Improving the Accuracy of NMR Structures of RNA by Means of Conformational Database Potentials of Mean Force as Assessed by Complete Dipolar Coupling Cross-ValidationClore, G.M., Kuszewski, J.
(2003) J.Am.Chem.Soc. 125: 1518-1525
- PubMed: 12568611
- DOI: 10.1021/ja028383j
- PubMed Abstract:
- Refinement of Local and Long Range Structural Order in Theophylline-Binding RNA Using Using 13C-1H Residual Dipolar Couplings and Restrained Molecular Dynamics.
Sibille, N.,Pardi, A.,Simorre, J.P.,Blackledge, M.
(2001) J.Am.Chem.Soc. 123: 12135
- Improving the Accuracy of NMR Structures of DNA by Means of a Database Potential of Mean Force Describing Base-Base Positional Interactions.
Kuszewski, J.,Schwieters, C.,Clore, G.M.
(2001) J.Am.Chem.Soc. 123: 3903
- Interlocking Structural Motifs Mediate Molecular Discrimination by a Theophylline-Binding RNA
Zimmermann, G.R.,Jenison, R.D.,Wick, C.L.,Simorre, J.P.,Pardi, A.
(1997) Nat.Struct.Mol.Biol. 4: 644
The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improv ...
The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nucleic acid torsion angle database potential consisting of various multidimensional torsion angle correlations; and an RNA specific base-base positioning potential that provides a simple geometric, statistically based, description of sequential and nonsequential base-base interactions. The former is based on 416 nucleic acid crystal structures solved at a resolution of =2 A and an R-factor =25%; the latter is based on 131 RNA crystal structures solved at a resolution of =3 A and an R-factor of =25%, and includes both the large and small subunits of the ribosome. The application of these two database potentials is illustrated for the structure refinement of an RNA aptamer/theophylline complex for which extensive NOE and residual dipolar coupling data have been measured in solution.
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0510, USA.