technique of MD simulation is still facing major challenges such as inadequacies in conformational sampling and force field accuracy. − The results from our work and other groups have revealed that simulations involving nucleic acids in general and RNA in particular, generate conformations that are not observed experimentally, thus motivating over the years a number of efforts to revise the AMBER and the CHARMM force fields to improve structural and thermodynamic predictions. − ,− ,, It should be noted that Nagan and co-workers and Mathews and co-workers have used the original Cornell et al and the updated FF99 force fields of the AMBER molecular modeling package, respectively, whereas Nilsson and co-workers used the latest CHARMM36 force field , with the current extension to include modified nucleotides . Notably, the force field parameters for the modifications used in these studies were not validated in any independent simulation.…”

“…These simulation results acquire a lot of significance for interpreting and understanding the experimental data on the structure and stability of tRNA (or their anticodon ASLs) when the native modifications were substituted by their unmodified counterparts. The unmodified or incompletely modified ASLs of tRNA Phe , tRNA Lys,3 , and tRNA Gly in solution studies were found to be destabilized and showed large deviation from their canonical structure. ,,− ,, It was suggested that the structures corresponded more to extended stems and shorter loops without evident U-turn conformation. ,,− ,, Although there were some structural differences between the crystal structures of the unmodified E. coli tRNA Phe and the completely modified structure of yeast tRNA Phe , the anticodon conformations were essentially the same .…”