1muv
From Proteopedia
(New page: 200px<br /><applet load="1muv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1muv" /> '''Sheared A(anti)-A(anti) Base Pairs in a Dest...) |
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| - | [[Image:1muv.gif|left|200px]]<br /><applet load="1muv" size=" | + | [[Image:1muv.gif|left|200px]]<br /><applet load="1muv" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1muv" /> | caption="1muv" /> | ||
'''Sheared A(anti)-A(anti) Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2'''<br /> | '''Sheared A(anti)-A(anti) Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The 5'(rGGCAAGCCU)(2) duplex contains tandem A.A pairs. The | + | The 5'(rGGCAAGCCU)(2) duplex contains tandem A.A pairs. The three-dimensional structure of the 5'(rGGCAAGCCU)(2) duplex was modeled by molecular dynamics and energy minimization with NMR-derived distance and dihedral angle restraints. Although the 5'(rCAAG)(2) loop is thermodynamically destabilizing by 1.1 kcal/mol, the tandem A.A pairs adopt a predominant conformation: a sheared anti-anti (A.A trans Hoogsteen/Sugar-edge) alignment similar to that observed in the crystal structure of the P4-P6 domain of the Tetrahymena thermophila intron [Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. (1996) Science 273, 1678-1685]. The NMR-derived structure of the 5'(rGGCAAGCCU)(2) duplex exhibits cross-strand hydrogen bonds from N3 of A4 to an amino hydrogen of A5 and from the 2' oxygen of the A4 sugar to the other amino hydrogen of A5. An intrastrand hydrogen bond is formed from the 2' OH hydrogen of A4 to O5' of A5. The cross-strand A5 bases are stacked. The Watson-Crick G-C regions are essentially A-form. The sheared anti-anti (A.A trans Hoogsteen/Sugar-edge) alignment provides potential contact sites for tertiary interactions and, therefore, is a possible target site for therapeutics. Thus, thermodynamically destabilizing internal loops can be preorganized for tertiary interactions or ligand binding. |
==About this Structure== | ==About this Structure== | ||
| - | 1MUV 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:// | + | 1MUV 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=1MUV OCA]. |
==Reference== | ==Reference== | ||
Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2., Znosko BM, Burkard ME, Schroeder SJ, Krugh TR, Turner DH, Biochemistry. 2002 Dec 17;41(50):14969-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12475246 12475246] | Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2., Znosko BM, Burkard ME, Schroeder SJ, Krugh TR, Turner DH, Biochemistry. 2002 Dec 17;41(50):14969-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12475246 12475246] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Burkard, M | + | [[Category: Burkard, M E.]] |
| - | [[Category: Krugh, T | + | [[Category: Krugh, T R.]] |
| - | [[Category: Schroeder, S | + | [[Category: Schroeder, S J.]] |
| - | [[Category: Turner, D | + | [[Category: Turner, D H.]] |
| - | [[Category: Znosko, B | + | [[Category: Znosko, B M.]] |
[[Category: aa mismatch]] | [[Category: aa mismatch]] | ||
[[Category: duplex]] | [[Category: duplex]] | ||
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[[Category: tandem mismatch]] | [[Category: tandem mismatch]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:59:15 2008'' |
Revision as of 11:59, 21 February 2008
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Sheared A(anti)-A(anti) Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2
Overview
The 5'(rGGCAAGCCU)(2) duplex contains tandem A.A pairs. The three-dimensional structure of the 5'(rGGCAAGCCU)(2) duplex was modeled by molecular dynamics and energy minimization with NMR-derived distance and dihedral angle restraints. Although the 5'(rCAAG)(2) loop is thermodynamically destabilizing by 1.1 kcal/mol, the tandem A.A pairs adopt a predominant conformation: a sheared anti-anti (A.A trans Hoogsteen/Sugar-edge) alignment similar to that observed in the crystal structure of the P4-P6 domain of the Tetrahymena thermophila intron [Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. (1996) Science 273, 1678-1685]. The NMR-derived structure of the 5'(rGGCAAGCCU)(2) duplex exhibits cross-strand hydrogen bonds from N3 of A4 to an amino hydrogen of A5 and from the 2' oxygen of the A4 sugar to the other amino hydrogen of A5. An intrastrand hydrogen bond is formed from the 2' OH hydrogen of A4 to O5' of A5. The cross-strand A5 bases are stacked. The Watson-Crick G-C regions are essentially A-form. The sheared anti-anti (A.A trans Hoogsteen/Sugar-edge) alignment provides potential contact sites for tertiary interactions and, therefore, is a possible target site for therapeutics. Thus, thermodynamically destabilizing internal loops can be preorganized for tertiary interactions or ligand binding.
About this Structure
1MUV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2., Znosko BM, Burkard ME, Schroeder SJ, Krugh TR, Turner DH, Biochemistry. 2002 Dec 17;41(50):14969-77. PMID:12475246
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