Quadruple‐Resonance Magic‐Angle Spinning NMR Spectroscopy of Deuterated Solid Proteins

¹H‐detected magic‐angle spinning NMR experiments facilitate structural biology of solid proteins, which requires using deuterated proteins. However, often amide protons cannot be back‐exchanged sufficiently, because of a possible lack of solvent exposure. For such systems, using ²H excitation instead of ¹H excitation can be beneficial because of the larger abundance and shorter longitudinal relaxation time, T₁, of deuterium. A new structure determination approach, “quadruple‐resonance NMR spectroscopy”, is presented which relies on an efficient ²H‐excitation and ²H‐¹³C cross‐polarization (CP) step, combined with ¹H detection. We show that by using ²H‐excited experiments better sensitivity is possible on an SH3 sample recrystallized from 30 % H₂O. For a membrane protein, the ABC transporter ArtMP in native lipid bilayers, different sets of signals can be observed from different initial polarization pathways, which can be evaluated further to extract structural properties.     

NMR Characterization of Complex p‐Oligophenyl Scaffolds by Means of Aliasing Techniques to Obtain Resolution‐Enhanced Two‐Dimensional Spectra

The usefulness of computer‐assisted aliasing to secure maximal resolution of signal clusters in ¹H‐ and ¹³C‐NMR spectra (which is essential for structure determination by HMBC 2D NMR spectroscopy) in minimal acquisition time is exemplified by the complete characterization of the two complementary p‐octiphenyls 1 and 2 with complex substitution patterns. The need for digital resolution near 1 Hz/pt to dissect the extensive signal clusters in the NMR spectra of these refined oligomers excluded structure determination under routine conditions. High resolution was secured by exploiting the low signal density in the ¹³C dimension of HMBC spectra by using computer‐assisted aliasing to maximize signal density. Based on the observed shifts in DEPT and ¹H‐decoupled ¹³C‐NMR spectra of 1 and 2 , computer‐assisted aliasing allowed to reduce the number of required time increments by a factor of 20 to 30 compared to full‐width spectra with identical resolution. Without signal‐to‐noise constraints, this computer‐assisted aliasing reduced the acquisition time for high‐resolution NMR spectra needed for complete characterization of refined oligomers 1 and 2 by the same factor (e.g., from over a day to about an hour). With resolved signal clusters in fully aliased HSQC and HMBC spectra, unproblematic structure determination of 1 and 2 is demonstrated by unambiguous assignment of all C‐ and H‐atoms. These findings demonstrate that computer‐assisted aliasing of the underexploited ¹³C dimension makes extensive molecular complexity accessible by conventional multidimensional heteronuclear NMR experiments without extraordinary efforts.     

Real‐Time Band‐Selective Homonuclear Proton Decoupling for Improving Sensitivity and Resolution in Phase‐Sensitive J‐Resolved Spectroscopy

Real‐time band‐selective homonuclear ¹H decoupling during data acquisition of z‐filtered J‐resolved spectroscopy produces ¹H‐decoupled ¹H NMR spectra and leads to sensitivity enhancement and improved resolution, and thus aids the measurement of J couplings and residual dipolar couplings in crowded regions of ¹H NMR spectrum. High quality spectra from peptides, organic molecules, and also from enantiomers dissolved in weakly aligned chiral media are reported.     

One‐ and two‐dimensional NMR characterization of N‐vinyl‐2‐pyrrolidone/methyl acrylate copolymers

N‐vinyl‐2‐pyrrolidone/methyl acrylate (V/M) copolymers were prepared by free‐radical bulk polymerization using benzoyl peroxide as an initiator. The copolymer composition of these copolymers was calculated from ¹H NMR spectra. The radical reactivity ratios for N‐vinyl‐2‐pyrrolidone (V) and methyl acrylate (M) were r_V = 0.09, r_M = 0.44. These reactivity ratios for the copolymerization of V and M were determined using the Kelen–Tudos and nonlinear least‐squares error‐in‐variable methods. The ¹³C{¹H} and ¹H NMR spectra of these copolymers overlapped and were complex. The complete spectral assignment of the ¹³C and ¹H NMR spectra were done with distortionless enhancement by polarization transfer and two dimensional ¹³C‐¹H heteronuclear single quantum correlation spectroscopic experiments. The two‐dimensional ¹H‐¹H homonuclear total correlation spectroscopic NMR spectrum showed the various bond interactions, thus inferring the possible structure of the copolymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2225–2236, 2002     

One‐ and two‐dimensional NMR characterization of N‐vinyl‐2‐pyrrolidone/methyl acrylate copolymers

N‐vinyl‐2‐pyrrolidone/methyl acrylate (V/M) copolymers were prepared by free‐radical bulk polymerization using benzoyl peroxide as an initiator. The copolymer composition of these copolymers was calculated from ¹H NMR spectra. The radical reactivity ratios for N‐vinyl‐2‐pyrrolidone (V) and methyl acrylate (M) were r_V = 0.09, r_M = 0.44. These reactivity ratios for the copolymerization of V and M were determined using the Kelen–Tudos and nonlinear least‐squares error‐in‐variable methods. The ¹³C{¹H} and ¹H NMR spectra of these copolymers overlapped and were complex. The complete spectral assignment of the ¹³C and ¹H NMR spectra were done with distortionless enhancement by polarization transfer and two dimensional ¹³C‐¹H heteronuclear single quantum correlation spectroscopic experiments. The two‐dimensional ¹H‐¹H homonuclear total correlation spectroscopic NMR spectrum showed the various bond interactions, thus inferring the possible structure of the copolymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2225–2236, 2002     

NMR analysis of mono‐ and difructosyllactosucrose synthesized by 1F‐fructosyltransferase purified from roots of asparagus (Asparagus officinalis L.)

Two novel oligosaccharides, mono‐ and difructosyllactosucrose {[O‐β‐D ‐fructofuranosyl‐(2 → 1)]_n‐β‐D ‐fructofuranosyl‐O‐[β‐D ‐galactopyranosyl‐(1 → 4)]‐α‐D ‐glucopyranoside, n = 1 and 2} were synthesized using 1^F‐fructosyltransferase purified form roots of asparagus (Asparagus officinalis L.). Their ¹H and ¹³C NMR spectra were assigned using several NMR techniques. The spectral analysis was started from two anomeric methines of aldose units, galactose and glucose, since they showed separate characteristic signals in their ¹H and ¹³C NMR spectra. After assignments of all the ¹H and ¹³C signals of two units of aldose, they were discriminated as galactose and glucose using proton–proton coupling constants. The HMBC spectrum revealed the galactose residue attached to C‐4 of glucose, fructose residue attached to the C‐1 of glucose, and further fructosyl fructose linkage extended from the glucosyl fructose residues. Copyright © 2002 John Wiley & Sons, Ltd.     

Site‐Resolved Backbone and Side‐Chain Intermediate Dynamics in a Carbohydrate‐Binding Module Protein Studied by Magic‐Angle Spinning NMR Spectroscopy

Magic‐angle spinning solid‐state NMR spectroscopy has been applied to study the dynamics of CBM3b–Cbh9A from Clostridium thermocellum (ctCBM3b), a cellulose binding module protein. This 146‐residue protein has a nine‐stranded β‐sandwich fold, in which 35 % of the residues are in the β‐sheet and the remainder are composed of loops and turns. Dynamically averaged ¹H‐¹³C dipolar coupling order parameters were extracted in a site‐specific manner by using a pseudo‐three‐dimensional constant‐time recoupled separated‐local‐field experiment (dipolar‐chemical shift correlation experiment; DIPSHIFT). The backbone‐Cα and Cβ order parameters indicate that the majority of the protein, including turns, is rigid despite having a high content of loops; this suggests that restricted motions of the turns stabilize the loops and create a rigid structure. Water molecules, located in the crystalline interface between protein units, induce an increased dynamics of the interface residues thereby lubricating crystal water‐mediated contacts, whereas other crystal contacts remain rigid.     

The Structure of N1‐Hydroxylophine N3‐Oxide (=1‐Hydroxy‐2,4,5‐ triphenyl‐1H‐imidazole 3‐Oxide) in the Solid State

The crystal structure of 1‐hydroxy‐2,4,5‐triphenyl‐1H‐imidazole 3‐oxide ( 1 ) has been determined from laboratory X‐ray powder‐diffraction data. The two independent molecules in the asymmetric unit form chains via O? H???O hydrogen bonds related by a twofold screw axis. One of the O???O distances is extremely short (2.32(1) and 2.43(1) Å). Solid‐state NMR spectroscopy (CPMAS) combined with calculation of absolute shieldings (GIAO/B3LYP/6‐31G*) allowed us to determine that the compound behaves as if the O? H???O hydrogen bond has the proton in the middle (single‐well potential), resulting in the near identity of both ¹⁵N‐NMR signals.     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.     

An Efficient Labelling Approach to Harness Backbone and Side‐Chain Protons in 1H‐Detected Solid‐State NMR Spectroscopy

¹H‐detection can greatly improve spectral sensitivity in biological solid‐state NMR (ssNMR), thus allowing the study of larger and more complex proteins. However, the general requirement to perdeuterate proteins critically curtails the potential of ¹H‐detection by the loss of aliphatic side‐chain protons, which are important probes for protein structure and function. Introduced herein is a labelling scheme for ¹H‐detected ssNMR, and it gives high quality spectra for both side‐chain and backbone protons, and allows quantitative assignments and aids in probing interresidual contacts. Excellent ¹H resolution in membrane proteins is obtained, the topology and dynamics of an ion channel were studied. This labelling scheme will open new avenues for the study of challenging proteins by ssNMR.     

Isolation and spectral study of 4‐methyl‐6,8‐dihydroxy‐7H‐benz[de]anthracen‐7‐one

4‐Methyl‐6,8‐dihydroxy‐7H‐benz[de]anthracen‐7‐one was isolated from the sap of Aloe by column chromatography. Its ¹H and ¹³C NMR spectra were completely assigned by utilizing two‐dimensional ¹H‐detected heteronuclear one‐bond (HMQC) and multiple‐bond (HMBC) chemical shift correlation experiments together with ¹H–¹H COSY and DEPT techniques. These techniques were also valuable in assigning the protons and carbons of those benzanthrone compounds which were previously incompletely reported because of the overlap of proton signals. The molecular structure was elucidated by 2D NMR analysis. The spectral properties (MS, IR and UV) are also presented. Copyright © 2003 John Wiley & Sons, Ltd.     

Iodine‐Catalyzed Synthesis of Spiro[1,3,4‐benzotriazepine‐2,3′‐indole]‐2′,5(1H,1′H)‐diones under Mild Conditions

The I₂‐catalyzed preparation of spiro[1,3,4‐benzotriazepine‐2,3′‐indole]‐2′,5(1H,1′H)‐diones from 2‐aminobenzohydrazide and isatins in MeCN at room temperature in good‐to‐excellent yields is described. The structure of 3 was corroborated spectroscopically (IR, ¹H‐ and ¹³C‐NMR, and EI‐MS data). A plausible mechanism for this type of reaction is proposed (Scheme 2).     

Facile Synthesis of 3,6‐Disubstituted‐1,2,4‐triazolo‐[3,4‐b]‐1,3,4‐thiadiazoles via Oxidative Cyclization of n‐Heteroaryl‐Substituted Hydrazones and Their Biological Activity

Fused 3,6‐disubstituted triazolothiadiazoles were synthesized in good yield from a rapid and convenient oxidative cyclization of N‐heteroaryl‐substituted hydrazones promoted by chloramine‐T trihydrate at ambient temperature. The structure of the synthesized compounds was confirmed by FTIR, ¹H NMR, ¹³C NMR, and mass spectral data. The synthesized compounds were evaluated for their antioxidant and antitubercular activities. All the compounds 5a‐i and 6a‐i showed good antitubercular activity. However, only compounds 5a‐i showed good antioxidant activity.     

The Impact of Long‐Range 1H‐15N Heteronuclear Shift Correlation Data on Computer‐Assisted Structure Elucidation: Posaconazole

Considerable work has been invested in the area of computer‐assisted structure elucidation (CASE) methods. As NMR techniques have been developed that provide more effective atom‐to‐atom connectivity information, it has become theoretically possible to do de novo structure elucidation based on 2D NMR datasets recorded for an unknown molecule. However, as annular (ring) nitrogen atoms become more prevalent in complex chemical structures, the ability to rely solely on ¹H and ¹³C homo‐ and hetero‐nuclear direct and long‐range connectivity information to solve a structure correspondingly diminishes. Hence, we now wish to report the results of an investigation into the application of CASE methods with and without long‐range ¹H‐¹⁵N data using posaconazole as a model compound, which has eight annular nitrogens in its structure. With the inclusion of ¹H‐¹⁵N data long‐range data, the structure could be successfully determined in a few hours. Excluding the ¹H‐¹⁵N data caused the program to generate millions of candidate structures, none of which fit the data well enough to be stored.     

Solid‐state NMR Study of the YadA Membrane‐Anchor Domain in the Bacterial Outer Membrane

MAS‐NMR was used to study the structure and dynamics at ambient temperatures of the membrane‐anchor domain of YadA (YadA‐M) in a pellet of the outer membrane of E. coli in which it was expressed. YadA is an adhesin from the pathogen Yersinia enterocolitica that is involved in interactions with the host cell, and it is a model protein for studying the autotransport process. Existing assignments were sucessfully transferred to a large part of the YadA‐M protein in the E. coli lipid environment by using ¹³C‐¹³C DARR and PDSD spectra at different mixing times. The chemical shifts in most regions of YadA‐M are unchanged relative to those in microcrystalline YadA‐M preparations from which a structure has previously been solved, including the ASSA region that is proposed to be involved in transition‐state hairpin formation for transport of the soluble domain. Comparisons of the dynamics between the microcrystalline and membrane‐embedded samples indicate greater flexibility of the ASSA region in the outer‐membrane preparation at physiological temperatures. This study will pave the way towards MAS‐NMR structure determination of membrane proteins, and a better understanding of functionally important dynamic residues in native membrane environments.     

Complete NMR assignment of 3, 4‐seco‐lup‐20(29)‐en‐3‐oic acid from Decatropis bicolor

Complete ¹H and ¹³C NMR chemical shift assignments for 3,4‐seco‐lup‐20(29)‐en‐3‐oic acid ( 1 ) have been established by means of two‐dimensional COSY, HSQC, HMBC and NOESY spectroscopic experiments as well as by analysis of MS data. Compound 1 was isolated from Decatropis bicolor (Zucc.) Radlk. (Rutaceae) in addition to six coumarins and one alkaloid of known structure. Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis of Isoxazole, 1, 2, 4‐Oxadiazole and (1H‐Pyrazol‐4‐yl)‐methanone Oxime Derivatives from N‐Hydroxy‐1H‐pyrazole‐4‐carbimidoyl Chloride and their Biological Activity

Some novel isoxazole‐, 1,2,4 oxadiazole‐, and (1H‐pyrazol‐4‐yl)‐methanone oxime derivatives were synthesized from N‐hydroxy‐1H‐pyrazole‐4‐carbimidoyl chloride and the structures of all products were identified by spectral data (¹H‐NMR, ¹³C‐NMR, IR, MS, and HRMS) and evaluated their antibacterial activity.     

Stacking Structure of Confined 1‐Butanol in SBA‐15 Investigated by Solid‐State NMR Spectroscopy

Understanding the complex thermodynamic behavior of confined amphiphilic molecules in biological or mesoporous hosts requires detailed knowledge of the stacking structures. Here, we present detailed solid‐state NMR spectroscopic investigations on 1‐butanol molecules confined in the hydrophilic mesoporous SBA‐15 host. A range of NMR spectroscopic measurements comprising of ¹H spin–lattice (T₁), spin–spin (T₂) relaxation, ¹³C cross‐polarization (CP), and ¹H,¹H two‐dimensional nuclear Overhauser enhancement spectroscopy (¹H,¹H 2D NOESY) with the magic angle spinning (MAS) technique as well as static wide‐line ²H NMR spectra have been used to investigate the dynamics and to observe the stacking structure of confined 1‐butanol in SBA‐15. The results suggest that not only the molecular reorientation but also the exchange motions of confined molecules of 1‐butanol are extremely restricted in the confined space of the SBA‐15 pores. The dynamics of the confined molecules of 1‐butanol imply that the ¹H,¹H 2D NOESY should be an appropriate technique to observe the stacking structure of confined amphiphilc molecules. This study is the first to observe that a significant part of confined 1‐butanol molecules are orientated as tilted bilayered structures on the surface of the host SBA‐15 pores in a time‐average state by solid‐state NMR spectroscopy with the ¹H,¹H 2D NOESY technique.     

113Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p

Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using ¹¹³Cd NMR experiments with ¹¹³Cd‐substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used ¹¹³Cd NMR spectroscopy during structure determination of Bud31p, a 157‐residue yeast protein containing an unusual Zn₃Cys₉ cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.     

First 13C‐NMR Assignments of Betaxanthins

Due to their inherent liability towards highly acidic conditions previously considered to be a prerequisite for data acquisition, betaxanthin structure dereplication by NMR spectroscopy has been scarcely reported and was, hitherto, exclusively based on ¹H‐NMR data interpretation. Applying only slightly acidic conditions, we herein report the first ¹³C‐NMR data of two betaxanthins, i.e., indicaxanthin ( 1 ), isolated from yellow‐orange cactus pear fruits (Opuntia ficus‐indica [L.] Mill . cv. ‘Gialla’), and of miraxanthin V ( 2 ) from yellow Swiss chard petioles (Beta vulgaris L. ssp. cicla [L.] Alef . cv. ‘Bright Lights’), as derived by gHSQC‐ and gHMQC‐NMR experiments and inverse detection.