Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR

Abstract

Intrinsic motions may allow HIV-1 transactivation response (TAR) RNA to change its conformation to form a functional complex with the Tat protein, which is essential for viral replication. Understanding the dynamic properties of TAR necessitates determining motion on the intermediate nanosecond-to-microsecond time scale. To this end, we performed solid-state deuterium NMR line-shape and T relaxation-time experiments to measure intermediate motions for two uridine residues, U40 and U42, within the lower helix of TAR. We infer global motions at rates of ∼10 s in the lower helix, which are much slower than those in the upper helix (∼10 s), indicating that the two helical domains reorient independently of one another in the solid-state sample. These results contribute to the aim of fully describing the properties of functional motions in TAR RNA.

RNA Dynamics by NMR Spectroscopy

“…[121] Examples:D robny and Varani could show ns-ms motions in TARR NA using deuterium solid-state NMR line shapes and T1 relaxation experiments on deuterated solid-state hairpin samples at different hydration levels. [122][123][124][125][126] Motions such as unstacking or base flipping out of the helix on the order of 10 7 s À1 and fast local motionso nt he order of 10 8 s À1 were sitespecifically observed from relaxation data, as described in refs. [124], [ 126].…”

“…Slower helical motionsc ould be determined from deuterium solid-state NMR line shapes for the upper and lower helix of TARi nt he ranges of % 10 6 and % 10 5 s À1 ,r espectively. [122] For analysis the two-site jump model is used to analyze the NMR data and extract exchange rates from line shape analysisand relaxation data. [124] Advantages, limitations, challenges:T hese results illustrate how solid-state NMR spectroscopy can provide dynamics data complementary to solution-state NMR experiments.…”

Advances in RNA 3D Structure Modeling Using Experimental Data

“…Moreover, there is no limitation in size of RNA and crystallization is not necessary (Marchanka et al, 2015). Some successful examples have been reported in both solution NMR (Davis et al, 2004;Latham et al, 2005;Keane et al, 2015;Orlovsky et al, 2020) and solid-state NMR (Marchanka et al, 2015(Marchanka et al, , 2018Huang et al, 2017;Yang and Wang, 2018).…”

A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints

“…However, it is important to note that our current understanding of HIV-1 TAR RNA structure, dynamics and function comes from the fundamental contribution of many different research groups, whose work, for the sake of brevity, will not be reviewed in this chapter. In particular, for the structure and dynamics by NMR of this molecule, the interested reader is directed to the recent work of the Drobny and Varani groups [78][79][80][81][82] .…”