Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy

Visualizing spatially correlated dynamics that directs RNA conformational transitions

RNAs fold into three-dimensional (3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals. RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways. However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using 'relativistic' sets of residual dipolar couplings (RDCs). Using this approach, we uncovered super-large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 53 degrees and 110 degrees in a highly correlated manner (R = 0.97) while simultaneously (R = 0.81-0.92) bending by about 94 degrees. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand-bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand-induced transitions along specific predefined conformational pathways.

NMR methods for studying quadruplex nucleic acids

Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.

Dynamics of large elongated RNA by NMR carbon relaxation

We present an NMR strategy for characterizing picosecond-to-nanosecond internal motions in uniformly 13C/15N-labeled RNAs that combines measurements of R1, R1rho, and heteronuclear 13C{1H} NOEs for protonated base (C2, C5, C6, and C8) and sugar (C1') carbons with a domain elongation strategy for decoupling internal from overall motions and residual dipolar coupling (RDC) measurements for determining the average RNA global conformation and orientation of the principal axis of the axially symmetric rotational diffusion. TROSY-detected pulse sequences are presented for the accurate measurement of nucleobase carbon R1 and R1rho rates in large RNAs. The relaxation data is analyzed using a model free formalism which takes into account the very high anisotropy of overall rotational diffusion (Dratio approximately 4.7), asymmetry of the nucleobase CSAs and noncollinearity of C-C, C-H dipolar and CSA interactions under the assumption that all interaction tensors for a given carbon experience identical isotropic internal motions. The approach is demonstrated and validated on an elongated HIV-1 TAR RNA (taum approximately 18 ns) both in free form and bound to the ligand argininamide (ARG). Results show that, while ARG binding reduces the amplitude of collective helix motions and local mobility at the binding pocket, it leads to a drastic increase in the local mobility of "spacer" bulge residues linking the two helices which undergo virtually unrestricted internal motions (S2 approximately 0.2) in the ARG bound state. Our results establish the ability to quantitatively study the dynamics of RNAs which are significantly larger and more anisotropic than customarily studied by NMR carbon relaxation.

Structure and dynamics of a molten globular enzyme

Although protein dynamics has been recognized as a potentially important contributor to enzyme catalysis, structural disorder is generally considered to reduce catalytic efficiency. This widely held assumption has recently been challenged by the finding that an engineered chorismate mutase combines high catalytic activity with the properties of a molten globule, a loosely packed and highly dynamic conformational ensemble. Taking advantage of the ordering observed upon ligand binding, we have now used NMR spectroscopy to characterize this enzyme in complex with a transition-state analog. The complex adopts a helix-bundle structure, as designed, but retains unprecedented flexibility on the millisecond timescale across its entire length. Moreover, pre-steady-state kinetics data show that binding occurs by an induced-fit mechanism on the same timescale as the enzymatic reaction, linking global conformational plasticity with efficient catalysis.

An improved picture of methyl dynamics in proteins from slowly relaxing local structure analysis of 2H spin relaxation

Protein dynamics is intimately related to biological function. Core dynamics is usually studied with 2H spin relaxation of the 13CDH2 group, analyzed traditionally with the model-free (MF) approach. We showed recently that MF is oversimplified in several respects. This includes the assumption that the local motion of the dynamic probe and the global motion of the protein are decoupled, the local geometry is simple, and the local ordering is axially symmetric. Because of these simplifications MF has yielded a puzzling picture where the methyl rotation axis is moving rapidly with amplitudes ranging from nearly complete disorder to nearly complete order in tightly packed protein cores. Our conclusions emerged from applying to methyl dynamics in proteins the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995-11006.), which can be considered the generalization of MF, with all the simplifications mentioned above removed. The SRLS picture derived here for the B1 immunoglobulin binding domain of peptostreptococcal protein L, studied over the temperature range of 15-45 degrees C, is fundamentally different from the MF picture. Thus, methyl dynamics is characterized structurally by rhombic local potentials with varying symmetries and dynamically by tenfold slower rates of local motion. On average, potential rhombicity decreases, mode-coupling increases, and the rate of local motion increases with increasing temperature. The average activation energy for local motion is 2.0 +/- 0.2 kcal/mol. Mode-coupling affects the analysis even at 15 degrees C. The accuracy of the results is improved by including in the experimental data set relaxation rates associated with rank 2 coherences.

Improved magnetization alignment schemes for spin-lock relaxation experiments

A pair of pulse schemes that spin-lock magnetization efficiently are presented. The design of the sequences benefited from a particularly simple relation that is derived describing to first order the evolution of any magnetization component due to the application of an off-resonance 90 degrees pulse. The sequences are shown theoretically and experimentally to significantly outperform the 90 degrees -delay-90 degrees element that is often used in current applications. It is shown that alignment of magnetization to within 1 degrees of the effective field can be obtained over a bandwidth extending between [-omega(SL), omega(SL)], where omega(SL) is the strength of the spin-lock field using a simple scheme that is an order of magnitude shorter than an adiabatic pulse that might also be used for a similar purpose.

Temperature dependence of fast dynamics in proteins

The temperature dependence of the internal dynamics of recombinant human ubiquitin has been measured using solution NMR relaxation techniques. Nitrogen-15 relaxation has been employed to obtain a measure of the amplitude of subnanosecond motion at amide N-H sites in the protein. Deuterium relaxation has been used to obtain a measure of the amplitude of motion of methyl-groups in amino-acid side chains. Data was obtained between 5 and 55 degrees C. The majority of amide N-H and methyl groups show a roughly linear (R(2)>0.75) temperature dependence of the associated Lipari-Szabo model-free squared generalized-order parameter (O(2)) describing the amplitude of motion. Interestingly, for those sites showing a linear response, the temperature dependence of the backbone is distinct from that of the methyl-bearing side chains with the former being characterized by a significantly larger Lambda-value, where Lambda is defined as d ln(1 - O)/d lnT. These results are comparable to the sole previous such study of the temperature dependence of protein motion obtained for a calmodulin-peptide complex. This suggests that the distinction between the main chain and methyl-bearing side chains may be general. Insight into the temperature dependence is gathered from a simple two-state step potential model.

Off-Resonance TROSY-Selected R1ρ Experiment with Improved Sensitivity for Medium- and High-Molecular-Weight Proteins

NMR spin relaxation techniques that utilize relaxation interference phenomena (TROSY) enable chemical exchange processes to be characterized in high-molecular-weight proteins. A TROSY-selected (TS) approach for measuring off-resonance R1rho relaxation in the spin-locked rotating reference frame is developed using three principles: (i) deuteration of nonexchangeable 1H sites to minimize remote dipole-dipole interactions, (ii) selective excitation of the slowly relaxing 15N doublet component to obtain optimal initial conditions, and (iii) selective inversion of one of the 15N doublet components to suppress cross-relaxation during the spin-lock period. The method is validated using [90%-15N, 70%-2H] ubiquitin at 280 K. The TROSY-selected R1rho experiment enables characterization of backbone dynamics on the microsecond time scale in large proteins.