Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins

Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation spectroscopy. However, the techniques developed so far have been applied primarily to proteins in the size range of 5–10 kDa, despite the fact that SSNMR has no inherent molecular weight limits. Rather, the degeneracy inherent to many 2D and 3D SSNMR spectra of larger proteins has prevented complete unambiguous chemical shift assignment. Here we demonstrate the implementation of 4D backbone chemical shift correlation experiments for assignment of solid proteins. The experiments greatly reduce spectral degeneracy at a modest cost in sensitivity, which is accurately described by theory. We consider several possible implementations and investigate the CANCOCX pulse sequence in detail. This experiment involves three cross polarization steps, from H to CA[i], CA[i] to N[i], and N[i] to C′[i−1], followed by a final homonuclear mixing period. With short homonuclear mixing times (<20 ms), backbone correlations are observed with high sensitivity; with longer mixing times (>200 ms), long-range correlations are revealed. For example, a single 4D experiment with 225 ms homonuclear mixing time reveals ∼200 uniquely resolved medium and long-range correlations in the 56-residue protein GB1. In addition to experimental demonstrations in the 56-residue protein GB1, we present a theoretical analysis of anticipated improvements in resolution for much larger proteins and compare these results in detail with the experiments, finding good agreement between experiment and theory under conditions of stable instrumental performance.     

Quantitative evaluation of NMR and MRI methods to measure sucrose concentrations in plants

Summary Developing pea (Pisum sativum L.) seeds were chosen to evaluate the performance of various nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) methods of detecting sucrose in plants. The methods included chemical shift selective imaging (CHESS), heteronuclear correlation via¹³C-¹H coupling (HMQC), and homonuclear correlation via¹H-¹H coupling (DQF). The same experiments were also performed on sucrose phantom samples to evaluate the methods in the absence of the line broadening observed in plant systems. Using the spin echo technique for multi-slice imaging, we could discern the detailed internal structure of the intact seed with a resolution of tens of microns. The proton spin-lattice relaxation time and linewidth as a function of the age of the seed were measured to optimize the efficiency of the NMR and MR experiments. The age-dependent changes in these NMR parameters are consistent with the accumulation of insoluble starch as age increases. Both the NMR and MRI results are in accord with the results of chemical analysis, which reveal that the sucrose concentration is higher in the embryo than in the seed coat, and glucose is at low concentration throughout the seed. Of the three methods for proton observation, the enhanced version of the CHESS approach (CD-CHESS) provides the best combination of sucrose detection and water suppression. Direct observation of¹³C is preferable to indirect detection using HMQC because of water signal bleed-through in samples with large (>200 Hz) linewidths.Abbreviations CD-CHESS continuous wave decoupling chemical shift selective imaging - CHESS chemical shift selective imaging - CSI chemical shift imaging - CW continuous wave - DQF homonuclear double quantum filtering - FOV field of view - FW fresh weight - GHMQC gradient version of the heteronuclear multiple quantum coherence     

C nuclear magnetic resonance study of 17α-substituted estradiols

We report the ¹³C NMR data for 20 compounds bearing a substituent (alkyl, alkenyl, alkynyl, alkylamide, spiro-γ-lactone, phenyl, benzyl, naphthyl, etc.) at the 17α-position of estradiol. The carbon assignments were done using 1D and 2D NMR experiments (distortionless enhancement by polarization transfer, homonuclear correlated spectroscopy, heteronuclear shift correlation, and heteronuclear shift correlation via long-range couplings). Only the chemical shifts of carbons 12–18, which surround the substitution site, were affected by the addition of a substituent. The magnitude of the effects (shielding or deshielding) was influenced by the 17α-substituent. The individual effects at these carbons were sufficiently distinctive to identify specific centers and should be valuable for signal assignment of a variety of 17α-derivatives of estradiol. In addition to carbon-skeleton assignment, we also report the carbon-substituent assignments.     

Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids

Triple resonance HCN and HCNCH experiments are reliable methods of establishing sugar-to-base connectivity in the NMR spectra of isotopicaly labeled oligonucleotides. However, with larger molecules the sensitivity of the experiments is drastically reduced due to relaxation processes. Since the polarization transfer between ¹³C and ¹⁵N nuclei relies on rather small heteronuclear coupling constants (11–12 Hz), the long evolution periods (up to 30–40 ms) in the pulse sequences cannot be avoided. Therefore any effort to enhance sensitivity has to concentrate on manipulating the spin system in such a way that the spin–spin relaxation rates would be minimized. In the present paper we analyze the efficiency of the two known approaches of relaxation rate control, namely the use of multiple-quantum coherence (MQ) and of the relaxation interference between chemical shift anisotropy and dipolar relaxation – TROSY. Both theoretical calculations and experimental results suggest that for the sugar moiety (H1-C1-N1/9) the MQ approach is clearly preferable. For the base moiety (H6/8-C6/8-N1/9), however, the TROSY shows results superior to the MQ suppression of the dipole–dipole relaxation at moderate magnetic fields (500 MHz) and the sensitivity improvement becomes dramatically more pronounced at very high fields (800 MHz). The pulse schemes of the triple-resonance HCN experiments with sensitivity optimized performance for unambiguous assignments of intra-residual sugar-to-base connectivities combining both approaches are presented.     

Band-selective 13C Homonuclear 3D Spectroscopy for Solid Proteins at High Field with Rotor-synchronized Soft Pulses

We demonstrate improved 3D ¹³C–¹³C–¹³C chemical shift correlation experiments for solid proteins, utilizing band-selective coherence transfer, scalar decoupling and homonuclear zero-quantum polarization transfer. Judicious use of selective pulses and a z-filter period suppress artifacts with a two-step phase cycle, allowing higher digital resolution in a fixed measurement time. The novel correlation of C^ali–C^ali–CX (C^ali for aliphatic carbons, CX for any carbon) reduces measurement time by an order of magnitude without sacrificing digital resolution. The experiment retains intensity from side-chain carbon resonances whose chemical shift dispersion is critical to minimize spectral degeneracy for large proteins with a predominance of secondary structure, such as β-sheet rich fibrillar proteins and α-helical membrane proteins. We demonstrate the experiment for the β1 immunoglobulin binding domain of protein G (GB1) and fibrils of the A30P mutant of α-synuclein, which is implicated in Parkinson’s disease. Selective pulses of duration comparable the rotor period give optimal performance, but must be synchronized with the spinning in non-trivial ways to minimize chemical shift anisotropy recoupling effects. Soft pulses with a small bandwidth-duration product are best for exciting the ~70 ppm bandwidth required for aliphatic-only dimensions.     

Determination of the rotational dynamics and pH dependence of the hydrogen exchange rates of the arginine guanidino group using NMR spectroscopy

Summary An improved version of the constant-time HSQC experiment is presented that gives uniform sensitivity over the complete ¹³C bandwidth in ¹³C−¹H correlation experiments without creating artifacts in the methyl and aromatic regions of the spectra. The improvement is achieved by replacing the refocussing ¹³C 180° pulse in the evolution time by a combination of a full-power (22 kHz) hyperbolic secant 180° pulse that inverts and refocusses the entire ¹³C window, immediately followed by a selective 180° pulse on the CO region. Further improvement in signal-to-noise in the aromatic and methyl regions, although less spectacular, is obtained by replacing the other two 180° ¹³C pulses in the INEPT parts of the pulse sequence by full-power hyperbolic secant pulses. Results of simulations and experimental data are presented that demonstrate the excellent performance of the hyperbolic secant pulse for broadband inversion and show that refocussing of transverse magnetization occurs over the same bandwidth, albeit with a ¹³C signal phase that depends quadratically on offset. A further modification, in which one of the selective pulses on the CO region is omitted, is also presented. Implications for other 2D and 3D experiments performed at high fields, where uniform ¹³C inversion and refocussing is desirable, are discussed.     

Robust refocusing of 13C magnetization in multidimensional NMR experiments by adiabatic fast passage pulses

We show that adiabatic fast passage (AFP) pulses are robust refocusing elements of transverse ¹³C magnetization in multidimensional NMR experiments. A pair of identical AFP pulses can refocus selected parts or a complete ¹³ C chemical shift range in ¹³C spectra. In the constant time ¹³C-¹H HSQC, replacement of attenuated rectangular pulses by selective AFP pulses results in a sensitivity enhancement of up to a factor of 1.8. In the 3D CBCA(CO)NH the signal-to-noise ratio is increased by a factor of up to 1.6.     

A TROSY relayed HCCH-COSY experiment for correlating adenine H2/H8 resonances in uniformly 13C-labeled RNA molecules

A new TROSY relayed HCCH-COSY pulse sequence is introduced for correlating adenine H2 and H8 resonances in ¹³C-labeled RNA molecules. The pulse scheme provides substantial improvements in signal-to-noise compared to previously suggested experiments, and therefore will be suitable for NMR studies of larger RNA molecules. The experiment provides ¹³C chemical shifts for all carbon nuclei in the adenine base. This is advantageous for resolving spectral overlap in larger RNA molecules and provides a starting point for measuring additional parameters for these carbons in the adenine spin system.     

Assignment Strategies for Large Proteins by Magic-Angle Spinning NMR: The 21-kDa Disulfide-Bond-Forming Enzyme DsbA

We present strategies for chemical shift assignments of large proteins by magic-angle spinning solid-state NMR, using the 21-kDa disulfide-bond-forming enzyme DsbA as prototype. Previous studies have demonstrated that complete de novo assignments are possible for proteins up to  ∼ 17 kDa, and partial assignments have been performed for several larger proteins. Here we show that combinations of isotopic labeling strategies, high field correlation spectroscopy, and three-dimensional (3D) and four-dimensional (4D) backbone correlation experiments yield highly confident assignments for more than 90% of backbone resonances in DsbA. Samples were prepared as nanocrystalline precipitates by a dialysis procedure, resulting in heterogeneous linewidths below 0.2 ppm. Thus, high magnetic fields, selective decoupling pulse sequences, and sparse isotopic labeling all improved spectral resolution. Assignments by amino acid type were facilitated by particular combinations of pulse sequences and isotopic labeling; for example, transferred echo double resonance experiments enhanced sensitivity for Pro and Gly residues; [2-¹³C]glycerol labeling clarified Val, Ile, and Leu assignments; in-phase anti-phase correlation spectra enabled interpretation of otherwise crowded Glx/Asx side-chain regions; and 3D NCACX experiments on [2-¹³C]glycerol samples provided unique sets of aromatic (Phe, Tyr, and Trp) correlations. Together with high-sensitivity CANCOCA 4D experiments and CANCOCX 3D experiments, unambiguous backbone walks could be performed throughout the majority of the sequence. At 189 residues, DsbA represents the largest monomeric unit for which essentially complete solid-state NMR assignments have so far been achieved. These results will facilitate studies of nanocrystalline DsbA structure and dynamics and will enable analysis of its 41-kDa covalent complex with the membrane protein DsbB, for which we demonstrate a high-resolution two-dimensional ¹³C-¹³C spectrum.     

2D and 3D TROSY-enhanced NOESY of 15N labeled proteins

Recently, several TROSY-based experiments have been designed for backbone chemical shift assignment and measurement of the NOEs of ²H, ¹³C and ¹⁵N labeled proteins. Here, we present TROSY-enhanced NOESY experiments, namely the 2D S3E-NOESY-S3E, 3D TROSY-NOESY-S3E and S3E-NOESY-TROSY experiments. These experiments use the spin-state selective excitation method (S3E), and have the TROSY effect in all the indirectly and directly detected dimensions, and so provide optimal resolution for amide protons. The first two experiments provide an additional useful feature in that the diagonal peaks of the amide proton region are cancelled or greatly reduced, allowing clear identification of NOE cross peaks that are close to diagonal peaks.     

Sensitivity improvement for correlations involving arginine side-chain Nε/Hε resonances in multi-dimensional NMR experiments using broadband 15N 180° pulses

Due to practical limitations in available ¹⁵N rf field strength, imperfections in ¹⁵N 180° pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino ¹⁵Nε (~85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg Nε–Hε groups, we have incorporated ¹⁵N broadband 180° pulses into 3D ¹⁵N-separated NOE-HSQC and HNCACB experiments. Two ¹⁵N-WURST pulses incorporated at the INEPT transfer steps of the 3D ¹⁵N-separated NOE-HSQC pulse sequence resulted in a ~1.5-fold increase in sensitivity for the Arg Nε–Hε signals at 800 MHz. For the 3D HNCACB experiment, five ¹⁵N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg¹Hε-¹⁵Nε-¹³Cγ/¹³Cδ correlation peaks was enhanced by a factor of ~1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg ¹Hε and ¹⁵Nε resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the ¹⁵Nε/¹Hε of Arg in 3D ¹⁵N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains.     

Biosynthesis of Cercosporin

¹³C NMR spectra were measured for 19 pyrethroids and their related compounds including allethrin, tetramethrin, resmethrin, furamethrin, phenothrin and permethrin. Complete assignment of chemical shifts was accomplished by relative spectral pattern, single-frequency off-resonance decoupling, benzene substituent effects, proton selective decoupling and use of shift reagents. The use of shift reagent was found to be especially efficient for assignment of ¹³C resonances. In the case of allethrin, the splittings of some resonance peaks were observed originating from diastereomerism.     

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° pulse. The sequences are shown theoretically and experimentally to significantly outperform the 90°-delay-90° element that is often used in current applications. It is shown that alignment of magnetization to within 1° of the effective field can be obtained over a bandwidth extending between [−ω_SL, ω_SL], where ω_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. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structural basis of ligand binding and release in insect pheromone-binding proteins: NMR structure of Antheraea polyphemus PBP1 at pH 4.5

The NMR structure of the Antheraea polyphemus pheromone-binding protein 1 at pH 4.5, ApolPBP1A, was determined at 20 degrees C. The structure consists of six alpha-helices, which are arranged in a globular fold that encapsulates a central helix alpha7 formed by the C-terminal polypeptide segment 131-142. The 3D arrangement of these helices is anchored by the three disulfide bonds 19-54, 50-108 and 97-117, which were identified by NMR. Superposition of the ApolPBP1A structure with the structure of the homologous pheromone-binding protein of Bombyx mori at pH 4.5, BmorPBPA, yielded an rmsd of 1.7 A calculated for the backbone heavy-atoms N, Calpha and C' of residues 10-142. In contrast, the present ApolPBP1A structure is different from a recently proposed molecular model for a low-pH form of ApolPBP1 that does not contain the central helix alpha7. ApolPBP1 exhibits a pH-dependent transition between two different globular conformations in slow exchange on the NMR chemical shift timescale similar to BmorPBP, suggesting that the two proteins use the same mechanism of ligand binding and ejection. The extensive sequence homology observed for pheromone-binding proteins from moth species further implies that the previously proposed mechanism of ligand ejection involving the insertion of a C-terminal helix into the pheromone-binding site is a general feature of pheromone signaling in moths.     

Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments

NMR spin relaxation experiments are used to characterize the dynamics of the backbone of ubiquitin. Chemical exchange processes affecting residues Ile 23, Asn 25, Thr 55, and Val 70 are characterized using on- and off-resonance rotating-frame 15N R1rho relaxation experiments to have a kinetic exchange rate constant of 25,000 sec(-1) at 280 K. The exchange process affecting residues 23, 25, and 55 appears to result from disruption of N-cap hydrogen bonds of the alpha-helix and possibly from repacking of the side chain of Ile 23. Chemical exchange processes affecting other residues on the surface of ubiquitin are identified using 1H-15N multiple quantum relaxation experiments. These residues are located near or at the regions known to interact with various enzymes of the ubiquitin-dependent protein degradation pathway.     

Chemical shift-dependent apparent scalar couplings: an alternative concept of chemical shift monitoring in multi-dimensional NMR experiments

The paper presents an alternative technique for chemical shift monitoring in a multi-dimensional NMR experiment. The monitored chemical shift is coded in the line-shape of a cross-peak through an apparent residual scalar coupling active during an established evolution period or acquisition. The size of the apparent scalar coupling is manipulated with an off-resonance radio-frequency pulse in order to correlate the size of the coupling with the position of the additional chemical shift. The strength of this concept is that chemical shift information is added without an additional evolution period and accompanying polarization transfer periods. This concept was incorporated into the three-dimensional triple-resonance experiment HNCA, adding the information of ¹H chemical shifts. The experiment is called HNCA^codedHA, since the chemical shift of ¹H is coded in the line-shape of the cross-peak along the ¹³C dimension.     

Three-dimensional 1H-TOCSY-relayed ct-[13C,1H]-HMQC for aromatic spin system identification in uniformly 13C-labeled proteins

Summary Three-dimensional ¹H-TOCSY-relayed ct-[¹³C,¹H]-HMQC is a novel experiment for aromatic spin system identification in uniformly ¹³C-labeled proteins, which is implemented so that it correlates the chemical shift of a given aromatic proton with those of the directly attached carbon and all vicinal protons. The ct-HMQC scheme is used both for overlay of the indirect ¹H and ¹³C chemical shift evolution periods and for the generation of ¹H-¹H antiphase magnetization to accelerate the ¹H-TOCSY magnetization transfer at short mixing times. As an illustration, data recorded for the 18 kDa protein cyclophilin A are presented. Since transverse relaxation of ¹³C-¹H zero-quantum and double-quantum coherences is to first order insensitive to ¹³C-¹H heteronuclear dipolar relaxation, the new experiment should work also for proteins with molecular weights above 20 kDa.     

Histidine side-chain dynamics and protonation monitored by 13C CPMG NMR relaxation dispersion

The use of ¹³C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically ¹³C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for ¹³C^ε1 nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from ¹⁵N backbone relaxation measurements. Compared to measurements of backbone nuclei, ¹³C^ε1 dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the ¹³C^ε1 dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.     

1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects

Summary In this study we report on the ¹H, ¹³C and ¹⁵N NMR chemical shifts for the random coil state and nearest-neighbor sequence effects measured from the protected linear hexapeptide Gly-Gly-X-Y-Gly-Gly (where X and Y are any of the 20 common amino acids). We present data for a set of 40 peptides (of the possible 400) including Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly, measured under identical aqueous conditions. Because all spectra were collected under identical experimental conditions, the data from the Gly-Gly-X-Ala-Gly-Gly series provide a complete and internally consistent set of ¹H, ¹³C and ¹⁵N random coil chemical shifts for all 20 common amino acids. In addition, studies were also conducted into nearest-neighbor effects on the random coil shift arising from a variety of X and Y positional substitutions. Comparisons between the chemical shift measurements obtained from Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly reveal significant systematic shift differences arising from the presence of proline in the peptide sequence. Similarly, measurements of the chemical shift changes occurring for both alanine and proline (i.e., the residues in the Y position) are found to depend strougly on the type of amino acid substituted into the X position. These data lend support to the hypothesis that sequence effects play a significant role in determining peptide and protein chemical shifts.     

15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9k in the apo, (Cd2+)1 and (Ca2+)2 states.

15N has been uniformly incorporated into the EF-hand Ca(2+)-binding protein calbindin D9k so that heteronuclear experiments can be used to further characterize the structure and dynamics of the apo, (Cd2+)1 and (Ca2+)2 states of the protein. The 15N NMR resonances were assigned by 2D 15N-resolved 1H experiments, which also allowed the identification of a number of sequential and medium-range 1H-1H contacts that are obscured by chemical shift degeneracy in homonuclear experiments. The 15N chemical shifts are analyzed with respect to correlations with protein secondary structure. In addition, the changes in 15N chemical shift found for the apo----(Cd2+)1----(Ca2+)2 binding sequence confirm that the effects on the protein are mainly associated with chelation of the first ion.