1ekw
From Proteopedia
(New page: 200px<br /><applet load="1ekw" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ekw" /> '''NMR STRUCTURE OF A DNA THREE-WAY JUNCTION'''...) |
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| - | [[Image:1ekw.gif|left|200px]]<br /><applet load="1ekw" size=" | + | [[Image:1ekw.gif|left|200px]]<br /><applet load="1ekw" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ekw" /> | caption="1ekw" /> | ||
'''NMR STRUCTURE OF A DNA THREE-WAY JUNCTION'''<br /> | '''NMR STRUCTURE OF A DNA THREE-WAY JUNCTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Homonuclear 3D NOESY-NOESY has shown great promise for the structural | + | Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (approximately 60 degrees) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (+/- 20 degrees) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method. |
==About this Structure== | ==About this Structure== | ||
| - | 1EKW is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1EKW is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKW OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Donne, D.]] | [[Category: Donne, D.]] | ||
| - | [[Category: Gorenstein, D | + | [[Category: Gorenstein, D G.]] |
| - | [[Category: Leontis, N | + | [[Category: Leontis, N B.]] |
| - | [[Category: Luxon, B | + | [[Category: Luxon, B A.]] |
[[Category: Thiviyanathan, V.]] | [[Category: Thiviyanathan, V.]] | ||
[[Category: dna]] | [[Category: dna]] | ||
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[[Category: unpaired bases]] | [[Category: unpaired bases]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:28:50 2008'' |
Revision as of 10:28, 21 February 2008
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NMR STRUCTURE OF A DNA THREE-WAY JUNCTION
Overview
Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (approximately 60 degrees) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (+/- 20 degrees) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method.
About this Structure
1EKW is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY., Thiviyanathan V, Luxon BA, Leontis NB, Illangasekare N, Donne DG, Gorenstein DG, J Biomol NMR. 1999 Jul;14(3):209-21. PMID:10481274
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