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. 2016 Oct 15;24(20):4826-4834.
doi: 10.1016/j.bmc.2016.06.037. Epub 2016 Jun 18.

Structural effects of modified ribonucleotides and magnesium in transfer RNAs

You Xu  1 , Alexander D MacKerell Jr  2 , Lennart Nilsson  3
Affiliations

Structural effects of modified ribonucleotides and magnesium in transfer RNAs

You Xu et al. Bioorg Med Chem. .

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, Escherichia 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 (J. Comput. Chem.2016, 37, 896), 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.

Keywords: Magnesium; Modified nucleotide; Molecular dynamics; Nucleic acids; Structure; Transfer RNA.

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Figures

Figure 1
Figure 1
Secondary and tertiary structure of tRNA. A) The secondary clover leaf structure of type 1 tRNAs (shorter VL). Each circle represents a nucleotide, and the anticodon nucleotides are solid squares. Dashes in the stems indicate WC base pairs. Each subdomain is colored differently and labeled. B) The average structure from one simulation of tRNAPhe with modified nucleotides and Mg2+ ions present, showing each subdomain using the same color scheme. Note that nucleotides 73-76 were removed in the simulations. The spheres are Mg2+ ions, where the green ones were in stable positions and the yellow ones were mobile in the simulations.
Figure 2
Figure 2
The percentage of base stacking in the anticodon of each run. Color scheme is black (WT), magenta (CAN), green (WTMG) and blue (CNMG).*36-37 stack for 1EHZ, 1YFG and 1FIR; 36-38 stack for 3CW5.
Figure 3
Figure 3
The sugar pucker distributions of nucleotides in the D loop from the simulations. The columns from left to right show 1EHZ, 1YFG, 3CW5 and 1FIR, respectively; rows from top to bottom show nucleotides 16, 17, G18, 20 and A21 respectively. The WT nucleotides in positions 16, 17 and 20 are shown in the individual panels. The combined distributions from two independent runs of each system are shown in the graphs. Color scheme is black (WT), magenta (CAN), green (WTMG) and blue (CNMG). The conformation in the crystal structure is shown as a vertical brown dashed line in each panel.
Figure 4
Figure 4
The sugar pucker (top) and glycosidic torsion (bottom) distributions of nucleotides in the V loop from the simulations. Within each graph, the columns from left to right show 1EHZ, 1YFG, 3CW5 and 1FIR, respectively; rows from top to bottom show nucleotides 46, 47 and 48, respectively. The WT nucleotides are shown in the individual panels. The combined distributions from two independent runs of each system are shown in the graphs. Color scheme is black (WT), magenta (CAN), green (WTMG) and blue (CNMG). The conformation in the crystal structure is shown as a vertical brown dashed line in each panel.
Figure 5
Figure 5
The root mean square fluctuation (RMSF) as a function of the nucleotide sequence (bottom) compared with the average experimental B-factors (top). The columns from left to right show 1EHZ, 1YFG, 3CW5 and 1FIR respectively. The graphs show averages from two independent runs of each system. Color scheme for B-factor is blue (backbone) and red (base); for RMSF it is black (WT), magenta (CAN), green (WTMG) and blue (CNMG); solid circles and lines, and open triangles and dashed lines, are used for backbone and base atoms, respectively.
Figure 6
Figure 6
Hydrogen bonds for base pairs in each trajectory vs simulation time. The rows from top to bottom show 1EHZ, 1YFG, 3CW5 and 1FIR, respectively. The colored strip indicates that the hydrogen bonds in the base pair are present. The first two columns show base pairs in ASL, the middle three columns (except 3rd col. in 3CW5 and 1FIR) are base pairs in TSL or between DSL and TSL, and the last three columns are base pairs between DSL and VL. Color scheme: black (WT), magenta (CAN), green (WTMG) and blue (CNMG).
Figure 7
Figure 7
The local structure of tRNAPhe (1EHZ) showing some modifications involving base pairs and magnesium ions. Each average structure of (A) A loop and (B) D loop was superimposed on the crystal structure. Color scheme is black (WT), magenta (CAN), green (WTMG) and slate (crystal); CNMG is not shown. The Mg2+ ions (spheres) have the same color as the tRNA. Some bases in WTMG are shown in atomic detail for visualization of hydrogen bonds (yellow dashed line).
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