Isotope-Filtered Affinity NMR

A double-editing pulse sequence has been developed that allows the direct observation of protein binding ligand(s) from a mixture of compounds. This technique should aid the discovery of lead pharmaceutical compounds. The proton NMR signals from protein and the nonbinding ligands are simultaneously eliminated using¹³C isotope editing and PFG diffusion-edited NMR. This new experiment is demonstrated using¹³C/¹⁵N-labeled stromelysin catalytic domain (SCD).     

Clean TROSY: compensation for relaxation-induced artifacts

TROSY pulse sequences for recording, e.g., (1)H-(15)N chemical shift correlation spectra of proteins are designed to select only one of four two-dimensional multiplet components. However, all of the variants published so far are prone to relaxation-induced artifacts at the positions of two of the other multiplet components. This article introduces modifications to the two spin-state-selective coherence transfer building blocks of the TROSY mixing sequence resulting in a clean TROSY spectrum with the artifacts largely suppressed. It works by having the new mixing sequence generate peaks of opposite phase at the positions of the relaxation artifacts. The clean TROSY pulse sequence is marginally shorter than the original one and contains the same pulses. Experimental demonstration is presented for the (15)N-labeled proteins RAP 17-97 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein) and EQT, equinatoxin II, from the Mediterranean anemone Actinia equina.     

Three-dimensional protein NMR TROSY-type (15)N-resolved (1)H(N)-(1)H(N) NOESY spectra with diagonal peak suppression

An earlier two-dimensional NOESY experiment with diagonal peak suppression in the (1)H(N)-(1)H(N) region is extended to three dimensions by including (15)N evolution while maintaining the TROSY approach throughout. The technique suppresses all anti-TROSY resonances by appropriate pulse sequence elements and for large molecules at high fields possible semi- and anti-TROSY artifacts are further suppressed by virtue of much shorter transverse relaxation times for these components. The new technique is demonstrated using an (15)N-labeled protein sample, RAP 17-97 (N-terminal domain of alpha2-macroglobulin Receptor Associated Protein), in H(2)O at 500 MHz.     

Three-dimensional 13C shift/1H-15N coupling/15N shift solid-state NMR correlation spectroscopy.

Triple-resonance experiments capable of correlating directly bonded and proximate carbon and nitrogen backbone sites of uniformly 13C- and 15N-labeled peptides in stationary oriented samples are described. The pulse sequences integrate cross-polarization from 1H to 13C and from 13C to 15N with flip-flop (phase and frequency switched) Lee-Goldburg irradiation for both 13C homonuclear decoupling and 1H-15N spin exchange at the magic angle. Because heteronuclear decoupling is applied throughout, the three-dimensional pulse sequence yields 13C shift/1H-15N coupling/15N shift correlation spectra with single-line resonances in all three frequency dimensions. Not only do the three-dimensional spectra correlate 13C and 15N resonances, they are well resolved due to the three independent frequency dimensions, and they can provide up to four orientationally dependent frequencies as input for structure determination. These experiments have the potential to make sequential backbone resonance assignments in uniformly 13C- and 15N-labeled proteins.     

13C natural abundance S3E and S3CT experiments for measurement of J coupling constants between 13Calpha or 1Halpha and other protons in a protein

It is demonstrated that the spin-state-selective pulse sequence elements, S3E and S3CT, previously introduced for measurement of J coupling constants in 15N-labeled proteins can be applied for work with peptides and proteins with 13C at the natural abundance level. In addition, a method is described for suppression of crosstalk caused by passive spin flips and pulse imperfections, which otherwise results in systematically underestimated J coupling constants and thereby inaccurate structural constraints. This method is also applicable for crosstalk suppression in applications of S3E and S3CT to 13C- or 15N-labeled samples. Experimental confirmation is obtained using a 10 mM BPTI sample focusing on 13C in the alpha position. The measured J coupling constants include 3J(HN-Halpha) and 3J(Halpha-Hbeta) related to the phi and chi1 angles, respectively.     

Protein dynamics measurements by TROSY-based NMR experiments

The described TROSY-based experiments for investigating backbone dynamics of proteins make it possible to elucidate internal motions in large proteins via measurements of T(1), T(2), and NOE of backbone (15)N nuclei. In our proposed sequences, the INEPT sequence is eliminated and the PEP sequence is replaced by the ST2-PT sequence from the HSQC-based experiments. This has the benefit of shortening the pulse sequences by 5.4 ms (=1/2J) and results in an increase in the intrinsic sensitivity of the proposed TROSY-based experiments. The TROSY-based experiments are on average of 13% more sensitive than the corresponding HSQC-based experiments on a uniformly (15)N-labeled Xenopus laevis calcium-bound calmodulin sample on a 750-MHz spectrometer at 5 degrees C. The amide proton linewidths of the TROSY-based experiments are 2-13 Hz narrower than those of the HSQC experiments. More sensitivity gain and higher resolution are expected if the protein sample is deuterated.     

Simple Two-Pulse Detection Scheme in Pulsed EPR for Studying Low-Frequency Nuclear Coherences

A microwave two-pulse sequence with a weak and long 180° first pulse and a hard 90° second pulse is employed to detect nuclear coherences in pulsed EPR. The coherences created by the first pulse are transferred after an evolution periodTinto an observable FID by the second pulse. The free induction is measured at some fixed delay after the second pulse; it is modulated whenTis varied. As the second pulse may be switched on immediately after the first pulse, the nuclear coherences may be detected immediately as they start to freely oscillate, without loss of information within the instrumental dead time. The method is demonstrated for a sample of the radical cation of¹⁵N-labeled bacteriochlorophylla.     

NMR relaxation and pulsed field gradient study of alginate bead porous media

Experiments are presented, which correlate molecular displacement with the multi-exponential T2 relaxation times of water flowing and diffusing through an alginate bead pack. Three systems were studied comprising beads of 3, 1 or < mm in diameter. T2-resolved propagators were obtained through a combined pulsed gradient stimulated echo (PGSTE) and Carr-Purcell-Meiboom-Gill (CPMG) experiment. Fourier transformation with respect to q produces a propagator for each echo in the CPMG train. Inverse Laplace transformation of the CPMG decays for each point (Z) in the propagator produced a two-dimensional propagator. Analysis of these two-dimensional propagators provided insight into the transport and exchange behaviour of water flowing through this system. This experiment has been simulated in a model bead structure and the resulting T2 relaxation time behaviour and T2-resolved propagators were found to be in good agreement with the experimental data. We also present a theoretical analysis of the response to the combined PGSTE/CPMG sequence in the simple model case of Pouseille flow in a cylindrical capillary, where diffusion to a surface sink is assumed to be the dominant relaxation mechanism.     

Spin-State-Selective TPPI: A New Method for Suppression of Heteronuclear Coupling Constants in Multidimensional NMR Experiments

A novel multidimensional NMR pulse sequence tool, spin-state-selective time-proportional phase incrementation (S(3) TPPI), is introduced. It amounts to application of different TPPIs on the two components of doublets so that their frequencies can be manipulated independently. The chief application is for suppression of large heteronuclear one-bond coupling constants in indirect dimensions of multidimensional experiments without interchanging the two transverse magnetization components of doublets as conventional decoupling does, which is advantageous when they relax at different rates such as by partial compensation of dipolar and CSA relaxation contributions. For experimental confirmation we use a sample of (15)N-labeled neural cell adhesion molecule modules 1 and 2, a protein with a molecular weight of about 20 kDa. The new tool is general and can be combined with many multidimensional NMR experiments for proteins.     

The Role of Coherence Transfer Efficiency in Design of TROSY-Type Multidimensional NMR Experiments

An improved method for TROSY-type (Pervushin et al., Proc. Natl. Acad. Sci. USA 94, 12366-12371 (1997)) heteronuclear two-dimensional correlation involving protons of negligible CSA is presented. Rather than applying a simple INEPT sequence for back-transfer to protons (Pervushin et al., J. Am. Chem. Soc. 120, 6394-6400 (1998)), we replace the pi/2 proton pulse in INEPT by a spin-state-selective coherence transfer element (Sorensen et al., J. Biomol. NMR 10, 181-186 (1997)) and maintain broadband decoupling during acquisition. Theoretically that results in a sensitivity enhancement of a factor of 2. The new method is demonstrated using a (13)C,(15)N-labeled protein sample, RAP 18-112 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein), at 750 MHz.     

An improved method for suppressing protein background in PFG NMR experiments to determine ligand diffusion coefficients in the presence of receptor

In NMR diffusion experiments to study ligand-protein binding equilibria, the spectral background due to broad protein resonances can contribute significantly to the measured ligand signal intensity resulting in erroneous binding affinities. One method to suppress the protein spectral background involves coupling a CPMG pulse train before or after the BPPSTE pulse sequence to allow for differential T(2) relaxation of the broad protein resonances. Here, we present an improved method, the Gradient Phase Encoded Spin-lock (GraPES) experiment that integrates the relaxation filter into the diffusion period. Compared with sequential CPMG-BPPSTE pulse sequences, GraPES offers effective suppression of the protein background with improved signal-to-noise ratios and shorter experiment times.     

1H detected 1H,15N correlation spectroscopy in rotating solids

We describe new correlation experiments suitable for determining long-range 1H-1H distances in 2H,15N-labeled peptides and proteins. The approach uses perdeuteration together with back substitution of exchangeable protons during sample preparation as a means of attenuating the strong 1H-1H dipolar couplings that broaden 1H magic angle spinning (MAS) spectra of solids. In the approach described here, we retain 100% of the 1H sensitivity by labeling and detecting all exchangeable sites. This is in contrast to homonuclear multiple pulse decoupling sequences that are applied during detection and that compromise sensitivity because of the requirement of sampling between pulses. As a result 1H detection provides a gain in sensitivity of >5 compared to the 15N detected version of the experiment (at a MAS frequency of 13.5kHz). The pulse schemes make use of the favorable dispersion of the amide 15Ns resonances in the protein backbone. The experiments are demonstrated on a sample of the uniformly 2H,15N-labeled dipeptide N-Ac-Val-Leu-OH and are analogous to the solution-state suite of HSQC-NOESY experiments. In this compound the 1H amide linewidths at 750MHz vary from approximately 0.67 ppm at omega(r)/2pi approximately 5kHz to approximately 0.20 ppm at omega(r)/2pi approximately 30kHz, indicating that useful resolution is available in the 1H spectrum via this approach. Since the experiments circumvent the problem of dipolar truncation in the 1H-1H spin system, they should make it possible to measure long-range distances in a uniformly labeled environment. Thus, we expect the experiments to be useful in constraining the global fold of a protein.     

Optimal control based NCO and NCA experiments for spectral assignment in biological solid-state NMR spectroscopy

We present novel pulse sequences for magic-angle-spinning solid-state NMR structural studies of (13)C,(15)N-isotope labeled proteins. The pulse sequences have been designed numerically using optimal control procedures and demonstrate superior performance relative to previous methods with respect to sensitivity, robustness to instrumental errors, and band-selective excitation profiles for typical biological solid-state NMR applications. Our study addresses specifically (15)N to (13)C coherence transfers being important elements in spectral assignment protocols for solid-state NMR structural characterization of uniformly (13)C,(15)N-labeled proteins. The pulse sequences are analyzed in detail and their robustness towards spin system and external experimental parameters are illustrated numerically for typical (15)N-(13)C spin systems under high-field solid-state NMR conditions. Experimentally the methods are demonstrated by 1D (15)N-->(13)C coherence transfer experiments, as well as 2D and 3D (15)N,(13)C and (15)N,(13)C,(13)C chemical shift correlation experiments on uniformly (13)C,(15)N-labeled ubiquitin.     

Identification of Spin Diffusion Pathways in Isotopically Labeled Biomolecules

One-dimensional NOE experiments applicable to labeled macromolecules are presented which allow the manipulation of specific spin diffusion pathways and thus unambiguously identify clandestine spins through which the direct NOE is mediated. A treatment of spin diffusion using average Liouvillian theory is shown to describe adequately these phenomena. Experiments are carried out on an 15N-labeled sample of human ubiquitin.     

The set of triple-resonance sequences with a multiple quantum coherence evolution period

The new pulse sequence building block that relies on evolution of heteronuclear multiple quantum coherences is proposed. The particular chemical shifts are obtained in multiple quadrature, using linear combinations of frequencies taken from spectra measured at different quantum levels. The pulse sequences designed in this way consist of small number of RF-pulses, are as short as possible, and could be applied for determination of coupling constants. The examples presented involve 2D correlations HNCO, HNCA, HN(CO)CA, and H(N)COCA via heteronuclear zero and double coherences, as well as 2D HNCOCA technique with simultaneous evolution of triple and three distinct single quantum coherences. Applications of the new sequences are presented for 13C,15N-labeled ubiquitin.     

Sensitivity-enhanced MQ-HCN-CCH-TOCSY and MQ-HCN-CCH-COSY pulse schemes for (13)C/(15)N labeled RNA oligonucleotides

Sensitivity enhanced multiple-quantum 3D HCN-CCH-TOCSY and HCN-CCH-COSY experiments are presented for the ribose resonance assignment of (13)C/(15)N-labeled RNA sample. The experiments make use of the chemical shift dispersion of N1/N9 of pyrimidine/purine to distinguish the ribose spin systems. They provide a complementary approach for the assignment of ribose resonance to the currently used HCCH-COSY and HCCH-TOCSY type experiments in which either (13)C or (1)H is utilized to separate the different ribose spin systems. The pulse schemes have been demonstrated on a 23-mer (13)C/(15)N-labeled RNA aptamer complexed with neomycin and tested on a 32-mer RNA complexed with a 23-residue peptide.     

Cross-correlations between low-γ nuclei in solids via a common dipolar bath

Correlation of chemical shifts of low-γ nuclei (such as 15N) is an important method for assignment of resonances in uniformly-labeled biological solids. Under static experimental conditions, an efficient mixing of low-γ nuclear spin magnetization can be achieved by a thermal contact to the common reservoir of dipole-dipole interactions in order to create 15N-15N, 13C-13C, or 15N-13C cross-peaks in a 2D correlation spectrum. A thermodynamic approach can be used to understand the mechanism of magnetization mixing in various 2D correlation pulse sequences. This mechanism is suppressed under magic-angle spinning, when mixing via direct cross-polarization with protons becomes more efficient. Experimental results are presented for single-crystalline and powder samples of 15N-labeled N-acetyl-L-15N-valyl-L-15N-leucine (NAVL). In addition to the thermodynamic analysis of mixing pulse sequences, two different new mixing sequences utilizing adiabatic pulses are also experimentally demonstrated.     

A high sensitivity 3D experiment for measuring Calpha-Halpha residual dipolar coupling constants

A new sensitivity improved approach is presented to measure the Calpha-Halpha scalar and dipolar coupling constants in 13C/15N-labeled proteins using a HA(CA)CONH scheme. The proposed experiment has significantly higher sensitivity than the previously published (HA)CA(CO)NH sequence, and provides accurate and straightforward measurements of the scalar and residual dipolar coupling constants. The sequence is easy to implement, and has been demonstrated on the C-terminal domain of the human Ku-80 protein (152 amino acid residues). On average, sensitivity is improved by 40% for both isotropic and anisotropic samples. The sensitivity enhancement is more pronounced for structured regions than unstructured regions, with an average of 50-60% enhancement being observed in the well-structured regions of the protein.     

New Multidimensional Editing Experiments for Measurement of Amide Deuterium Isotope Effects on CChemical Shifts inC,N-Labeled Proteins

Novel multidimensional NMR pulse sequences for measurement of the three- and four-bond amide deuterium isotope effect on the chemical shifts of¹³C^βin proteins are presented. The sequences result in editing into two subspectra of a heteronuclear triple resonance spectrum {ω(N), ω(C^β), ω(H^α)} according to there being a deuterium or a proton attached to¹⁵N for the pertinent correlations. The new experiments are demonstrated by an application to the first module of the¹³C,¹⁵N-labeled protein RAP 18-112 (N-terminal module of α₂-macroglobulin receptor associated protein).     

Three-Dimensional C Shift/H–N Coupling/N Shift Solid-State NMR Correlation Spectroscopy

Triple-resonance experiments capable of correlating directly bonded and proximate carbon and nitrogen backbone sites of uniformly ¹³C- and ¹⁵N-labeled peptides in stationary oriented samples are described. The pulse sequences integrate cross-polarization from ¹H to ¹³C and from ¹³C to ¹⁵N with flip-flop (phase and frequency switched) Lee–Goldburg irradiation for both ¹³C homonuclear decoupling and ¹H–¹⁵N spin exchange at the magic angle. Because heteronuclear decoupling is applied throughout, the three-dimensional pulse sequence yields ¹³C shift/¹H–¹⁵N coupling/¹⁵N shift correlation spectra with single-line resonances in all three frequency dimensions. Not only do the three-dimensional spectra correlate ¹³C and ¹⁵N resonances, they are well resolved due to the three independent frequency dimensions, and they can provide up to four orientationally dependent frequencies as input for structure determination. These experiments have the potential to make sequential backbone resonance assignments in uniformly ¹³C- and ¹⁵N-labeled proteins.