Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin

NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from (1)H, (13)C, and (15)N nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with (13)C and (15)N. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective (13)C labeling and one-dimensional (1D) (13)C NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by (13)C[(13)C] constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective (15)N labeling and 1D (15)N NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D (13)C[(15)N] difference decoupling experiments. (6) Signals from (1)H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D (1)H[(13)C] experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone (15)N signals from nine of the 22 residues and ambiguous assignments for five of the others.     

High resolution 1H-detected solid-state NMR spectroscopy of protein aliphatic resonances: access to tertiary structure information

Biological magic angle spinning (MAS) solid-state nuclear magnetic resonance spectroscopy has developed rapidly over the past two decades. For the structure determination of a protein by solid-state NMR, routinely (13)C,(13)C distance restraints as well as dihedral restraints are employed. In protonated samples, this is achieved by growing the bacterium on a medium which contains [1,3]-(13)C glycerol or [2]-(13)C glycerol to dilute the (13)C spin system. Labeling schemes, which rely on heteronuclei, are insensitive both for detection and in terms of quantification of distances, since they are relying on low-γ nuclei. Proton detection can in principle provide a gain in sensitivity by a factor of 8 and 31, compared to the (13)C or (15)N detected version of the experiment. We report here a new labeling scheme, which enables (1)H-detection of aliphatic resonances with high resolution in MAS solid-state NMR spectroscopy. We prepared microcrystals of the SH3 domain of chicken α-spectrin with 5% protonation at nonexchangeable sites and obtained line widths on the order of 25 Hz for aliphatic (1)H resonances. We show further that (13)C resolved 3D-(1)H,(1)H correlation experiments yield access to long-range proton-proton distances in the protein.     

13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase

In this report, the use of 13C direct detection has been pursued in 2D experiments (13C-13C COSY, 13C-13C COCAMQ, 13C-13C NOESY) to detect broad lines in nuclear magnetic resonance spectra of paramagnetic metalloproteins. The sample is a monomeric oxidized copper, zinc superoxide dismutase. Thanks to direct detection probeheads, cryogenic technology, and implementation of 13C band-selective homodecoupling, many broadened signals were detected. Proton signals for the same residues escaped detection in 1H and 1H-15N HSQC experiments because of the broadening. Only the 13C signals which experience large contact coupling escaped detection, i.e., the 13C nuclei of the metal coordinated histidines. Otherwise, nuclei as close to copper(II) as 4 A can be detected. Paramagnetic-based restraints can in principle be used for solution structure determination of paramagnetic metalloproteins and in copper(II) proteins in particular. The present study is significant also for the study of large diamagnetic proteins for which proton relaxation makes proton-based spectroscopy not adequate.     

A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins

A general strategy is proposed to assign aliphatic side-chain resonances of large 13C,15N-labeled proteins without deuteration, using 4D 13C,15N-edited NOESY and MQ-(H)CCH-TOCSY experiments on the basis of prior assignments of backbone and 13Cbeta resonances. The strategy has been tested on a 214 residue protein (DdCAD-1) and applied to a chain-selectively 13C,15N-labeled hemoglobin (65 kDa). About 96 and 80% aliphatic side-chain spins in DdCAD-1 and hemoglobin have been assigned, respectively. The strategy proposed here will be very useful for the structure determination and dynamics characterization of large proteins by NMR.     

Observation of individual transitions in magnetically equivalent spin systems

Individual transitions of magnetically equivalent spin systems such as methyl groups residing on isotropically tumbling molecules in solution usually cannot be observed as multiplet-split NMR lines. We propose a pair of NMR experiments, 2D [13C,1Halphaalpha]Methyl and [13C,1Hbetabeta]Methyl HSQC, to overcome this limitation and enable direct and selective observation of individual 1H transitions in 13C-labeled methyl spin systems. Immediate applications include quantitative measurements of 1H-1H residual dipolar couplings (RDC) and cross-correlated relaxation between 1H chemical shift anisotropy and 1H-1H dipole-dipole interactions. The use of the experiments for the measurement of RDCs is demonstrated with two proteins, one weakly aligned by means of Pf1 phages and the other using a naturally present paramagnetic heme group.     

Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy

A novel approach for detection of ligand binding to a protein in solid samples is described. Hydrated precipitates of the anti-apoptotic protein Bcl-xL show well-resolved (13)C-(13)C 2D solid-state NMR spectra that allow site-specific assignment of resonances for many residues in uniformly (13)C-enriched samples. Binding of a small peptide or drug-like organic molecule leads to changes in the chemical shift of resonances from multiple residues in the protein that can be monitored to characterize binding. Differential chemical shifts can be used to distinguish between direct protein-ligand contacts and small conformational changes of the protein induced by ligand binding. The agreement with prior solution-state NMR results indicates that the binding pocket in solid and liquid samples is similar for this protein. Advantages of different labeling schemes involving selective (13)C enrichment of methyl groups of Ala, Val, Leu, and Ile (Cdelta1) for characterizing protein-ligand interactions are also discussed. It is demonstrated that high-resolution solid-state NMR spectroscopy on uniformly or extensively (13)C-enriched samples has the potential to screen proteins of moderate size ( approximately 20 kDa) for ligand binding as hydrated solids. The results presented here suggest the possibility of using solid-state NMR to study ligand binding in proteins not amenable to solution NMR.     

Improved NMR methods for the direct 13C-satellite-selective excitation in overlapped 1H-NMR spectra

Improved pulsed-field gradient echo methods are presented and discussed for the direct selective excitation of the (13)C-satellite lines in overcrowded (1)H NMR spectra of small molecules. Sensitivity enhancements in (13)C spin-state selection can be achieved by combining multiple-proton-frequency excitation and Hadamard phase encoding. Several satellite-selective (SATSEL) NMR experiments are proposed and exemplified by measuring the sign and the magnitude of small, long-range proton-carbon coupling constants for (1)H resonances showing several levels of signal overlapping.     

2D-NMR对Phyllfofenone-A(Ⅰ)的~1H和~(13)C的完全指定

采用多种二维NMR技术,并借助一维NOE差谱以及INAPT技术对新二倍半萜Phyllo-fenone-A(Ⅰ)的全部质子和碳信号进行了归属,并纠正了前人对其类似物的一些碳谱峰指定的错误。     

Paramagnetic 1H NMR spectrum of nickel(II) pseudoazurin: investigation of the active site structure and the acid and alkaline transitions

The paramagnetic (1)H NMR spectrum of Ni(II) pseudoazurin [(PA)Ni(II)] possesses a number of resonances exhibiting sizable Fermi-contact shifts. These have been assigned to protons associated with the four ligating amino acids, His40, Cys78, His81, and Met86. The shifts experienced by the C(gamma)H protons of the axial Met86 ligand are unprecedented compared to other Ni(II)- and Co(II)-substituted cupredoxins (the C(gamma)(1)H signal is found at 432.5 ppm at 25 degrees C). The large shift of protons of the axial Met86 ligand highlights a strong Ni(II)-S(Met) interaction in (PA)Ni(II). The paramagnetic (1)H NMR spectrum of (PA)Ni(II) is altered by decreasing and increasing the pH value from 8.0. At acidic pH a number of the hyperfine-shifted resonances undergo limited changes in their chemical shift values. This effect is assigned to the surface His6 residue whose protonation results in a structural modification of the active site. Increasing the pH value from 8.0 has a more significant effect on the paramagnetic (1)H NMR spectrum of (PA)Ni(II), and the alkaline transition can now be assigned to two surface lysine residues close to the active site of the protein. The effect of altering pH on the (1)H NMR spectrum of Ni(II) pseudoazurin is smaller than that previously observed in the Cu(II) protein indicating more limited structural rearrangements at the non-native metal site.     

Novel 13C‐detected NMR Experiments for the Precise Detection of RNA Structure

Up to now, NMR spectroscopic investigations of RNA have utilized imino proton resonances as reporters for base pairing and RNA structure. The nucleobase amino groups are often neglected, since most of their resonances are broadened beyond detection due to rotational motion around the C–NH₂ bond. Here, we present ¹³C‐detected NMR experiments for the characterization of all RNA amino groups irrespective of their motional behavior. We have developed a C(N)H‐HDQC experiment that enables the observation of a complete set of sharp amino resonances through the detection of proton‐NH₂ double quantum coherences. Further, we present an “amino”‐NOESY experiment to detect NOEs to amino protons, which are undetectable by any other conventional NOESY experiment. Together, these experiments allow the exploration of additional chemical shift information and inter‐residual proton distances important for high‐resolution RNA secondary and tertiary structure determination.     

NMR analysis of conformationally dependent (n)J(C, H) and (n)J(C, C) in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe and a site-specifically labeled isotopologue thereof

An array of NMR spectroscopy experiments have been carried out to obtain conformationally dependent (1)H,(13)C- and (13)C,(13)C-spin-spin coupling constants in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe. The trisaccharide was synthesized with (13)C site-specific labeling at C2' and C2″, i.e. in the rhamnosyl groups in order to alleviate (1)H spectral overlap. This facilitated the measurement of a key trans-glycosidic proton-proton cross-relaxation rate using 1D (1)H,(1)H-T-ROESY experiments as well as a (3)J(C, H) coupling employing 1D (1)H,(13)C-long-range experiments, devoid of potential interference from additional J coupling. By means of both the natural abundance compound and the (13)C-labeled sample 2D (1)H,(13)C-J-HMBC and (1)H,(13)C-HSQC-HECADE NMR experiments, total line-shape analysis of (1)H NMR spectra and 1D (13)C NMR experiments were employed to extract (3)J(C, H) , (2)J(C, H), (3)J(C, C), and (1)J(C, C) coupling constants. The (13)C site-specific labeling facilitates straightforward determination of (n)J(C, C) as the splitting of the (13)C natural abundance resonances. This study resulted in eight conformationally dependent coupling constants for the trisaccharide and illustrates the use of (13)C site-specific labeling as a valuable approach that extends the 1D and 2D NMR methods in current use to attain both hetero- and homonuclear spin-spin coupling constants that subsequently can be utilized for conformational analysis.     

Progress in 13C and 1H solid-state nuclear magnetic resonance for paramagnetic systems under very fast magic angle spinning

High-resolution solid-state NMR (SSNMR) of paramagnetic systems has been largely unexplored because of various technical difficulties due to large hyperfine shifts, which have limited the success of previous studies through depressed sensitivity/resolution and lack of suitable assignment methods. Our group recently introduced an approach using "very fast" magic angle spinning (VFMAS) for SSNMR of paramagnetic systems, which opened an avenue toward routine analyses of small paramagnetic systems by (13)C and (1)H SSNMR [Y. Ishii et al., J. Am. Chem. Soc. 125, 3438 (2003); N. P. Wickramasinghe et al., ibid. 127, 5796 (2005)]. In this review, we discuss our recent progress in establishing this approach, which offers solutions to a series of problems associated with large hyperfine shifts. First, we demonstrate that MAS at a spinning speed of 20 kHz or higher greatly improves sensitivity and resolution in both (1)H and (13)C SSNMR for paramagnetic systems such as Cu(II)(DL-alanine)(2)H(2)O (Cu(DL-Ala)(2)) and Mn(acac)(3), for which the spectral dispersions due to (1)H hyperfine shifts reach 200 and 700 ppm, respectively. Then, we introduce polarization transfer methods from (1)H spins to (13)C spins with high-power cross polarization and dipolar insensitive nuclei enhanced by polarization transfer (INEPT) in order to attain further sensitivity enhancement and to correlate (1)H and (13)C spins in two-dimensional (2D) SSNMR for the paramagnetic systems. Comparison of (13)C VFMAS SSNMR spectra with (13)C solution NMR spectra revealed superior sensitivity in SSNMR for Cu(DL-Ala)(2), Cu(Gly)(2), and V(acac)(3). We discuss signal assignment methods using one-dimensional (1D) (13)C SSNMR (13)C-(1)H rotational echo double resonance (REDOR) and dipolar INEPT methods and 2D (13)C(1)H correlation SSNMR under VFMAS, which yield reliable assignments of (1)H and (13)C resonances for Cu(Ala-Thr). Based on the excellent sensitivity/resolution and signal assignments attained in the VFMAS approach, we discuss methods of elucidating multiple distance constraints in unlabeled paramagnetic systems by combing simple measurements of (13)C T(1) values and anisotropic hyperfine shifts. Comparison of experimental (13)C hyperfine shifts and ab initio calculated shifts for alpha- and beta-forms of Cu(8-quinolinol)(2) demonstrates that (13)C hyperfine shifts are parameters exceptionally sensitive to small structural difference between the two polymorphs. Finally, we discuss sensitivity enhancement with paramagnetic ion doping in (13)C SSNMR of nonparamagnetic proteins in microcrystals. Fast recycling with exceptionally short recycle delays matched to short (1)H T(1) of approximately 60 ms in the presence of Cu(II) doping accelerated 1D (13)C SSNMR for ubiquitin and lysozyme by a factor of 7.3-8.4 under fast MAS at a spinning speed of 40 kHz. It is likely that the VFMAS approach and use of paramagnetic interactions are applicable to a variety of paramagnetic systems and nonparamagnetic biomolecules.     

Recent developments in the <Superscript>13</Superscript>C NMR spectroscopic analysis of paramagnetic hemes and heme proteins

Despite the wealth of information that has been obtained from the study of paramagnetic hemes and heme proteins by ¹H NMR spectroscopy, there are certain limitations imposed by the nature of paramagnetically affected resonances that are difficult to overcome. Although it has long been recognized that ¹³C NMR spectroscopy is likely to be a powerful complementary technique to overcome some of these limitations, the low sensitivity and low natural abundance of ¹³C nuclei has resulted in a lag in the application of ¹³C NMR spectroscopy to the study of paramagnetic hemes and heme proteins. The tremendous advances in methodology and instrumentation witnessed in the NMR field, coupled to the advent of recombinant DNA methods that have made possible the preparation and purification of significant quantities of proteins, and the biosynthesis of ¹³C-labeled heme, have contributed to an increased interest in the study of paramagnetic heme active sites by ¹³C NMR spectroscopy. As a consequence, ¹³C NMR spectroscopy is emerging as a powerful tool to study heme electronic structure and structure–function relationships in heme-containing proteins. In this report we strive to summarize some of the recent developments in the analysis of paramagnetic hemes and heme-containing proteins by ¹³C NMR spectroscopy.     

Rapid recycle (13)C',(15)N and (13)C,(13)C' heteronuclear and homonuclear multiple quantum coherence detection for resonance assignments in paramagnetic proteins: example of Ni(2+)-containing acireductone dioxygenase

NMR resonance assignments in the vicinity of paramagnetic metals in proteins are often difficult or impossible to make using conventional 1H detected 2-D and 3-D methods due to paramagnetic line broadening. The applicability of 13Calpha{13C'} and 13C'{15N} multiple quantum coherence methods for residue-specific assignments of resonances near paramagnetic centers is described, using the Ni2+-containing enzyme acireductone dioxygenase as an example.     

2D NMR对Sarcophine所有^1H NMR和^1^3C NMR归属的指定

从中国南海软珊瑚Sarcophyton molle中分离得到大环二萜内酯Sarcophine(1)。本文利用^1H-^1H COSY，HMQC，HMBC等二维谱手段首次对Sarcophine所有^1H NMR、^1^3C NMR的信号归属进行了完全的指定。并第一次报道了其^1^3C NMR数据。     

NMR of heparin API: investigation of unidentified signals in the USP-specified range of 2.12–3.00 ppm

This article addresses the identification and quantification of the chemical species resulting in resonances at 2.17 and 2.25 ppm in the ¹H nuclear magnetic resonance (NMR) spectrum of pharmaceutical-grade heparin sodium. The NMR signals in question were first confirmed to arise from chemical moieties covalently attached to the heparin molecule through NMR diffusion experiments as well as chemical treatment of heparin active pharmaceutical ingredient (API) containing the resonances. The material responsible for the extra NMR signals was then demonstrated by NMR spiking studies to be something other than oversulfated chondroitin sulfate and was finally identified as an O-acetylation product of heparin through ¹³C labeling experiments with subsequent NMR analysis. The extent of O-acetylation was quantified using three orthogonal techniques: ¹H NMR, ion chromatography, and headspace gas chromatography/mass spectrometry. The results of this work showed good agreement between the three quantitative methods developed to analyze the signals in the United States Pharmacopeia-specified region of 2.12–3.00 ppm for heparin API.     

Structural analysis of alanine tripeptide with antiparallel and parallel beta-sheet structures in relation to the analysis of mixed beta-sheet structures in Samia cynthia ricini silk protein fiber using solid-state NMR spectroscopy

The structural analysis of natural protein fibers with mixed parallel and antiparallel beta-sheet structures by solid-state NMR is reported. To obtain NMR parameters that can characterize these beta-sheet structures, (13)C solid-state NMR experiments were performed on two alanine tripeptide samples: one with 100% parallel beta-sheet structure and the other with 100% antiparallel beta-sheet structure. All (13)C resonances of the tripeptides could be assigned by a comparison of the methyl (13)C resonances of Ala(3) with different [3-(13)C]Ala labeling schemes and also by a series of RFDR (radio frequency driven recoupling) spectra observed by changing mixing times. Two (13)C resonances observed for each Ala residue could be assigned to two nonequivalent molecules per unit cell. Differences in the (13)C chemical shifts and (13)C spin-lattice relaxation times (T(1)) were observed between the two beta-sheet structures. Especially, about 3 times longer T(1) values were obtained for parallel beta-sheet structure as compared to those of antiparallel beta-sheet structure, which could be explicable by the difference in the hydrogen-bond networks of both structures. This very large difference in T(1) becomes a good measure to differentiate between parallel or antiparallel beta-sheet structures. These differences in the NMR parameters found for the tripeptides may be applied to assign the parallel and antiparallel beta-sheet (13)C resonances in the asymmetric and broad methyl spectra of [3-(13)C]Ala silk protein fiber of a wild silkworm, Samia cynthia ricini.     

Heteronuclear Cross‐Relaxation Effects in the NMR Spectroscopy of Hyperpolarized Targets

Dissolution dynamic nuclear polarization (DNP) enables high‐sensitivity solution‐phase NMR experiments on long‐lived nuclear spin species such as ¹⁵N and ¹³C. This report explores certain features arising in solution‐state ¹H NMR upon polarizing low‐γ nuclear species. Following solid‐state hyperpolarization of both ¹³C and ¹H, solution‐phase ¹H NMR experiments on dissolved samples revealed transient effects, whereby peaks arising from protons bonded to the naturally occurring ¹³C nuclei appeared larger than the typically dominant ¹²C‐bonded ¹H resonances. This enhancement of the satellite peaks was examined in detail with respect to a variety of mechanisms that could potentially explain this observation. Both two‐ and three‐spin phenomena active in the solid state could lead to this kind of effect; still, experimental observations revealed that the enhancement originates from ¹³C→¹H polarization‐transfer processes active in the liquid state. Kinetic equations based on modified heteronuclear cross‐relaxation models were examined, and found to well describe the distinct patterns of growth and decay shown by the ¹³C‐bound ¹H NMR satellite resonances. The dynamics of these novel cross‐relaxation phenomena were determined, and their potential usefulness as tools for investigating hyperpolarized ensembles and for obtaining enhanced‐sensitivity ¹H NMR traces was explored.     

Tailoring 13C labeling for triple-resonance solid-state NMR experiments on aligned samples of proteins

In order to develop triple-resonance solid-state NMR spectroscopy of membrane proteins, we have implemented several different (13)C labeling schemes with the purpose of overcoming the interfering effects of (13)C-(13)C dipole-dipole couplings in stationary samples. The membrane-bound form of the major coat protein of the filamentous bacteriophage Pf1 was used as an example of a well-characterized helical membrane protein. Aligned protein samples randomly enriched to 35% (13)C in all sites and metabolically labeled from bacterial growth on media containing [2-(13)C]-glycerol or [1,3-(13)C]-glycerol enables direct (13)C detection in solid-state NMR experiments without the need for homonuclear (13)C-(13)C dipole-dipole decoupling. The (13)C-detected NMR spectra of Pf1 coat protein show a substantial increase in sensitivity compared to the equivalent (15)N-detected spectra. The isotopic labeling pattern was analyzed for [2-(13)C]-glycerol and [1,3-(13)C]-glycerol as metabolic precursors by solution-state NMR of micelle samples. Polarization inversion spin exchange at the magic angle (PISEMA) and other solid-state NMR experiments work well on 35% random fractionally and metabolically tailored (13)C-labeled samples, in contrast to their failure with conventional 100% uniformly (13)C-labeled samples.