Abstract
Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.
Highlights
Intramolecular folding of RNA secondary structures drives tertiary conformation of RNA molecules [1,2,3]
SimRNA Evaluated 3D Properties of HIVNL4-3 50 -untranslated region (UTR) Beginning with 50 -Capped-Guanosine
Perspective on the capability of SimRNA to simulate HIV RNA was developed by comparing in silico constraints of centroid 2D or no secondary structure inputs
Summary
Intramolecular folding of RNA secondary structures drives tertiary conformation of RNA molecules [1,2,3]. Within the 50 -UTR, unspliced proviral transcripts engage host ribonucleoproteins (RNPs) that catalyze splicing or translation to virion proteins, or viral nucleocapsid RNPs drive pairs of RNA molecules into diploid genomic RNPs (gRNPs) to be packaged into virions. Ample secondary structure information is available on individual segments of the HIV 50 -UTR that are necessary for dimerization and packaging of diploid gRNA into virions [6,9,12,13,14,15,16,17,18,19,20]. U5-AUG pairing orients the dimer initiation sequence (DIS) for intermolecular dimerization and the core encapsidation signal (CES) for nucleocapsid binding, and packaging of the diploid genomic ribonucleoprotein into virions [8]
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