The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.
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ABSTRACT:
SUBMITTER: Lee CW
PROVIDER: S-EPMC3086565 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem-loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem-loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem-loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5' and 3' stacking pattern, a sheared A-A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.
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Project description:Nucleoside base modifications can alter the structures and dynamics of RNA molecules and are important in tRNAs for maintaining translational fidelity and efficiency. The unmodified anticodon stem-loop from Escherichia coli tRNA(Phe) forms a trinucleotide loop in solution, but Mg2+ and dimethylallyl modification of A37 N6 destabilize the loop-proximal base pairs and increase the mobility of the loop nucleotides. The anticodon arm has three additional modifications, psi32, psi39, and A37 C2-thiomethyl. We have used NMR spectroscopy to investigate the structural and dynamical effects of psi32 on the anticodon stem-loop from E.coli tRNA(Phe). The psi32 modification does not significantly alter the structure of the anticodon stem-loop relative to the unmodified parent molecule. The stem of the RNA molecule includes base pairs psi32-A38 and U33-A37 and the base of psi32 stacks between U33 and A31. The glycosidic bond of psi32 is in the anti configuration and is paired with A38 in a Watson-Crick geometry, unlike residue 32 in most crystal structures of tRNA. The psi32 modification increases the melting temperature of the stem by approximately 3.5 degrees C, although the psi32 and U33 imino resonances are exchange broadened. The results suggest that psi32 functions to preserve the stem integrity in the presence of additional loop modifications or after reorganization of the loop into a translationally functional conformation.
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Project description:MotivationCanonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. A rapid predictor would facilitate the annotation of CDR structures in the large amounts of repertoire data now becoming available from next generation sequencing experiments.ResultsSCALOP annotates CDR canonical forms for antibody sequences, supported by an auto-updating database to capture the latest cluster information. Its accuracy is comparable to that of a standard structural predictor but it is 800 times faster. The auto-updating nature of SCALOP ensures that it always attains the best possible coverage.Availability and implementationSCALOP is available as a web application and for download under a GPLv3 license at opig.stats.ox.ac.uk/webapps/scalop.Supplementary informationSupplementary data are available at Bioinformatics online.
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