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| | {{STRUCTURE_1rht| PDB=1rht | SCENE= }} | | {{STRUCTURE_1rht| PDB=1rht | SCENE= }} |
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| - | '''24-MER RNA HAIRPIN COAT PROTEIN BINDING SITE FOR BACTERIOPHAGE R17 (NMR, MINIMIZED AVERAGE STRUCTURE)'''
| + | ===24-MER RNA HAIRPIN COAT PROTEIN BINDING SITE FOR BACTERIOPHAGE R17 (NMR, MINIMIZED AVERAGE STRUCTURE)=== |
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| - | ==Overview==
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| - | The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The imino proton spectrum is consistent with base pairing requirements for coat protein binding known from biochemical studies. All 185 of the nonexchangeable protons were assigned using a variety of homonuclear 2D and 3D NMR methods. Measurements of nuclear Overhauser enhancements and two-quantum correlations were made at 500 MHz. New procedures were developed to characterize as many resonances as possible, including deconvolution and path analysis methods. An average of 21 distance constraints per residue were used in molecular dynamics calculations to obtain preliminary folded structures for residues 3-21. The unpaired A8 residue is stacked in the stem, and the entire region from G7 to C15 in the upper stem and loop appears to be flexible. Several of these residues have a large fraction of S-puckered ribose rings, rather than the N-forms characteristic of RNA duplexes. There is considerable variation in the low-energy loop conformations that satisfy the distance constraints at this preliminary level of refinement. The Shine-Dalgarno ribosome binding site is exposed, and only two apparently weak base pairs would have to break for the 16S ribosomal RNA to bind and the ribosome to initiate translation of the replicase gene. Although the loop form must be regarded as tentative, the known interaction sites with the coat protein are easily accessible from the major groove side of the loop.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_7756280}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 7756280 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_7756280}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RHT OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RHT OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Nmr]] | | [[Category: Nmr]] |
| | [[Category: Rna]] | | [[Category: Rna]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:30:55 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 07:26:46 2008'' |
Revision as of 04:26, 29 July 2008
Template:STRUCTURE 1rht
24-MER RNA HAIRPIN COAT PROTEIN BINDING SITE FOR BACTERIOPHAGE R17 (NMR, MINIMIZED AVERAGE STRUCTURE)
Template:ABSTRACT PUBMED 7756280
About this Structure
Full experimental information is available from OCA.
Reference
Proton NMR and structural features of a 24-nucleotide RNA hairpin., Borer PN, Lin Y, Wang S, Roggenbuck MW, Gott JM, Uhlenbeck OC, Pelczer I, Biochemistry. 1995 May 16;34(19):6488-503. PMID:7756280
Page seeded by OCA on Tue Jul 29 07:26:46 2008
