2jse
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(New page: 200px<br /><applet load="2jse" size="350" color="white" frame="true" align="right" spinBox="true" caption="2jse" /> '''NMR reveals absence of hydrogen bonding in a...)
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Revision as of 10:08, 23 January 2008
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NMR reveals absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.
Overview
NMR studies provide insights into structural features of internal loops., These insights can be combined with thermodynamic studies to generate, models for predicting structure and energetics. The tandem mismatch, internal loop, %@mt;sys@%, %@sx@%3'C%@bold@%UA%@rsf@%C5'%@be@%5'G%@bold@%UG%@rsf@%G3'%@sxx@%%@mx@% , has been studied by NMR. The NMR structure reveals an internal loop with, no hydrogen bonding between the loop bases and with the G in the AG, mismatch flipped out of the helix. The sequence of this internal loop is, highly conserved in rRNA. The loop is located in the large ribosomal, subunit and is part of a conserved 58-nt fragment that is the binding, domain of ribosomal protein L11. Structural comparisons between variants, of this internal loop in crystal structures of the 58-nt domain complexed, with L11 protein and of the large ribosomal subunit (LSU) suggest that, this thermodynamically destabilizing internal loop is partially, preorganized for tertiary interactions and for binding L11. A model for, predicting the base pairing and free energy of 2 x 2 nucleotide internal, loops with a purine-purine mismatch next to a pyrimidine-pyrimidine, mismatch is proposed on the basis of the present NMR structure and, previously reported thermodynamics.
About this Structure
2JSE is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR Reveals the Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop from Ribosomal RNA(,)., Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH, Biochemistry. 2007 Nov 6;46(44):12665-12678. Epub 2007 Oct 11. PMID:17929882
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