Addressing the overlap problem in the quantitative analysis of two dimensional NMR spectra: application to (15)N relaxation measurements

Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation

Recent studies suggest that the fast timescale motion of methyl-bearing side chains may play an important role in mediating protein activity. These motions have been shown to encapsulate the residual conformational entropy of the folded state that can potentially contribute to the energetics of protein function. Here, we provide an overview of how to characterize these motions using nuclear magnetic resonance (NMR) spin relaxation methods. The strengths and limitations of several techniques are highlighted in order to assist with experimental design. Particular emphasis is placed on the practical aspects of sample preparation, data collection, data fitting, and statistical analysis. Additionally, discussion of the recently refined "entropy meter" is presented and its use in converting NMR observables to conformational entropy is illustrated. Taken together, these methods should yield new insights into the complex interplay between structure and dynamics in protein function.

Triple resonance ¹⁵Ν NMR relaxation experiments for studies of intrinsically disordered proteins

Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] chemical shifts very often observed within intrinsically disordered proteins complicates utilization of standard 2D HN correlated spectra because a limited number of amino acids can be characterized. Here we present a suite of triple resonance HNCO-type NMR experiments for measurements of five [Formula: see text] relaxation parameters ([Formula: see text], [Formula: see text], NOE, cross-correlated relaxation rates [Formula: see text] and [Formula: see text]) in doubly [Formula: see text],[Formula: see text]-labeled proteins. We show that the third spectral dimension combined with non-uniform sampling provides relaxation rates for almost all residues of a protein with extremely poor chemical shift dispersion, the C terminal domain of [Formula: see text]-subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by [Formula: see text] only showed that the presence of [Formula: see text] has a negligible effect on [Formula: see text], [Formula: see text], and on the cross-relaxation rate (calculated from NOE and [Formula: see text]), and that these relaxation rates can be used to calculate accurate spectral density values. Partially [Formula: see text]-labeled sample was used to test if the observed increase of [Formula: see text] [Formula: see text] in the presence of [Formula: see text] corresponds to the [Formula: see text] dipole-dipole interactions in the [Formula: see text],[Formula: see text]-labeled sample.

Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

Optimized linear prediction for radial sampled multidimensional NMR experiments

Radial sampling in multidimensional NMR experiments offers greatly decreased acquisition times while also providing an avenue for increased sensitivity. Digital resolution remains a concern and depends strongly upon the extent of sampling of individual radial angles. Truncated time domain data leads to spurious peaks (artifacts) upon FT and 2D FT. Linear prediction is commonly employed to improve resolution in Cartesian sampled NMR experiments. Here, we adapt the linear prediction method to radial sampling. Significantly more accurate estimates of linear prediction coefficients are obtained by combining quadrature frequency components from the multiple angle spectra. This approach results in significant improvement in both resolution and removal of spurious peaks as compared to traditional linear prediction methods applied to radial sampled data. The 'averaging linear prediction' (ALP) method is demonstrated as a general tool for resolution improvement in multidimensional radial sampled experiments.

Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins

Resonance assignment of intrinsically disordered proteins is made difficult by the extensive spectral overlaps. High-resolution 3D and 4D spectra are thus essential for this purpose. We have adapted the series of 3D BEST-experiments proposed by Lescop et al. [E. Lescop, P. Schanda, B. Brutscher, A set of BEST triple-resonance experiments for time-optimized protein resonance assignment, J. Magn. Reson. 187 (2007) 163-169] to the case of unfolded proteins. Longer acquisitions in the indirect dimensions are obtained by implementing semi-constant time evolution and sparse sampling. Using maximum entropy reconstruction for the indirect dimensions, the artifact intensity due to sparse sampling can be reduced to a level similar to the other sources of noise. The reduction of the sampled increments and the shorter duration of individual transients makes it possible to record a 4D experiment with reasonable resolution in less than 60 h.

15N H/D-SOLEXSY experiment for accurate measurement of amide solvent exchange rates: application to denatured drkN SH3

Amide solvent exchange rates are regarded as a valuable source of information on structure/dynamics of unfolded (disordered) proteins. Proton-based saturation transfer experiments, normally used to measure solvent exchange, are known to meet some serious difficulties. The problems mainly arise from the need to (1) manipulate water magnetization and (2) discriminate between multiple magnetization transfer pathways that occur within the proton pool. Some of these issues are specific to unfolded proteins. For example, the compensation scheme used to cancel the Overhauser effect in the popular CLEANEX experiment is not designed for use with unfolded proteins. In this report we describe an alternative experimental strategy, where amide (15)N is used as a probe of solvent exchange. The experiment is performed in 50% H(2)O-50% D(2)O solvent and is based on the (HACACO)NH pulse sequence. The resulting spectral map is fully equivalent to the conventional HSQC. To fulfill its purpose, the experiment monitors the conversion of deuterated species, (15)N(D), into protonated species, (15)N(H), as effected by the solvent exchange. Conceptually, this experiment is similar to EXSY which prompted the name of (15)N(H/D)-SOLEXSY (SOLvent EXchange SpectroscopY). Of note, our experimental scheme, which relies on nitrogen rather than proton to monitor solvent exchange, is free of the complications described above. The developed pulse sequence was used to measure solvent exchange rates in the chemically denatured state of the drkN SH3 domain. The results were found to correlate well with the CLEANEX-PM data, r = 0.97, thus providing a measure of validation for both techniques. When the experimentally measured exchange rates are converted into protection factors, most of the values fall in the range 0.5-2, consistent with random-coil behavior. However, elevated values, ca. 5, are obtained for residues R38 and A39, as well as the side-chain indole of W36. This is surprising, given that high protection factors imply hydrogen bonding or hydrophobic burial not expected to occur in a chemically denatured state of a protein. We, therefore, hypothesized that elevated protection factors are an artefact arising from the calculation of the reference (random-coil) exchange rates. To confirm this hypothesis, we prepared samples of several short peptides derived from the sequence of the drkN SH3 domain; these samples were used to directly measure the reference exchange rates. The revised protection factors obtained in this manner proved to be close to 1.0. These results also have implications for the more compact unfolded state of drkN SH3, which appears to be fully permeable to water as well, with no manifestations of hydrophobic burial.

Projected [(1)H, (15)N]-HMQC-[ (1)H, (1)H]-NOESY for large molecular systems: application to a 121 kDa protein-DNA complex

We present a projected [(1)H,(15)N]-HMQC-[(1)H,(1)H]-NOESY experiment for observation of NOE interactions between amide protons with degenerate (15)N chemical shifts in large molecular systems. The projection is achieved by simultaneous evolution of the multiple quantum coherence of the nitrogen spin and the attached proton spin. In this way NOE signals can be separated from direct-correlation peaks also in spectra with low resolution by fully exploiting both (1)H and (15)N frequency differences, such that sensitivity can be increased by using short maximum evolution times. The sensitivity of the experiment is not dependent on the projection angle for projections up to 45 degrees and no additional pulses or delays are required as compared to the conventional 2D [(1)H,(15)N]-HMQC-NOESY. The experiment provides two distinct 2D spectra corresponding to the positive and negative angle projections, respectively. With a linear combination of 1D cross-sections from the two projections the unavoidable sensitivity loss in projection spectra can be compensated for each particular NOE interaction. We demonstrate the application of the novel projection experiment for the observation of an NOE interaction between two sequential glycines with degenerate (15)N chemical shifts in a 121.3 kDa complex of the linker H1 histone protein with a 152 bp linear DNA.

Hadamard NMR spectroscopy for relaxation measurements of large (>35 kDa) proteins

Here we present a suite of pulse sequences for the measurement of (15)N T(1), T(1rho) and NOE data that combine traditional TROSY-based pulse sequences with band-selective Hadamard frequency encoding. The additive nature of the Hadamard matrix produces much reduced resonance overlap without the need for an increase in the dimensionality of the experiment or a significant decrease in the signal to noise ratio. We validate the accuracy of these sequences in application to ubiquitin and demonstrate their utility for relaxation measurements in Escherichia coli Class II fructose 1,6-bisphosphate aldolase (FBP-aldolase), a 358 residue 78 kDa dimeric enzyme.

Resolving overlap in two-dimensional NMR spectra: nuclear Overhauser effects in a polysaccharide

Overlapping resonances in the two-dimensional nuclear Overhauser (NOESY) spectrum of the O-antigenic polysaccharide from Escherichia coli O147 have been resolved by recording a tilted projection of a three-dimensional NOESY-HSQC spectrum, where the carbon-13 and proton evolutions are linked together. Through the introduction of small contributions from the appropriate carbon-13 shifts, a cluster of five unresolved proton peaks is separated into its components without the need to perform the full three-dimensional measurement, a time saving of at least an order of magnitude.

Resolving ambiguities in two-dimensional NMR spectra: the 'TILT' experiment

Ambiguities in two-dimensional nuclear magnetic resonance spectra due to overlap are usually resolved by recording a three-dimensional version of the experiment. It is shown that a simpler solution is to record a tilted projection of the three-dimensional spectrum, derived by Fourier transformation of the time-domain signal acquired while the two evolution parameters are varied simultaneously at the appropriate rates. By avoiding the need to record the full three-dimensional spectrum, this saves an order of magnitude in measurement time. The tilt technique is illustrated by reference to degenerate responses in the TOCSY and NOESY spectra of a small protein, agitoxin, where the 1H and 15N frequencies are incremented in tandem.