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Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

ABSTRACT: The HIV-1 transactivation response element (TAR) RNA binds a variety of proteins and is a target for developing anti-HIV therapies. TAR has two primary binding sites: a UCU bulge and a CUGGGA apical loop. We used NMR residual dipolar couplings, carbon spin relaxation (R(1) and R(2)), and relaxation dispersion (R(1rho)) in conjunction with molecular dynamics and mutagenesis to characterize the dynamics of the TAR apical loop and investigate previously proposed long-range interactions with the distant bulge. Replacement of the wild-type apical loop with a UUCG loop did not significantly affect the structural dynamics at the bulge, indicating that the apical loop and the bulge act largely as independent dynamical recognition centers. The apical loop undergoes complex dynamics at multiple timescales that are likely important for adaptive recognition: U31 and G33 undergo limited motions, G32 is highly flexible at picosecond-nanosecond timescales, and G34 and C30 form a dynamic Watson-Crick basepair in which G34 and A35 undergo a slow (approximately 30 mus) likely concerted looping in and out motion, with A35 also undergoing large amplitude motions at picosecond-nanosecond timescales. Our study highlights the power of combining NMR, molecular dynamics, and mutagenesis in characterizing RNA dynamics.

SUBMITTER: Dethoff EA

PROVIDER: S-EPMC2553144 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature

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Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

Dethoff Elizabeth A EA Hansen Alexandar L AL Musselman Catherine C Watt Eric D ED Andricioaei Ioan I Al-Hashimi Hashim M HM

Biophysical journal 20080711 8

The HIV-1 transactivation response element (TAR) RNA binds a variety of proteins and is a target for developing anti-HIV therapies. TAR has two primary binding sites: a UCU bulge and a CUGGGA apical loop. We used NMR residual dipolar couplings, carbon spin relaxation (R(1) and R(2)), and relaxation dispersion (R(1rho)) in conjunction with molecular dynamics and mutagenesis to characterize the dynamics of the TAR apical loop and investigate previously proposed long-range interactions with the dis ...[more]

PMID: 18621815

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Project description:Over the past 15 years, researchers have extended the multidimensional techniques which originated with NMR in the 1970s to infrared and visible coherent spectroscopy. These advances have dramatically enhanced the temporal resolution from the microsecond to the femtosecond regime. NMR spectroscopists have developed principles for the design of pulse sequences that enhance selected spectral features and reveal desired dynamical events. Extending these principles to the optical regime offers numerous opportunities for narrowing the line shapes in specific directions, unraveling weak cross-peaks from otherwise congested spectra, and controlling the interferences between quantum pathways. We can achieve these enhancements by shaping the spectral and temporal profiles of the pulses. Pulse polarization shaping may lead to unique probes of time-dependent chirality. In this Account, we compare two types of signals. The first, the photon echo, is generated in the direction -k(1) + k(2) + k(3), and the second, double quantum coherence, is detected at +k(1) + k(2) - k(3). Here k(1), k(2), and k(3) are the wave vectors of the three incoming pulses in chronological order. We illustrate the novel information extracted from these signals by simulations of three physical systems. In the first system, spectra of GaAs semiconductor quantum wells provide a direct look at many-body electron correlation effects. We directly observe specific projections of the many-electron wave function, which we can use to test the quality of various levels of computational techniques for electronic structure. Secondly, the spectra of photosynthetic aggregates reveal couplings between chromophores, quantum coherence signatures of chromophore entanglement, and energy-transfer pathways. Using some fundamental symmetries of pulse polarization configurations of nonlinear signals, we can construct superpositions of signals designed to better distinguish among various coherent and incoherent exciton transport pathways and amplify subtle variations among different species of the Fenna-Matthews-Olson (FMO) antenna complex. Both of the first two applications require femtosecond pulses of light in the visible range. The third application demonstrates how resonant core spectroscopy may be used to generate core excitations that are highly localized at selected atoms. Such signals can monitor the motions of valence electron wavepackets in real space with atomic spatial resolution. These future X-ray applications will require attosecond bright X-ray sources, which are currently being developed in several labs. Common principles underlie these techniques in coherent spectroscopy for spins, valence electrons, and core electronic excitations, spanning frequencies from radiowaves to hard X-rays.

Dataset Information

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

Publications

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

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