Probing Invisible,Excited Protein States by Non‐Uniformly Sampled Pseudo‐4D CEST Spectroscopy

Chemical exchange saturation transfer (CEST) NMR spectroscopy is a powerful tool for studies of slow timescale protein dynamics. Typical experiments are based on recording a large number of 2D data sets and quantifying peak intensities in each of the resulting planes. A weakness of the method is that peaks must be resolved in 2D spectra, limiting applications to relatively small proteins. Resolution is significantly improved in 3D spectra but recording uniformly sampled data is time‐prohibitive. Here we describe non‐uniformly sampled HNCO‐based pseudo‐4D CEST that provides excellent resolution in reasonable measurement times. Data analysis is done through fitting in the time domain, without the need of reconstructing the frequency dimensions, exploiting previously measured accurate peak positions in reference spectra. The methodology is demonstrated on several protein systems, including a nascent form of superoxide dismutase that is implicated in neurodegenerative disease.     

Accelerated NMR Spectroscopy with Low‐Rank Reconstruction

Accelerated multi‐dimensional NMR spectroscopy is a prerequisite for high‐throughput applications, studying short‐lived molecular systems and monitoring chemical reactions in real time. Non‐uniform sampling is a common approach to reduce the measurement time. Here, a new method for high‐quality spectra reconstruction from non‐uniformly sampled data is introduced, which is based on recent developments in the field of signal processing theory and uses the so far unexploited general property of the NMR signal, its low rank. Using experimental and simulated data, we demonstrate that the low‐rank reconstruction is a viable alternative to the current state‐of‐the‐art technique compressed sensing. In particular, the low‐rank approach is good in preserving of low‐intensity broad peaks, and thus increases the effective sensitivity in the reconstructed spectra.     

Bacteriophage Tail‐Tube Assembly Studied by Proton‐Detected 4D Solid‐State NMR

Obtaining unambiguous resonance assignments remains a major bottleneck in solid‐state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three‐dimensional (3D) spectra are used. Here, we present a proton‐detected 4D solid‐state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non‐uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail‐tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.     

Lamp‐based wavelength‐resolved fluorescence detection for protein capillary electrophoresis: Setup and detector performance

A lamp‐based fluorescence detection (Flu) system for CE was extended with a wavelength‐resolved (WR) detector to allow recording of full protein emission spectra. WRFlu was achieved using a fluorescence cell that employs optical fibres to lead excitation light from a Xe‐Hg lamp to the capillary window and protein fluorescence emission to a spectrograph equipped with a CCD. A 280 nm band pass filter etc. together with a 300 nm short pass cut‐off filter was used for excitation. A capillary cartridge was modified to hold the detection cell in a commercial CE instrument enabling WRFlu in routine CE. The performance of the WRFlu detection was evaluated and optimised using lysozyme as model protein. Based on reference spectral data, a signal‐intensity adjustment was introduced to correct for transmission losses in the detector optics that occurred for lower protein emission wavelengths. CE‐WRFlu of lysozyme was performed using BGEs of 50 mM sodium phosphate (pH 6.5 or 3.0) and a charged‐polymer coated capillary. Using the 3‐D data set, signal averaging over time and emission‐wavelength intervals was carried out to improve the S/N of emission spectra and electropherograms. The detection limit for lysozyme was 21 nM, providing sufficient sensitivity to obtain spectral information on protein impurities.     

Non‐Uniform Sampling and J‐UNIO Automation for Efficient Protein NMR Structure Determination

High‐resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non‐uniform sampling (NUS) of 3D heteronuclear‐resolved [¹H,¹H]‐NOESY data yielded two‐ to three‐fold savings of instrument time for structure determinations of soluble proteins. With the 152‐residue protein NP_372339.1 from Staphylococcus aureus and the 71‐residue protein NP_346341.1 from Streptococcus pneumonia we show that high‐quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data.     

Theoretical studies on triaryamine‐based p‐type D‐D‐π‐A sensitizer

Development of triaryamine‐based nonmetallic dye sensitizers is a hot topic in the solar cell research. A series of triaryamine‐based dyes WS1 – WS7 were designed with W1 as the prototype. Density functional theory (DFT) and time‐dependent‐DFT calculations were used to investigate the effects of the attached donor D on the absorption spectra and electronic properties of the dyes. The light‐harvesting efficiency (LHE), hole injection force (ΔG_inj), dye regeneration force (ΔG_reg), and charge recombination force (ΔG_CR) for all the dyes were predicted. The insertion of D not only results in a red shift in the absorption spectra for all dyes but also achieves a broader absorption for visible light. Compared with that of the prototype, the absorption peak of the dye WS7 has a red shift of 95 nm and an oscillator strength increase of 29%. The absorption peak of WS7 is wider and stronger, and the absorption range extends to 900 nm. The LHE and ΔG_reg values of WS7 are 0.991 and ?1.49 eV, respectively. On overall evaluation, WS7 is a promising candidate of a p‐type dye sensitizer with good light absorption and dye regeneration efficiency.     

Extending the Sensitivity of CEST NMR Spectroscopy to Micro‐to‐Millisecond Dynamics in Nucleic Acids Using High‐Power Radio‐Frequency Fields

Biomolecules undergo motions on the micro‐to‐millisecond timescale to adopt low‐populated transient states that play important roles in folding, recognition, and catalysis. NMR techniques, such as Carr–Purcell–Meiboom–Gill (CPMG), chemical exchange saturation transfer (CEST), and R_1ρ are the most commonly used methods for characterizing such transitions at atomic resolution under solution conditions. CPMG and CEST are most effective at characterizing motions on the millisecond timescale. While some implementations of the R_1ρ experiment are more broadly sensitive to motions on the micro‐to‐millisecond timescale, they entail the use of selective irradiation schemes and inefficient 1D data acquisition methods. Herein, we show that high‐power radio‐frequency fields can be used in CEST experiments to extend the sensitivity to faster motions on the micro‐to‐millisecond timescale. Given the ease of implementing high‐power fields in CEST, this should make it easier to characterize micro‐to‐millisecond dynamics in biomolecules.     

A biuret‐derived,MS‐cleavable cross‐linking reagent for protein structural analysis: A proof‐of‐principle study

Chemical cross‐linking combined with mass spectrometry (XL‐MS) and computational modeling has evolved as an alternative method to derive protein 3D structures and to map protein interaction networks. Special focus has been laid recently on the development and application of cross‐linkers that are cleavable by collisional activation as they yield distinct signatures in tandem mass spectra. Building on our experiences with cross‐linkers containing an MS‐labile urea group, we now present the biuret‐based, CID‐MS/MS‐cleavable cross‐linker imidodicarbonyl diimidazole (IDDI) and demonstrate its applicability for protein cross‐linking studies based on the four model peptides angiotensin II, MRFA, substance P, and thymopentin.     

(+)‐N‐Formylnorglaucine Rotamers from Unonopsis stipitata Diels

(+)‐N‐formylnorglaucine ( 1 ), an aporphine alkaloid containing a formyl group linked to the heterocyclic nitrogen, was isolated from the leaves of Unonopsis stipitata, an Amazon medicinal plant. The chemical structure was characterized based on 1D‐ and 2D‐NMR spectroscopy and HR‐ESI‐MS. NMR spectra revealed that 1 is composed of two rotamers ( 1a and 1b ) in a ratio of approximately 2:1. In addition, the fragmentation behavior of 1 displayed an unusual fragmentation pattern compared to regular aporphine alkaloids. Thus, this compound is reported for the first time as a natural product in this study.     

Computational Study of the One‐ and Two‐Dimensional Infrared Spectra of a Proton‐Transfer Mode in a Hydrogen‐Bonded Complex Dissolved in a Polar Nanocluster

The signatures of nanosolvation on the one‐ and two‐dimensional (1D and 2D) IR spectra of a proton‐transfer mode in a hydrogen‐bonded complex dissolved in polar solvent molecule nanoclusters of varying size are elucidated by using mixed quantum–classical molecular dynamics simulations. For this particular system, increasing the number of solvent molecules successively from N=7 to N=9 initiates the transition of the system from a cluster state to a bulk‐like state. Both the 1D and 2D IR spectra reflect this transition through pronounced changes in their peak intensities and numbers, but the time‐resolved 2D IR spectra also manifest spectral features that uniquely identify the onset of the cluster‐to‐bulk transition. In particular, it is observed that in the 1D IR spectra, the relative intensities of the peaks change such that the number of peaks decreases from three to two as the size of the cluster increases from N=7 to N=9. In the 2D IR spectra, off‐diagonal peaks are observed in the N=7 and N=8 cases at zero waiting time, but not in the N=9 case. It is known that there are no off‐diagonal peaks in the 2D IR spectrum of the bulk version of this system at zero waiting time, so the disappearance of these peaks is a unique signature of the onset of bulk‐like behavior. Through an examination of the trajectories of various properties of the complex and solvent, it is possible to relate the emergence of these off‐diagonal peaks to an interplay between the vibrations of the complex and the solvent polarization dynamics.     

Identification of a lipid‐related peak set to enhance the interpretation of TOF‐SIMS data from model and cellular membranes

Principal component analysis (PCA) of time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) data enables differentiating structurally similar molecules according to linear combinations of multiple peaks in their spectra. However, in order to use PCA to correctly identify variations in lipid composition between samples, the discrimination achieved must be based on chemical differences that are related to the lipid species, and not sample‐associated contamination. Here, we identify the positive‐ion TOF‐SIMS peaks that are related to phosphatidylcholine lipid headgroups and tail groups by PCA of spectra acquired from lipid isotopologs. We demonstrate that restricting PCA to a contaminant‐free lipid‐related peak set reduces the variability in the spectra acquired from lipid samples that is due to contaminants, which enhanced differentiating different lipid standards, but adversely affected the contrast in PC scores images of phase‐separated lipid membranes. We also show that PCA of a restricted data set consisting of the peaks related to lipids and amino acids increases the likelihood that the discrimination of TOF‐SIMS data acquired from intact cells is based on differences in the lipids and proteins on the cell surface, and not sample‐specific contamination without compromising sample discrimination. We expect that the lipid‐related peak database established herein will facilitate interpreting the TOF‐SIMS data and PCA results from studies of both model and cellular membranes, and enhance identifying the origins of the peaks that contribute to discriminating different types of cells. Copyright © 2011 John Wiley & Sons, Ltd.     

Root‐mean‐square‐deviation‐based rapid backbone resonance assignments in proteins

We have shown that the methodology based on the estimation of root‐mean‐square deviation (RMSD) between two sets of chemical shifts is very useful to rapidly assign the spectral signatures of ¹H^N, ¹³C^α, ¹³C^β, ¹³C′, ¹H^α and ¹⁵N spins of a given protein in one state from the knowledge of its resonance assignments in a different state, without resorting to routine established procedures (manual and automated). We demonstrate the utility of this methodology to rapidly assign the 3D spectra of a metal‐binding protein in its holo‐state from the knowledge of its assignments in apo‐state, the spectra of a protein in its paramagnetic state from the knowledge of its assignments in diamagnetic state and, finally, the spectra of a mutant protein from the knowledge of the chemical shifts of the corresponding wild‐type protein. The underlying assumption of this methodology is that, it is impossible for any two amino acid residues in a given protein to have all the six chemical shifts degenerate and that the protein under consideration does not undergo large conformational changes in going from one conformational state to another. The methodology has been tested using experimental data on three proteins, M‐crystallin (8.5 kDa, predominantly β‐sheet, for apo‐ to holo‐state), Calbindin (7.5 kDa, predominantly α‐helical, for diamagnetic to paramagnetic state and apo to holo) and EhCaBP1 (14.3 kDa, α‐helical, the wild‐type protein with one of its mutant). In all the cases, the extent of assignment is found to be greater than 85%. Copyright © 2010 John Wiley & Sons, Ltd.     

Study of near‐symmetric cyclodextrins by compressed sensing 2D NMR

The compressed sensing NMR (CS‐NMR) is an approach to processing of nonuniformly sampled NMR data. Its idea is to introduce minimal l_p‐norm (0 < p ≤ 1) constraint to a penalty function used in a reconstruction algorithm. Here, we demonstrate that 2D CS‐NMR spectra allow the full spectral assignment of near‐symmetric β‐cyclodextrin derivatives (mono‐modified at the C6 position). The application of CS‐NMR ensures experimental time saving and the resolution improvement, necessary because of very low chemical shift dispersion. In the overnight experimental time, the set of properly resolved 2D NMR spectra required for the unambiguous assignment of mono(6‐deoxy‐6‐(1‐1,2,3‐triazo‐4‐yl)‐1‐propane‐3‐O‐(phenyl)) β‐cyclodextrin was obtained. The highly resolved HSQC spectrum was reconstructed from 5.12% of the data. Moreover, reconstructed 2D HSQC–TOCSY spectrum yielded information about the correlations within one sugar unit, and 2D HSQC–NOESY technique allowed the sequential assignment of the glucosidic units. Copyright © 2013 John Wiley & Sons, Ltd.     

Preparation of few‐layer two‐dimensional polymers by self‐assembly of bola‐amphiphilic small molecules

Two bola‐amphiphilic small molecules, based on the diphenylanthracene skeleton structure, namely, BASM‐1 and its functionalized small molecule BASM‐2 , were designed and synthesized. The self‐assembly behavior and mechanism of these two molecules in aqueous solution were studied. The supramolecular two‐dimensional (2D) layer and the covalent 2D polymers were, respectively, prepared by these two molecules. What is more, the transverse size of the covalent 2D polymer laminates increased with the extension of the polymerization time. Atomic force microscopy results showed that both free‐standing single‐layer 2D polymers and few layer laminates with two to three molecular layers were obtained. So our work provides a simple and efficient method for directly preparing independent both supramolecular 2D polymers and covalent 2D polymers in liquid phase which is of great significance. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1748–1755     

Preparation and characterization of a novel dual‐retention mechanism mixed‐mode stationary phase with PEG 400 and succinic anhydride as ligand for protein separation in WCX and HIC modes

A novel dual‐retention mechanism mixed‐mode stationary phase based on silica gel functionalized with PEG 400 and succinic anhydride as the ligand was prepared and characterized by infrared spectra and elemental analysis. Because of the ligand containing PEG 400 and carboxyl function groups, it displayed hydrophobic interaction chromatography (HIC) characteristic in a high‐salt‐concentration mobile phase, and weak cation exchange chromatography (WCX) characteristic in a low‐salt‐concentration mobile phase. As a result, it can be employed to separate proteins with both WCX and HIC modes. The resolution and selectivity of the stationary phase was evaluated under both HIC and WCX modes with protein standards, and its performance was comparable to that of conventional ion‐exchange chromatography and HIC columns. The results indicated that the novel dual‐retention mechanism column, in many cases, could replace two individual WCX and HIC columns as a ‘2D column’. In addition, the mixed retention mechanism of proteins on this ‘2D column’ was investigated with stoichiometric displacement theory for retention of solute in liquid chromatography in detail in order to understand why the dual‐retention mechanism column has high resolution and selectivity for protein separation under WCX and HIC modes, respectively. Based on this ‘2D column’, a new 2DLC technology with a single column was developed. It is very important in proteome research and recombinant protein drug production to save column expense and simplify the processes in biotechnology. Copyright © 2013 John Wiley & Sons, Ltd.     

On‐bead combinatorial synthesis and imaging of europium(III)‐based paraCEST agents aids in identification of chemical features that enhance CEST sensitivity

The rate of water exchange between the inner sphere of a paramagnetic ion and bulk water is an important parameter in determining the magnitude of the chemical exchange saturation transfer signal from paramagnetic CEST agents (paraCEST). This is governed by various geometric, steric and ligand field factors created by macrocyclic ligands surrounding the paramagnetic metal ion. Our previous on‐bead combinatorial studies of di‐peptoid–europium(III)–1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA)–tetraamide complexes revealed that negatively charged groups in the immediate vicinity of the metal center strongly enhances the CEST signal. Here, we report a solid phase synthesis and on‐bead imaging of 76 new DOTA derivatives that are developed by coupling with a single residue onto each of the three arms of a DOTA–tetraamide scaffold attached to resin beads. This single residue predominantly carries negatively charged groups blended with various physico‐chemical characteristics. We found that non‐bulky negatively charged groups are best suited at the immediate vicinity of the metal ion, while positive, bulky and halogen containing moieties suppress the CEST signal. Copyright © 2017 John Wiley & Sons, Ltd.     

A toolbox of HSQC experiments for small molecules at high 13C‐enrichment. Artifact‐free,fully 13C‐homodecoupled and JCC‐encoding pulse sequences

A set of modified HSQC experiments designed for the study of ¹³C‐enriched small molecules is introduced. It includes an improved sensitivity‐enhanced HSQC experiment eliminating signal artifacts because of high‐order ¹³C magnetization terms generated at high ¹³C enrichment. A broadband homonuclear ¹³C decoupling sequence based on Zangger and Sterk's method simplifies the complex ¹³C–¹³C multiplet structure in the F1 dimension of HSQC. When recording spectra at high resolution, the combination with a multiple‐site modulation of the selective pulse outperforms the constant‐time HSQC in terms of sensitivity and reliability. Finally, two pulse sequences reintroducing selected J_CC couplings with selective pulses facilitate their assignments and measurements either in the splitting of the resulting doublets or by modulation of the signal amplitude. A sample of uniformly 92% ¹³C‐enriched cholesterol is used as an example. Copyright © 2013 John Wiley & Sons, Ltd.     

Multidimensional solid‐state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C‐labeled Arabidopsis primary cell walls

Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high‐resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic‐angle‐spinning (MAS) solid‐state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with ¹³C and their NMR spectra were compared. Recent ¹³C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D ¹³C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. ¹³C spin–lattice relaxation times and ¹H rotating‐frame spin–lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near‐native conditions. Copyright © 2012 John Wiley & Sons, Ltd.     

Improved Large‐Scale Liquid‐Phase Synthesis and High‐Temperature NMR Characterization of Short ­(F‐)PNAs

We report on a large‐scale synthesis of F‐PNA trimer 10 and PNA trimer 11 . The key improvement is the facile two‐step synthesis of (2,4‐difluoro‐5‐methylphenyl)acetic acid ( 2 ). Water solubility of the corresponding F‐PNA oligomer 10 was achieved by synthesizing solubility enhancer 5a , which is twofold positively charged and only consists of inherent structural elements of PNA. Protected and unpaired PNA n‐mers exist in a mixture of 2ⁿ conformers undergoing slow exchange and leading to complicated NMR spectra. Structure analysis was improved by recording ¹H‐ and ¹³C‐NMR spectra at elevated temperatures above the coalescence point. Fully protected backbone derivatives show sharp resonances where expected, and spectra of protected PNAs are remarkably simplified, thereby allowing an interpretation for the first time. Both trimers 10 and 11 are considered as building blocks for a self‐replicating system based on PNA.     

Travelling‐wave ion mobility and negative ion fragmentation of high‐mannose N‐glycans

The isomeric structure of high‐mannose N‐glycans can significantly impact biological recognition events. Here, the utility of travelling‐wave ion mobility mass spectrometry for isomer separation of high‐mannose N‐glycans is investigated. Negative ion fragmentation using collision‐induced dissociation gave more informative spectra than positive ion spectra with mass‐different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling‐wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N‐glycans released from the well‐characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross‐sectional data, details of the negative ion collision‐induced dissociation spectra of all resolved isomers are discussed. Copyright © 2016 John Wiley & Sons, Ltd.