1o15
From Proteopedia
(New page: 200px<br /><applet load="1o15" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o15" /> '''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THE...) |
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| - | [[Image:1o15.gif|left|200px]]<br /><applet load="1o15" size=" | + | [[Image:1o15.gif|left|200px]]<br /><applet load="1o15" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1o15" /> | caption="1o15" /> | ||
'''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS'''<br /> | '''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The description of the nonbonded contact terms used in simulated annealing | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1O15 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with TEP as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1O15 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=TEP:'>TEP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O15 OCA]. |
==Reference== | ==Reference== | ||
Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation., Clore GM, Kuszewski J, J Am Chem Soc. 2003 Feb 12;125(6):1518-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12568611 12568611] | Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation., Clore GM, Kuszewski J, J Am Chem Soc. 2003 Feb 12;125(6):1518-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12568611 12568611] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Clore, G | + | [[Category: Clore, G M.]] |
[[Category: Kuszewski, J.]] | [[Category: Kuszewski, J.]] | ||
[[Category: TEP]] | [[Category: TEP]] | ||
[[Category: ribonucleic acid]] | [[Category: ribonucleic acid]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:12:11 2008'' |
Revision as of 12:12, 21 February 2008
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THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS
Overview
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.
About this Structure
1O15 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation., Clore GM, Kuszewski J, J Am Chem Soc. 2003 Feb 12;125(6):1518-25. PMID:12568611
Page seeded by OCA on Thu Feb 21 14:12:11 2008
