DSSR in the validation of NMR RNA structures

With great interest, I read the article titled Improving NMR Structures of RNA by Bermejo et al. As is well-known, solution NMR structures of RNA normally exhibit more steric clashes and conformational ambiguities than their crystal X-ray counterparts. The paper introduces an improved force field, RNA-ff1, for structure elucidation with Xplor-NIH. By adopting realistic atom radii and a new statistical torsional potential, the RNA-ff1 force field significantly enhances covalent geometry and MolProbity validation scores (in steric contacts and backbone conformation) in the seven tested NMR datasets.

I am glad to see that DSSR is mentioned in the Section titled Analysis of Known Structural Motifs:

… The program DSSR (Lu et al., 2015) (part of the 3DNA software suite [Lu and Olson, 2003, 2008]) was used to evaluate the stacking configuration of successive base pairs (i.e., ‘‘steps’’) within the helical stems of the systems in the present calculations. The most interesting trends are observed for the base-pair step parameters slide (Figure 4K) and rise (Figure 4L), which respectively measure an in-plane dislocation and the vertical displacement of a step relative to a local mid-step reference frame (Lu and Olson, 2003; for analysis of all step parameters, see Figure S1). Relative to A-form parameters in high-resolution X-ray structures (Olson et al., 2001) (Figures 4K and 4L, dashed lines), the average slide of all but one of the original NMR models (PDB: 1O15) is small in absolute value (Figure 4K). … Moreover, four out of the seven original PDB models display an average rise considerably larger than the expected 3.32 Å (the van der Waals separation distance between bases, not to be confused with the helical rise, measured relative to the helical axis, expected to be 2.83 Å for A-form [Olson et al., 2001]).

As an example, the single stem of PDB: 2KOC’s representative structure, assumed to be an A-form helix (Nozinovic et al., 2010), displays a particularly large separation between base pairs C3–G12 and A4–U11 (rise: 4.33 Å) that is visually evident when compared with that of the RNA-ff1 representative model (rise: 3.33 Å ) (Figure 6A). Indeed, this base-pair step defies conformational classification by DSSR in the PDB: 2KOC structure, while it is assigned as A-form (along with the rest of the stem) in the RNA-ff1 structure.

Through the text, the term “stem” or “helical stem” is used consistently, in line with the nomenclatures adopted by DSSR. It is worth noting that DSSR also derives a complete set of backbone conformational parameters, including the assignment of sugar-phosphate backbone suites. The backbone parameters constitutes only a small portion of what DSSR has to offer, and they are written to the auxiliary file dssr-torsions.txt by default.





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