1yfv
From Proteopedia
(New page: 200px<br /><applet load="1yfv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yfv" /> '''STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3...) |
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| - | [[Image:1yfv.gif|left|200px]]<br /><applet load="1yfv" size=" | + | [[Image:1yfv.gif|left|200px]]<br /><applet load="1yfv" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1yfv" /> | caption="1yfv" /> | ||
'''STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE'''<br /> | '''STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif | + | The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived restraints for 78 interproton distances (per strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26 dihedral angles (per strand). The G x A mismatch structures are similar to those observed in a DNA duplex [Li, Y., Zon, G., & Wilson, W. D. (1991) Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., & Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G 2-amino and A 6-amino protons are within hydrogen-bonding distance of a phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and G-G stacking is observed between the G x A mismatches. This contrasts with the poor stacking observed between the G x A mismatches and closing G x C base pairs. The stems are basically A-form with all bases in the anti conformation and all nonterminal sugars in the C3'-endo conformation. The structure rationalizes previous thermodynamic, circular dichroism, and imino proton NMR results and suggests tandem G x A mismatches in RNA may provide a contact site for tertiary interactions. |
==About this Structure== | ==About this Structure== | ||
| - | 1YFV 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:// | + | 1YFV 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=1YFV OCA]. |
==Reference== | ==Reference== | ||
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics., SantaLucia J Jr, Turner DH, Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8251479 8251479] | Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics., SantaLucia J Jr, Turner DH, Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8251479 8251479] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Junior, J | + | [[Category: Junior, J Santalucia.]] |
| - | [[Category: Turner, D | + | [[Category: Turner, D H.]] |
[[Category: 2-d nmr]] | [[Category: 2-d nmr]] | ||
[[Category: anti-parallel rna duplex]] | [[Category: anti-parallel rna duplex]] | ||
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[[Category: ribonucleic acid]] | [[Category: ribonucleic acid]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:04:56 2008'' |
Revision as of 14:04, 21 February 2008
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STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE
Overview
The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived restraints for 78 interproton distances (per strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26 dihedral angles (per strand). The G x A mismatch structures are similar to those observed in a DNA duplex [Li, Y., Zon, G., & Wilson, W. D. (1991) Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., & Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G 2-amino and A 6-amino protons are within hydrogen-bonding distance of a phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and G-G stacking is observed between the G x A mismatches. This contrasts with the poor stacking observed between the G x A mismatches and closing G x C base pairs. The stems are basically A-form with all bases in the anti conformation and all nonterminal sugars in the C3'-endo conformation. The structure rationalizes previous thermodynamic, circular dichroism, and imino proton NMR results and suggests tandem G x A mismatches in RNA may provide a contact site for tertiary interactions.
About this Structure
1YFV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics., SantaLucia J Jr, Turner DH, Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:8251479
Page seeded by OCA on Thu Feb 21 16:04:56 2008
