Limits...
Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.

Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH - J Phys Chem B (2011)

Bottom Line: A set of 50 ns simulations with revised χ torsions (AMBER99χ force field) gives two primary conformations, consistent with the NMR spectra.For the rest of the simulation, random-coil structures and a stable non-A-form conformation inconsistent with NMR spectra were seen.Evidently, the AMBER99χ force field improves structural predictions for single-stranded GACC RNA compared to the AMBER99 force field, but further force field improvements are needed.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.

Show MeSH

Related in: MedlinePlus

Overlap of the NMR modeled (black) and AMBER99χ force field predicted (red) conformations of major (left) and minor (right) species. Predicted structures are average from fifteen 50 ns unrestrained simulations starting from A-form. Heavy atom rmsd of major and minor conformations with respect to NMR modeled structures are 0.6 and 0.9 Å, respectively (see text and Figure S4 for detail). Values of dihedral angles for structures are given in the Supporting Information. Major and minor conformations generated during 1.9 μs simulation are similar to these (see Figure S4).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3140773&req=5

fig5: Overlap of the NMR modeled (black) and AMBER99χ force field predicted (red) conformations of major (left) and minor (right) species. Predicted structures are average from fifteen 50 ns unrestrained simulations starting from A-form. Heavy atom rmsd of major and minor conformations with respect to NMR modeled structures are 0.6 and 0.9 Å, respectively (see text and Figure S4 for detail). Values of dihedral angles for structures are given in the Supporting Information. Major and minor conformations generated during 1.9 μs simulation are similar to these (see Figure S4).

Mentions: GACC presumably has an ensemble of structures in rapid exchange that contribute to the NMR spectrum. Simulated annealing with NMR restraints was used to see if any particular structures are consistent with the NMR data. The protocol described in the Methods section generated 182 out of 200 structures with constraint energies less than 0.1 kcal/mol. Of these structures, two had energies greater than the mean plus the standard deviation. As a result, 180 out of 200 structures were analyzed. Cluster analyses showed that 116 and 32 represent A-form-like major and first minor conformations, respectively (Figures 5 and S4 and Tables S9 and S10). Another 18 structures represent a second A-form-like minor conformation with an average energy less favorable than both the major and first minor conformations (Figure S4). Both minor conformations have a flipped, upside down C4 sugar, but with different backbone orientations (Figure S4). The flipped C4 sugar conformation is consistent with weak C3H6–C4H2′ and C3H3′-C4H2′ NOEs that were observed, but not used as restraints. The major and first minor conformations have stacking between G1/A2, A2/C3, and C3/C4, while the C3/C4 stacking is missing in the second minor conformation. With the exception of the flipped C4, the structures generated by simulated annealing are largely A-form-like.


Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.

Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH - J Phys Chem B (2011)

Overlap of the NMR modeled (black) and AMBER99χ force field predicted (red) conformations of major (left) and minor (right) species. Predicted structures are average from fifteen 50 ns unrestrained simulations starting from A-form. Heavy atom rmsd of major and minor conformations with respect to NMR modeled structures are 0.6 and 0.9 Å, respectively (see text and Figure S4 for detail). Values of dihedral angles for structures are given in the Supporting Information. Major and minor conformations generated during 1.9 μs simulation are similar to these (see Figure S4).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3140773&req=5

fig5: Overlap of the NMR modeled (black) and AMBER99χ force field predicted (red) conformations of major (left) and minor (right) species. Predicted structures are average from fifteen 50 ns unrestrained simulations starting from A-form. Heavy atom rmsd of major and minor conformations with respect to NMR modeled structures are 0.6 and 0.9 Å, respectively (see text and Figure S4 for detail). Values of dihedral angles for structures are given in the Supporting Information. Major and minor conformations generated during 1.9 μs simulation are similar to these (see Figure S4).
Mentions: GACC presumably has an ensemble of structures in rapid exchange that contribute to the NMR spectrum. Simulated annealing with NMR restraints was used to see if any particular structures are consistent with the NMR data. The protocol described in the Methods section generated 182 out of 200 structures with constraint energies less than 0.1 kcal/mol. Of these structures, two had energies greater than the mean plus the standard deviation. As a result, 180 out of 200 structures were analyzed. Cluster analyses showed that 116 and 32 represent A-form-like major and first minor conformations, respectively (Figures 5 and S4 and Tables S9 and S10). Another 18 structures represent a second A-form-like minor conformation with an average energy less favorable than both the major and first minor conformations (Figure S4). Both minor conformations have a flipped, upside down C4 sugar, but with different backbone orientations (Figure S4). The flipped C4 sugar conformation is consistent with weak C3H6–C4H2′ and C3H3′-C4H2′ NOEs that were observed, but not used as restraints. The major and first minor conformations have stacking between G1/A2, A2/C3, and C3/C4, while the C3/C4 stacking is missing in the second minor conformation. With the exception of the flipped C4, the structures generated by simulated annealing are largely A-form-like.

Bottom Line: A set of 50 ns simulations with revised χ torsions (AMBER99χ force field) gives two primary conformations, consistent with the NMR spectra.For the rest of the simulation, random-coil structures and a stable non-A-form conformation inconsistent with NMR spectra were seen.Evidently, the AMBER99χ force field improves structural predictions for single-stranded GACC RNA compared to the AMBER99 force field, but further force field improvements are needed.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.

Show MeSH
Related in: MedlinePlus