R1ρ relaxation for two-site chemical exchange: General approximations and some exact solutions

Miloushev, Vesselin Z.; Palmer, Arthur G.

doi:10.1016/j.jmr.2005.07.023

Cited by 59 publications

(57 citation statements)

References 19 publications

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“…1B and Fig. S2) using the Laguerre equation (32) yielded an ES population (p B ∼ 0.26-0.66%) and lifetime (τ = 1.2-3.1 ms) very similar to that measured previously (16) for the slow-exchanging apical loop residues (p B = ∼0.4% and τ = ∼2 ms). Indeed, all of the R1ρ data showing signs of slow exchange could be combined into a single two-state global fit yielding p B = 0.40 ± 0.05% and τ = 2.1 ± 0.3 ms (Table S1).…”

Section: Resultssupporting

confidence: 74%

Invisible RNA state dynamically couples distant motifs

Lee

Dethoff

Al‐Hashimi

2014

Proc. Natl. Acad. Sci. U.S.A.

113

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Using on-and off-resonance carbon and nitrogen R1ρ NMR relaxation dispersion in concert with mutagenesis and NMR chemical shift fingerprinting, we show that the transactivation response element RNA from the HIV-1 exists in dynamic equilibrium with a transient state that has a lifetime of ∼2 ms and population of ∼0.4%, which simultaneously remodels the structure of a bulge, stem, and apical loop. This is accomplished by a global change in strand register, in which bulge residues pair up with residues in the upper stem, causing a reshuffling of base pairs that propagates to the tip of apical loop, resulting in the creation of three noncanonical base pairs. Our results show that transient states can remodel distant RNA motifs and possibly give rise to mechanisms for rapid long-range communication in RNA that can be harnessed in processes such as cooperative folding and ribonucleoprotein assembly.NMR spectroscopy | dynamics | R1ρ relaxation dispersion | nucleic acids I t is now well-established that RNA sequences do not code for a single static structure, but rather, many conformations that populate energetic minima along a free-energy landscape (1, 2). Cellular inputs, ranging from changes in temperature and pH to the binding of proteins, other RNAs, and ligands, can preferentially stabilize select conformations along the landscape, resulting in dynamic changes in RNA structure that drive the multistep catalytic cycles of ribozymes (3), regulatory activities of riboswitches (4) and other RNA-based switches (5), and the dynamic assembly and disassembly of ribonucleoprotein (RNP) complexes (6).A common mode of RNA dynamics involves rearrangements in secondary structure that can melt or create entire hairpins, and thereby expose or sequester key regulatory elements that are several nucleotides long (1,4,7,8). Such secondary structural transitions entail large kinetic barriers, so they are often catalyzed by RNA-binding proteins (9), ATP-dependent chaperones (10), or otherwise occur by modulating cotranscriptional folding (5, 11). Recently, NMR R1ρ relaxation dispersion experiments (12-15) in concert with mutagenesis (16) have helped uncover more labile RNA secondary structural transitions that can take place without assistance from external cofactors at rates that are 2-4 orders of magnitude faster than larger-scale secondary structural rearrangements. These transitions entail excursions away from the energetically favorable ground state (GS) toward lowpopulated (typically populations <15%) and short-lived (lifetime < milliseconds) species often referred to as "excited states" (ES) (12, 13). These invisible RNA ES feature localized reshuffling of base pairing in and around noncanonical motifs such as bulges, internal loops, and apical loops (16) which can also expose or sequester functionally important residues or promote ATPindependent large-scale changes in secondary structure (14, 15). These faster and more localized changes in secondary structure may meet unique demands in RNA-based regulatory functions (16).Using...

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Section: Resultssupporting

confidence: 74%

Invisible RNA state dynamically couples distant motifs

Lee

Dethoff

Al‐Hashimi

2014

Proc. Natl. Acad. Sci. U.S.A.

113

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“…In two special cases, that of equal populations, p 1 ) p 2 , or that of placement of the rf carrier at the average resonance frequency of the two sites, ω rf ) (Ω 1 + Ω 2 )/2, the following result is obtained 26 This expression has an improved performance over those of eqs 31 and 34, as illustrated in Figure 5. ( 1 + 2k ex 2 (p 1 ω e1 2 + p 2 ω e2 2 )…”

Section: Rotating-frame Relaxationmentioning

confidence: 91%

“…Results for the linear three-site system given by eq 13 are obtained by interchanging the site 1 and 2 indices in eqs [26][27][28][29]. The general fast exchange solution reduces for the two-site system to in which k ex ) k 12 + k 21 .…”

Section: Rotating-frame Relaxationmentioning

confidence: 99%

Characterization of the Dynamics of Biomacromolecules Using Rotating-Frame Spin Relaxation NMR Spectroscopy

2006

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“…[12, 27–29] Studies have also examined the robustness with which exchange parameters can be characterized using R1ρ data for systems in slow exchange (k ex ~ 20 milliseconds) with the aid of weak spin lock fields (typically as low as 25–100 Hz). [15, 24, 30, 31] However, the reliability of exchange parameters obtained from R1ρ relaxation dispersion data for systems in fast exchange has not been thoroughly investigated.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange

Bothe

Stein

Al‐Hashimi

2014

Journal of Magnetic Resonance

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Spin relaxation in the rotating frame (R1ρ) is a powerful NMR technique for characterizing fast microsecond timescale exchange processes directed toward short-lived excited states in biomolecules. At the limit of fast exchange, only kex = k1 + k−1 and Φıx = pGpE(Δω)2 can be determined from R1ρ data limiting the ability to characterize the structure and energetics of the excited state conformation. Here, we use simulations to examine the uncertainty with which exchange parameters can be determined for two state systems in intermediate-to-fast exchange using off-resonance R1ρ relaxation dispersion. R1ρ data computed by solving the Bloch-McConnell equations reveals small but significant asymmetry with respect to offset (R1ρ(ΔΩ) ≠ R1ρ(−ΔΩ)), which is a hallmark of slow-to-intermediate exchange, even under conditions of fast exchange for free precession chemical exchange line broadening (kex/Δω > 10). A grid search analysis combined with bootstrap and Monte-Carlo based statistical approaches for estimating uncertainty in exchange parameters reveals that both the sign and magnitude of Δω can be determined at a useful level of uncertainty for systems in fast exchange (kex/Δω < 10) but that this depends on the uncertainty in the R1ρ data and requires a thorough examination of the multidimensional variation of χ2 as a function of exchange parameters. Results from simulations are complemented by analysis of experimental R1ρ data measured in three nucleic acid systems with exchange processes occurring on the slow (kex/Δω = 0.2; pE = ~ 0.7%), fast (kex/Δω = ~10–16; pE = ~13%) and very fast (kex = 39,000 s−1) chemical shift timescales.

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R1ρ relaxation for two-site chemical exchange: General approximations and some exact solutions

Cited by 59 publications

References 19 publications

Invisible RNA state dynamically couples distant motifs

Invisible RNA state dynamically couples distant motifs

Characterization of the Dynamics of Biomacromolecules Using Rotating-Frame Spin Relaxation NMR Spectroscopy

Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange

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