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Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins.

Haribabu arthanari.

1. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215

2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115

Koh Takeuchi

3. Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 135-0064 Tokyo, Japan

Abhinav Dubey

Gerhard wagner.

The first recognition of protein breathing was more than 50 years ago. Today, we are able to detect the multitude of interaction modes, structural polymorphisms, and binding-induced changes in protein structure that direct function. Solution-state NMR spectroscopy has proved to be a powerful technique, not only to obtain high-resolution structures of proteins, but also to provide unique insights into the functional dynamics of proteins. Here, we summarize recent technical landmarks in solution NMR that have enabled characterization of key biological macromolecular systems. These methods have been fundamental to atomic resolution structure determination and quantitative analysis of dynamics over a wide range of time scales by NMR. The ability of NMR to detect lowly populated protein conformations and transiently formed complexes plays a critical role in its ability to elucidate functionally important structural features of proteins and their dynamics.

Graphical abstract

Introduction

Solution-state NMR has contributed significantly in providing unique, quantitative, atomic resolution insights into the structures, dynamics, and interactions of biological macromolecules ( Fig. 1 ). The versatility of NMR was illustrated early in applications to the analysis of protein dynamics. Even before NMR methods for protein structure determination had been established, the technique revealed unexpected dynamic events in proteins, such as the presence of aromatic ring flips [ 1 ], which tracked with periodic opening motions in the protein conformation. Other studies during the same period detected breathing in protein structures by residue-specific amide proton exchange [ 2 , 3 ].

The versatility of NMR to dissect the dynamics, interactions, and high-resolution structures of macromolecules and the methodological developments that have enabled these applications.

Since then, not only has protein structure determination by NMR become possible, continuously evolving NMR technologies have allowed the structures of large macromolecular complexes to be solved, the dynamics of proteins to be quantitatively characterized, and the relevance for function to be illuminated ( Figure 1 ). NMR is unique amongst the structure-determination approaches in its ability to provide quantitative thermodynamic and kinetic insights into protein dynamics without requiring modification of the protein. Furthermore, NMR can detect lowly populated protein conformations and transiently formed protein complexes. All these applications have required new methodological developments, including advances in protein expression, stable isotope labeling, and assignment strategies. Here we will highlight the recent technical developments that have enabled us to access more complex protein systems.

NMR signal detection and resonance assignment of high molecular weight proteins

NMR studies on larger proteins are complicated by faster transverse relaxation rates, broader linewidths, and overall spectral crowding due to the increase in the number of peaks. Three main areas of technical advancement have facilitated the application of NMR to large molecular weight systems and aided the measurement of protein dynamics in multiple time regimes: 1) advances in protein expression and site-specific labeling, 2) the development of new NMR methodologies, particularly new experimental designs (pulse programs) and data acquisition schemes and 3) advances in instrumentation and probe design. In the following sections, we will discuss recent critical achievements in each area.

Advances in protein expression and site-specific labeling

Labeling proteins through isotopic enrichment with NMR-active stable isotopes is a critical aspect of NMR spectroscopy. Recent developments have enabled amino-acid-specific and site-specific labeling, both of which greatly reduce spectral complexity and improve relaxation properties, a critical factor when tackling large molecular weight systems. Whereas previously, the necessity for labeling meant that certain categories of proteins were off-limits, methods now exist to label proteins in eukaryotic and cell-free expression systems, which means that a greater repertoire of systems can be studied by NMR.

Methyl Labeling:

Methyl moieties have favorable properties for NMR. These advantageous properties arise from the fast rotation of methyl groups, which is independent from the overall correlation time of the protein, and the three-fold higher signal intensity due to the three chemically equivalent methyl protons.

These advantages can be harnessed through the use of selective methyl labeling in a deuterated background, significantly reducing transverse relaxation rates in a Methyl-TROSY (HMQC) experiment, and thus enabling the analysis of the structure and dynamics of substantially larger proteins up to 1 MDa in size [ 4 , 5 ]. When using the appropriate metabolic/amino acid precursors in E. coli , the methyls of Ala, Ile, Leu, Met, Thr, and Val can be specifically labeled with 13 C and 1 H isotopes, while the remainder of the protein is 12 C-based and deuterated [ 6 , 7 ].

To be effective the methyl TROSY effect requires high-level deuteration around the methyl groups. Methyl labeling in a high deuteration background is possible in yeast, but additional effort is required to incorporate the metabolic precursors needed to obtain high levels of Leu/Val (LV) labeling [ 8 – 10 ]. Some proteins, however, can only be expressed in mammalian or insect cell expression systems, and these cells cannot survive in fully deuterated culture medium. Recently, it was shown that conditions favorable for the methyl TROSY effect can be achieved by culturing insect cells with a limited selection of deuterated amino acids [ 11 , 12 ]. Alternatively, to avoid this restriction in the expression system, extensive searching for conditions that allow protein expression in yeast and/or E. coli may be undertaken. The best and most recent example of this achievement has been the expression of G-protein-coupled receptors (GPCRs) in P. pastoris [ 13 – 17 ] and E. coli in combination with directed evolution [ 18 , 19 ]. There are several strategies to produce proteins with methyl-specific labeling using in vitro expression systems; however, most require extensive chemical synthesis of labeled amino acids. One exception is a cost-effective method of methyl labeling in vitro that uses crude hydrolyzed ILV-labeled OmpX inclusion bodies, which can be obtained with high yield from E. coli [ 20 ].

Efficient 19 F Labeling:

In addition to methyl-selective labeling, site-specific 19 F labeling has been used to analyze the dynamics of sites of interest. Taking advantage of the high sensitivity of 19 F chemical shifts to the local chemical environment, site-specific 19 F labeling has been successfully utilized to examine the functional dynamics of GPCRs [ 13 , 15 , 21 – 23 ]. The isotopic enrichment strategies are primarily based on the labeling of a minimal cysteine version of the target protein with trifluoromethyl (CF 3 ) probes, such as 2,2,2-trifluoroethanethiol, 2-bromo-N-(4-(trifluoromethyl)phenyl) acetamide (BTFMA), or N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA). These cysteine-reactive labels allow sensitive 19 F-signal detection even from large and dynamic protein systems. It should be noted that NMR studies of GPCRs using BTFMA or 3-BTFMA observed dramatically improved chemical shift dispersion when compared to the use of trifluoroacetanilide probes, a difference that might be due to the direct conjugation of the phenyl group to the CF 3 substituent in the reagent [ 15 , 22 , 24 ].

Aromatic Labeling and TROSY:

Side chains of aromatic amino acids are bulky and often buried in the hydrophobic core of proteins. For these reasons, they can be excellent probes for generating NMR distance constraints, detecting dynamic events, and reporting on protein function. However, the strong scalar couplings and small chemical shift differences between the 13 C atoms pose challenges for NMR studies. These disadvantages can be overcome by site-specific 13 C labeling of aromatic side chains. Using [1- 13 C] glucose as the carbon source, the δ position of Phe and Tyr, the δ2/ε1 positions of His, and the δ1/ε2/ ε3 positions of Trp can be specifically labeled with 13 C, while keeping the remaining sites unlabeled [ 25 ].

Isolated 1 H 13 C labeling at the δ positions of Phe and Tyr can be achieved by providing [ 2 H, 12 C] pyruvate and [4- 13 C] erythrose to E. coli grown in deuterium oxide, thus allowing accurate relaxation measurements by removing interference from remote 1 H and 13 C nuclei [ 26 ]. The removal of the strong scalar 1 J cc coupling by alternating 13 C and 12 C labeling simplifies the aromatic carbon spectrum. This allows sensitive and high-resolution detection of aromatic TROSY signals, which can be used to obtain valuable intramolecular and intermolecular crosspeaks from the NOESY spectra of protein complexes [ 27 ]. A recent comprehensive study reported site-selective 13 C labeling of all 20 amino acids through the use of [1-, 2-, 3-, or 4- 13 C] erythrose supplemented with [U- 12 C] glucose. Applying the results of these studies has enabled the development of custom aromatic-residue labeling schemes tailored to diverse research problems [ 28 ].

Recently, we developed the aromatic 19 F- 13 C TROSY experiment, which takes advantage of the remarkable relaxation properties of 19 F- 13 C spin pairs of aromatic amino acid side chains and nucleotide bases to disperse 19 F resonances in two-dimensional spectra [ 29 ]. The technique allowed a complete mapping of the tyrosine 19 F- 13 C signals of a 180-kDa protein and provides a powerful background-free NMR probe for proteins and nucleic acids.

Development of new NMR pulse programs and data acquisition methods

NMR resonances harbor information about structure and dynamics at atomic resolution, and there exist specific NMR methods to extract this information for a given system. However, a substantial fraction of the experimental effort is dedicated to correlating each resonance to a specific atom in the primary sequence of the protein. In this section we will discuss the recent developments in methods for resonance assignment and analysis of structure and dynamics.

NMR methods for resonance assignment

For the assignment of methyl groups, besides brute force mutation-based strategies, methods to correlate methyl resonances to their corresponding main-chain 15 N and 13 Cα chemical shifts have been previously proposed [ 30 – 33 ]. More recently, Kerfah et al published a convenient method to establish CH 3 -specific NMR assignment of Ala, Ile, Leu, and Val methyl groups in high molecular weight proteins using a single sample [ 34 ]. This new approach requires the use of precursors in protein expression to linearly label branched amino acids with 13 C/ 2 H and to stereo-specifically label methyl groups with 13 C/ 1 H. An out-and-back-style NMR experiment with TOCSY transfer correlates 1 H CH3 , 13 C CH3 and 13 C aliph (which includes 13 Cα) to facilitate sequence specific resonance assignments.

Assigning side chain methyl resonances is possible without prior backbone assignment (reviewed in [ 31 ]); however, triple resonance experiments, such as the HNCA and HN(CA)CB, facilitate methyl assignment and are still advantageous. Methyl resonance assignments can also be established using covariance NMR to directly correlate assigned amide resonances and unassigned methyl resonances via indirect correlations to Cα and Cβ nuclei [ 35 ]. Resonance overlap can be resolved by combining covariance with spectral derivatives. Here, we take the derivative of the spectrum along the frequency dimension, prior to performing covariance, to emphasize the peak maxima [ 36 , 37 ].

Recently, we reported a primarily nuclear-Overhauser-effect (NOE)-based assignment of the methyl signals of the OmpX membrane protein in a phospholipid nanodisc (~100+ kDa). The combination of spin-label data and residual dipolar couplings resulted in a refined solution-state NMR structure of this model membrane protein in a phospholipid bilayer [ 38 ].

In large molecular weight systems, high-resolution in the 13 Cα dimension is restricted by peak broadening and decreased sensitivity stemming from the one-bond scalar coupling with 13 Cβ. To mitigate this problem, a labeling strategy was developed that utilizes a mixture of 2- 13 C and 3- 13 C pyruvate as the carbon source during protein expression. Labeling with this pyruvate combination suppresses one-bond 1 J αβ couplings, provides enhanced resolution for the Cα resonance, and yields amino-acid-species-specific peak shapes that arise from residual J couplings [ 39 ]. By this approach, near-complete backbone resonance assignment of a 42 kDa protein was achieved using a single HNCA, the most sensitive of the triple resonance experiments with sequential information.

Multidimensional NMR spectroscopy at ultra-high magnetic fields (> 1GHz) requires radiofrequency (rf) pulses capable of covering the increased spectral bandwidths, and at these field strengths, the commonly used rectangular pulses reach their limits. Thus, Ramsey-type cooperative pulses were introduced to achieve an excitation bandwidth of 100 kHz with a 20 kHz maximum rf field, which is a more than three- fold improvement when compared to excitation by rectangular pulses [ 40 ]. A novel low-power, broadband heteronuclear decoupling pulse designed using optimal control theory was also developed that surmounts shortcomings of composite pulse decoupling and adiabatic decoupling [ 41 ]. Optimal control theory has also facilitated the development of sophisticated homonuclear decoupling pulses for use in the acquisition of high-resolution 13 Cα spectra. Use of these pulses enables selective inclusion of the one-bond 13 Cα- 13 Cβ scalar coupling, which helps to identify residue types in an HNCA spectrum [ 42 ].

Direct detection of low γ nuclei.

Although 15 N and 13 C have low intrinsic sensitivity as measured by peak volume, slow transverse relaxation due to the low γ renders peaks both narrow and intense, giving direct detection of these nuclei competitive sensitivity. These types of direct-detection experiments are in fact the method of choice for intrinsically disordered proteins (IDPs) where the traditional direct dimension of 1 H/ 15 N spin pairs has little resolving power due to inherently reduced dispersion in chemical shifts [ 43 ]. There are a wide range of applications for 13 C-detected experiments including assignment strategies [ 44 – 46 ], which have been extensively utilized in the analysis of IDPs as well as metal-containing proteins. It should be noted that relaxation of 13 Cα nuclei is significantly reduced by deuteration and favors spectroscopy with alpha carbons for higher molecular weights over 13 CO detection [ 47 – 49 ]. The main drawback in detecting 13 Cα nuclei is the 13 CO and 13 Cβ coupling, which can be managed by double-IPAP selection [ 45 ], or alternating 13 C- 12 C labeling [ 47 ].

Beside 13 C direct-detection experiments, 15 N direct-detection experiments with TROSY selection represent a promising alternative for large proteins that cannot be deuterated, such as those expressed in insect cells. Since 15 N transverse relaxation is least affected by dipolar interactions with nearby protons, direct nitrogen detection may also be advantageous for the study of larger complexes [ 50 ].

Fast NMR methods

NMR studies of complex protein systems require resolution achievable only through time-consuming multidimensional NMR experiments. The experimental time increases nonlinearly with the number and lengths of the indirect dimensions. Two major factors contributing to this increase in acquisition time are the long interscan delays (seconds) and the nature of acquiring multidimensional experiments through a series of modulated FIDs ( Figure 2 ). By taking these areas of inefficiency into account, a variety of techniques have been developed to save time in data acquisition for sampling-limited systems. These techniques include SOFAST/BEST experiments [ 51 , 52 ], ultrafast experiment [ 53 ], non-uniform sampling in indirect dimension(s) (see reviews [ 54 – 56 ], etc.), covariance NMR [ 36 ], acquisition through multiple receivers [ 57 ], reduced dimensionality and projection spectroscopy [ 58 – 60 ], and Hadamard encoding [ 61 ].

Illustrating fast data acquisition for NMR using non-uniform sparse sampling (NUS) and reducing interscan delay (SOFAST/BEST).

The SOFAST/BEST experiment shortens the long interscan delay by returning 1 H magnetization back to the z-axis between scans and applying longitudinal optimization. In longitudinal optimization, a subset of protons is band-selectively excited while the remaining protons serve as a sink enabling faster relaxation of the spins of interest. Dipolar-coupling-mediated NOEs between protons means that this z-axis population increases the longitudinal relaxation rate, and ultimately allows faster recycling. This approach, however, requires a population of aliphatic protons to serve as the relaxation sink and is, thus, less suitable for perdeuterated proteins. The need for a series of modulated FIDs in multidimensional experiments can also be minimized by reducing the dimensionality of indirect dimensions with G-matrix Fourier transform (GFT) spectroscopy [ 62 ] as well as APSY [ 63 ].

Non-uniform sampling (NUS), in which only a subset of increments is acquired in the indirect dimensions, is an alternative way to achieve fast acquisition. NUS data subsequently employs non-Fourier techniques for reconstructing the frequency domain spectra. These methods allow the acquisition of 3-and 4-dimensional experiments at high resolution that would otherwise be impossible to record in a reasonable period of time [ 64 , 65 ]. There are several strategies in reconstituting the sparsely obtained data, which differ in their demand on computational resources. It is now common practice to collect 10-20% of the full data grid for 3D experiments and 1-5% for 4D experiments without significantly eliminating spectral content. It should be noted that the current reconstruction methods are sufficiently linear so that NUS can be used in structure determination as well as in relaxation experiments. NUS can also contribute to optimizing the sensitivity of experiments within a fixed experimental time through an optimally weighted random sampling of decaying signals according to a Poisson distribution of gap lengths [ 66 , 67 ]. The sensitivity gains from NUS have been previously estimated using analytical procedures [ 68 , 69 ]. It is important to point out that NUS and SOFAST/BEST experiments can be used in combination, thus increasing the overall time efficiency of the resulting NMR experiment [ 69 , 70 ].

Random Quadrature Detection (RQD) is another method to speed up the acquisition of multidimensional NMR experiments. In higher dimension experiments, every grid point in the indirect dimension needs to be recorded twice, in quadrature, to faithfully encode the frequencies. Hoch and coworkers were the first to show that it is sufficient to randomly record only one of the two phases in quadrature detection for each point in the Nyquist grid of the indirect dimension [ 71 ]. Applying this method of random phase detection alone would provide a factor of 2 3 = 8 in time savings for a 4D experiment. Recent work has shown that RQD can successfully be combined with NUS for 4D experiments and can also be applied for gradient- selection experiments [ 72 ]. RQD adds another dimension to NUS. Combining RQD and NUS provides greater flexibility and coverage while sampling the indirect Nyquist grid, as compared to using NUS alone.

Advances in instrumentation and probe design; new detection schemes

The above-mentioned advances in NMR experiment and pulse design have been supported by innovations in hardware design. High-field magnets above 1 GHz are now becoming commercially available and promise improved resolution and sensitivity. Helium recycling magnets and nitrogen-cooled cryoprobes have significantly reduced the demand for helium, which reduces NMR running costs stemming from the increasing price of this noble gas, thereby facilitating the acquisition of long experiments without interruption by cryogen fills. It should be noted that the recycling systems currently available produce vibrations that introduce T1 noise, something that reduces spectral quality, and which will need to be addressed in future systems through better hardware design. New state-of-the-art NMR consoles and probes generate higher power and more stable pulses. Using consoles with multiple receivers, several nuclei can be detected simultaneously, which enables the acquisition of different NMR experiments in parallel, thus maximizing the information obtained within a given experimental period. High rf power applied to samples generates heat, especially during experiments. The load from decoupling pulses changes as a function of evolution time period, and this demands better control in sample absolute temperature across different experiments and instruments. To cope with this, the concept of a “T-lock” was introduced, which automatically maintains the sample at a constant temperature by locking the temperature-sensitive chemical shift of a reference spin through an electronic feedback loop [ 73 ].

The use of cryogenic probes where the receiver coils and preamplifiers are cooled to liquid helium (or liquid nitrogen) temperature greatly reduces thermal noise in the NMR spectra and is almost indispensable for biological samples with limited solubility. While the sensitivity of cryogenic probes suffers when samples are in high salt buffers, this intolerance can be partially compensated using a probe design that fits rectangular salt tolerant tubes [ 74 ] or through the use of specially designed sample tubes containing a cavity within magnetic susceptibility-matched glass [ 75 ]. There are also several variations of cryogenic probes that provide better sensitivity for 15 N/ 13 C detection by positioning the coils closer to the sample. The newer cryogenic probes also have longer detection coils, which provide additional sensitivity. It should be noted that cryogenic probes are better at dissipating heat and are suitable for heavy-duty pulses, which is particularly useful in experiments that use CMPG blocks, such as R 2 , R 1ρ , relaxation dispersion experiments, etc.

Emerging NMR methods for studies of protein structure and dynamics

The basic solution NMR strategy for protein structure determination has not changed significantly since it was established; however, combining NMR-based approaches with computational strategies promises to reduce the quantity of experimental data required for structure determination [ 76 – 79 ]. The resolution-adapted structural recombination (RASREC)-Rosetta protocol, which is an improved version of CS-ROSETTA, has successfully used sparse NOE data to determine the structures (median Cα RMSD <2 Å) of 11 proteins with sizes up to 40 kDa [ 77 ]. In addition, state-of-the-art tools, such as FLYA, UNIO, 4D-CHAINS, and AUDANA, allow automated simultaneous resonance assignment and structure determination [ 80 – 83 ], and have the potential to significantly reduce the effort required to determine high-resolution NMR structures.

The versatility of NMR as a technique has enabled hybrid approaches that improve the accuracy of NMR-derived structures by combining chemical shift data with additional structural information, such as residual dipolar coupling (RDC), paramagnetic relaxation enhancement (PRE), and/or pseudo-contact chemical shift (PCS) data [ 84 – 87 ]. One such hybrid approach improves the quality of structures by utilizing solvent paramagnetic relaxation enhancements by a soluble paramagnetic compound (sPREs) as a measure of to-surface distances [ 88 ]. PRE and PCS data have also been used to characterize transient encounter complexes [ 89 , 90 ], alternate binding modes [ 91 ], changes in relative domain orientations [ 92 – 95 ], long-range order in intrinsically disordered proteins [ 96 ], protein-ligand interactions [ 97 , 98 ], and protein translation along the DNA helix [ 99 ].

Experimental strategies to dissect protein dynamics and their relationship to biological function are still being actively developed, and some are already capable of assessing very high molecular weight systems ( Figure 3 ). A landmark strategy that has been used extensively is the relaxation dispersion (RD) experiment. The beauty of this experiment is its ability to detect very lowly populated states (<1%), to quantify their populations, and to measure their chemical shifts and state-exchange rates. Previously, the method was limited to a narrow timescale window (~ sub ms). High-power RD techniques have been enabled by the larger power allowance of recently-developed cryogenically cooled probes, which now allow coverage of a wider time window up to several μs [ 100 ]. High-power RD measurements under super-cooled temperatures can also be used to obtain the exchange-rate, temperature dependence and allow access to sub-μs dynamics at physiological temperatures by the use of an Arrhenius extrapolation [ 101 ]. Temperature and magnetic field dependent changes in relaxation rates can also be used to measure local activation energies of dynamic processes along the chain in IDPs [ 102 ].

Time scale of molecular dynamics that is accessible for each experimental design in studying macromolecules with molecular weights ranging from 10 kDa to > 100 kDa.

The absence of small chemical shift differences between alternative states often prevents detection of conformational exchange; in these cases, analysis of multi-quantum (MQ) transverse relaxation rates can be used to obtain significantly larger dispersion profiles for methyl groups [ 103 ], as well as for main chain amide groups [ 104 ]. Field-dependent MQ relaxation analyses for methyl groups was developed to dissect the slow conformational equilibrium found in higher molecular weight systems [ 105 , 106 ]. Although their timescale window partially overlaps with that of RD experiments, slower timescales can also be covered by a variety of CEST experiments [ 107 ].

For faster timescales, methyl relaxation violated coherence transfer experiments have been used to quantitatively analyze side-chain dynamics [ 108 ]. This strategy has been used to quantify changes in the fast dynamics of methyl-bearing amino acids, which can be used empirically as an “entropy meter’ for estimating changes in conformational entropy in multiple-protein interaction systems [ 109 , 110 ]. Relaxation violated coherence transfer has also been expanded to 19 F to monitor the fast dynamics of the CF 3 moiety [ 111 ].

Recently, two-field NMR spectroscopy has been proposed to study dynamics more quantitatively. This approach has the sensitivity advantage of increased magnetic fields and limits the disadvantage of line broadening by shuttling the sample between high and low fields in a single NMR experiment [ 112 ].

Conclusion and future perspectives

The versatility of solution NMR spectroscopy opens a plethora of experimental approaches for characterizing protein structure, dynamics, and interactions. Numerous techniques have co-evolved with the introduction of new labeling methods, better hardware engineering, such as the development of high field magnets, optimized spectrometer electronics, and higher sensitivity probes. NMR also provides greater freedom in the selection of experimental conditions that more closely mimic physiological situations. This has been utilized in particular by in-cell NMR, which permits the analysis of structures and even potentially the dynamic behavior of proteins inside living cells [ 113 – 119 ]. Varying the temperature and pressure conditions in an experiment allows assessment of the thermodynamic characteristics of a protein [ 120 – 122 ], as otherwise undetectable high-energy states are stabilized. The unique insight into structure and dynamics provided by NMR can be integrated with data generated from other structural methods [ 123 – 126 ], such as X-ray crystallography, small-angle X-ray scattering (SAXS), and electron cryomicroscopy, to create an integrated view of proteins at a molecular level, which will be essential to understand how they function.

• NMR yields quantitative data on the dynamics of solution-state protein structures.
• NMR’s impact is enhanced by continuous innovation in assignment techniques.
• Improvements in hardware and experimental design have extended the reach of NMR.
• NMR provides access to lowly-populated invisible states.
• nformation provided by NMR is unique and complements other biophysical techniques.

Acknowledgements:

We thank Kendra E. Leigh for helpful discussions during the preparation of this manuscript.

This work was supported by NIH grants GM047467, GM129026 and AI037581 to G. W., by the Claudia Adams Barr Program for Innovative Cancer Research to HA, and by JSPS KAKENHI Grant Number JP18K19415 to KT.

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Solution NMR backbone assignments of the N-terminal Zα-linker-Zβ segment from Homo sapiens ADAR1p150

Affiliations.

• 1 Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
• 2 Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
• 3 Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA. [email protected].
• 4 Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA. [email protected].
• PMID: 33742389
• PMCID: PMC9199369
• DOI: 10.1007/s12104-021-10017-8

Adenosine-to-inosine (A-to-I) editing of a subset of RNAs in a eukaryotic cell is required in order to avoid triggering the innate immune system. Editing is carried out by ADAR1, which exists as short (p110) and long (p150) isoforms. ADAR1p150 is mostly cytoplasmic, possesses a Z-RNA binding domain (Zα), and is only expressed during the innate immune response. A structurally homologous domain to Zα, the Zβ domain, is separated by a long linker from Zα on the N-terminus of ADAR1 but its function remains unknown. Zβ does not bind to RNA in isolation, yet the binding kinetics of the segment encompassing Zα, Zβ and the 95-residue linker between the two domains (Zα-Zβ) are markedly different compared to Zα alone. Here we present the solution NMR backbone assignment of Zα-Zβ from H. Sapiens ADAR1. The predicted secondary structure of Zα-Zβ based on chemical shifts is in agreement with previously determined structures of Zα and Zβ in isolation, and indicates that the linker is intrinsically disordered. Comparison of the chemical shifts between the individual Zα and Zβ domains to the full Zα-Zβ construct suggests that Zβ may interact with the linker, the function of which is currently unknown.

Keywords: ADAR1; Backbone chemical shift assignment; Editing; Protein domains; Protein structure and dynamics; Z-RNA.

© 2021. The Author(s), under exclusive licence to Springer Nature B.V.

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Conflict of interest statement

Conflict of interest

The authors declare they have no conflict of interest.

Figure 1.. The Zα and Zβ domains…

Figure 1.. The Zα and Zβ domains of ADAR1p150.

(a) Domain organization of ADAR1: Zα…

Figure 2.. Assigned 1 H- 15 N…

Figure 2.. Assigned 1 H- 15 N HSQC spectra of Zα, Zβ, and Zα-Zβ.

Shown are the 1…

Figure 3.. Secondary Structure Propensity Score of…

Figure 3.. Secondary Structure Propensity Score of Zα-Zβ of ADAR1.

The Secondary Structure Propensity score…

Figure 4.. Chemical shift perturbations between Zα…

Figure 4.. Chemical shift perturbations between Zα and Zβ in isolation versus Zα-Zβ.

(a) Overlay…

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and Zahn, Michael and Burmann, Irena Matecko and Bibow, Stefan and Hiller, Sebastian. --> Journal of the American Chemical Society, 140 (36). pp. 11252-11260. --> Full text not available from this repository. Official URL: Downloads: Faculties and Departments: 05 Faculty of Science > Departement Biozentrum > Structural Biology & Biophysics > Structural Biology (Hiller) UniBasel Contributors: and Item Type: Article, refereed Article Subtype: Research Article Publisher: American Chemical Society ISSN: 0002-7863 e-ISSN: 1520-5126 Note: Publication type according to Uni Basel Research Database: Journal article Identification Number: Last Modified: 01 Mar 2023 10:53 Deposited On: 10 Feb 2020 15:28 Repository Staff Only: item control page Woonghee Lee, Arash Bahrami, Hesam Dashti, Hamid R. Eghbalnia, Marco Tonelli, William M. Westler, John L. Markley. (2019) Journal of Biomolecular NMR. 73(5): 213-222. [click to read] This is the I-PINE web server. Please let us know any unexpected behavior from this server . You can also use PINE from here . I-PINE accepts, as input, the sequence of the protein plus peak lists (or spin systems) from a variety of NMR experiments and offers automated backbone and sidechain assignments, detection and automated correction of potential referencing problems or inconsistent assignments, secondary structure determination, 3D structure prediction, cysteine oxidation, proline isomerization and hydrophobic core detection. Most jobs take only a few minutes. The results will be accessible from provided URL and job identification number and also sent to the user via email (optional). If you do not receive any email including spam folder longer than a few hours, please contact NMRFAM . I-PINE supports more types of input NMR data than its precursor PINE including from three- and four-dimensional NOE experiments, achieves more accurate and complete chemical shift assignments, and supports more comprehensive visualization of chemical shift based analysis of protein structure and dynamics. Users of the I-PINE web server can not only submit unassigned peak lists or spin systems but also sets of previously assigned chemical shifts as inputs. The output of I-PINE is available in formats used as input by other software packages. A user can choose one of three interfaces when submitting a job to the I-PINE web server ( http://i-pine.nmrfam.wisc.edu ): a CLI (command-line user interface) with a versatile python script pyIPINE.py , a GUI (graphical user interface) with the PINE-SPARKY.2 plugin of the popular NMR analysis software package NMRFAM-SPARKY , or a WUI (web-based user interface). A single submission to I-PINE automatically achieves what previously required multiple tedious discrete tasks. Submitted data are kept confidential and are not viewable by others. Complete output information is available in a custom-built web page, which is accessible from the job identification number. Amino acid sequences (1-letter / 3-letter) Peak lists in (NMRFAM/UCSF)-SPARKY / XEASY / NMRView / NMRDraw / PINE formats Spin systems Pre-assignments Selective labels Atomic coordinates Empty .prot to get XEASY results When you look at an NMR spectrum, do you see only a bunch of disordered lines or peaks? Then you have come to the right place. This site was established to provide people interested in NMR with a library of NMR spectroscopy problems. Interpretation of spectra is a skill that requires pattern recognition and/or practice to master the chaos. This site provides one dimensional spectra of different nuclei, COSY, HSQC, HMBC and some less common spectra of various compounds for you to interpret, together with worked solutions. Hopefully, these problems will provide a useful resource to help you better understand NMR spectral interpretation. A series of about 50 problems is available in printable form. The print version will not be developed further. The PDF documents are still available (german only). Get them here: The step-by-step approach works nearly perfectly on the desktop and most tablets. On cellular phones, PowerPoint documents are sometimes displayed incorrectly. There is a workaround, but it is unfortunately much too complicated to be practical. As an alternative, all documents can be saved locally. Feel free to follow the download links. A free PowerPoint viewer is available in both the iOS and Android AppStores. As a bonus, there would be no need for a permanent internet connection. Of course, this offline method also works with desktop computers. The author is always grateful for criticism, suggestions, references to errors and information about the design via email: Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. View all journals Explore content About the journal Publish with us Sign up for alerts Published: 26 May 2023 Solution-state nuclear magnetic resonance spectroscopy of crystalline cellulosic materials using a direct dissolution ionic liquid electrolyte Lukas Fliri   ORCID: orcid.org/0000-0001-5555-8659 1 , Katja Heise 1 , Tetyana Koso   ORCID: orcid.org/0000-0002-0429-3205 2 , Aleksandar R. Todorov   ORCID: orcid.org/0000-0001-9147-4874 2 , Daniel Rico del Cerro 2 , Sami Hietala 2 , Juha Fiskari 3 , Ilkka Kilpeläinen 2 , Michael Hummel 1 & Alistair W. T. King   ORCID: orcid.org/0000-0003-3142-9259 2 , 4   Nature Protocols volume  18 ,  pages 2084–2123 ( 2023 ) Cite this article 1932 Accesses 15 Citations 5 Altmetric Metrics details Solution-state NMR Structure elucidation Synthesis and processing Owing to its high sustainable production capacity, cellulose represents a valuable feedstock for the development of more sustainable alternatives to currently used fossil fuel-based materials. Chemical analysis of cellulose remains challenging, and analytical techniques have not advanced as fast as the development of the proposed materials science applications. Crystalline cellulosic materials are insoluble in most solvents, which restricts direct analytical techniques to lower-resolution solid-state spectroscopy, destructive indirect procedures or to ‘old-school’ derivatization protocols. While investigating their use for biomass valorization, tetralkylphosphonium ionic liquids (ILs) exhibited advantageous properties for direct solution-state nuclear magnetic resonance (NMR) analysis of crystalline cellulose. After screening and optimization, the IL tetra- n -butylphosphonium acetate [P 4444 ][OAc], diluted with dimethyl sulfoxide- d 6 , was found to be the most promising partly deuterated solvent system for high-resolution solution-state NMR. The solvent system has been used for the measurement of both 1D and 2D experiments for a wide substrate scope, with excellent spectral quality and signal-to-noise, all with modest collection times. The procedure initially describes the scalable syntheses of an IL, in 24–72 h, of sufficient purity, yielding a stock electrolyte solution. The dissolution of cellulosic materials and preparation of NMR samples is presented, with pretreatment, concentration and dissolution time recommendations for different sample types. Also included is a set of recommended 1D and 2D NMR experiments with parameters optimized for an in-depth structural characterization of cellulosic materials. The time required for full characterization varies between a few hours and several days. This is a preview of subscription content, access via your institution Access options Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription 24,99 € / 30 days cancel any time Subscribe to this journal Receive 12 print issues and online access 251,40 € per year only 20,95 € per issue Buy this article Purchase on SpringerLink Instant access to full article PDF Prices may be subject to local taxes which are calculated during checkout Similar content being viewed by others Optimizing chemistry at the surface of prodrug-loaded cellulose nanofibrils with MAS-DNP Solid-state 31 P NMR mapping of active centers and relevant spatial correlations in solid acid catalysts 3D sub-nanometer analysis of glucose in an aqueous solution by cryo-atom probe tomography Data availability. The data related to the results shown in this protocol are included in this document and in the supporting primary research papers 25 , 26 . MacLeod, M., Arp, H. P. 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A.W.T.K. gratefully acknowledges funding by the Academy of Finland (project no. 311255, ‘WTF-Click-Nano’). K.H. gratefully acknowledges the postdoctoral grant received from the Academy of Finland (project no. 333905). Author information Authors and affiliations. Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland Lukas Fliri, Katja Heise & Michael Hummel Materials Chemistry Division, Department of Chemistry, University of Helsinki, Helsinki, Finland Tetyana Koso, Aleksandar R. Todorov, Daniel Rico del Cerro, Sami Hietala, Ilkka Kilpeläinen & Alistair W. T. King Fibre Science and Communication Network (FSCN), Mid Sweden University, Sundsvall, Sweden Juha Fiskari VTT Technical Research Centre of Finland Ltd, Espoo, Finland Alistair W. T. King You can also search for this author in PubMed   Google Scholar Contributions A.W.T.K and T.K., designed and developed the workflows presented in this protocol. L.F., K.H. and M.H. implemented the protocol in a more technology-orientated environment and addressed the occurring translational barriers. L.F. and A.R.T. contributed optimized metathesis schemes for the ionic liquid starting from commercial sources. S.H. provided solid-state NMR spectra and expertise. D.R.d.C. and J.F. provided samples, discussion and experimentation regarding the adaptation of the protocol to other substrates, as presented in the ‘Anticipated results’ section. L.F. and A.W.T.K. drafted, reviewed and edited the manuscript with significant input from K.H., T.K. and M.H. I.K. provided funding for the basic research (initial articles) and advice on presentation of the subject matter. All authors read and agreed on the final version of the manuscript. Corresponding authors Correspondence to Michael Hummel or Alistair W. T. King . Ethics declarations Competing interests. The authors declare no competing financial interests. Peer review Peer review information. Nature Protocols thanks Jun Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Additional information Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Related links Key references using this protocol King, A. W. T. et al. Biomacromolecules 19 , 2708–2720 (2018): https://doi.org/10.1021/acs.biomac.8b00295 Koso, T. et al. Cellulose 27 , 7929–7953 (2020): https://doi.org/10.1007/s10570-020-03317-0 Extended data Extended data fig. 1 multiplicity-edited hsqc of acetylated mcc.. Multiplicity-edited HSQC of acetylated MCC showing significant peak superposition ([P 4444 ][OAc]:DMSO- d 6 1:4 wt%, 65 °C, 5 wt%; 600 MHz 1 H frequency. For multiplicity edited HSQC green = CH, blue = CH 2 ). Extended Data Fig. 2 Effect of diffusing-editing on the 1 H 1D data for surface acetylated MCC. Comparison of the quantitative 1 H spectrum ( a ) with the diffusion edited 1 H spectrum ( b ) allows to quickly assess the introduction of functionalities of species exhibiting resonances in the heavily crowded IL spectral region ([P 4444 ][OAc]:DMSO- d 6 1:4 wt%, 65 °C, 5 wt%; 600 MHz 1 H frequency). Extended Data Fig. 3 Utility of the 2D HSQC-TOCSY experiment for further peak assignment of cellulose derivatives. ( a ) HSQC-TOCSY in the full view allows to further assign the AGA moiety over interactions of the C1 signal with peaks in the crowded areas., ( b ) HSQC-TOCSY with zoom into the C2–C5 region shows that full characterisation of the spin system can be possible. However, owing to strong superpositions with the AGU, NRE and RE moieties the peak assignments can become tedious. Spectra shown with diffusion-edited 1 H trace (top trace) and 13 C trace (left trace). AGU = anhydroglucose unit; AGA = anhydroglucopyranosiduronic acid unit; NRE = non-reducing end; RE = reducing end. In the spectra HSQC correlations are shown in green (CH) and blue (CH 2 ) and TOCSY correlations are shown in gray. Extended Data Fig. 4 Diffusion-edited 1 H spectra of food insects. Diffusion-edited 1 H spectra ([P 4444 ][OAc]:DMSO- d 6 1:4 wt%, 65 °C, 5 wt%, 600 MHz) for fruit flies, damselfly tail and whole food crickets, after Wiley milling and dissolution. Supplementary information Supplementary information. Supplementary Figs. 1–12 and Note. Rights and permissions Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Reprints and permissions About this article Cite this article. Fliri, L., Heise, K., Koso, T. et al. Solution-state nuclear magnetic resonance spectroscopy of crystalline cellulosic materials using a direct dissolution ionic liquid electrolyte. Nat Protoc 18 , 2084–2123 (2023). https://doi.org/10.1038/s41596-023-00832-9 Download citation Received : 05 April 2022 Accepted : 17 March 2023 Published : 26 May 2023 Issue Date : July 2023 DOI : https://doi.org/10.1038/s41596-023-00832-9 Share this article Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative This article is cited by Complete 1h and 13c nmr assignment of cellulose oligomer in licl/dmso. Atsushi Sasaki Tatsuhiro Konishi Ryosuke Kusumi Cellulose (2024) Insights into the borohydride reduction of dialdehyde cellulose: the dilemma of competing reduction and β-elimination reactions Jonas Simon Lukas Fliri Antje Potthast Cellulose (2023) By submitting a comment you agree to abide by our Terms and Community Guidelines . If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. Quick links Explore articles by subject Guide to authors Editorial policies Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. Biomolecular NMR Assignments Provides an avenue for depositing these data into a public database at BioMagResBank. Assignment Notes are published in biannual editions in June and December. No page charges or fees for online color images. Optional color images in print and open access publication fees apply. Christina Redfield Latest issue Volume 18, Issue 1 Latest articles Solution nmr backbone assignment of the n-terminal tandem zα1-zα2 domains of z-dna binding protein 1. Lily G. Beck Jeffrey B. Krall Beat Vögeli NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans -editing enzyme Antonia D. Duran Eric M. Danhart Mark P. Foster Solution NMR backbone resonance assignment of the full-length resistance-related calcium-binding protein Sorcin Kathleen Joyce Carillo Chemical shift assignments of the α-actinin C-terminal EF-hand domain bound to a cytosolic C0 domain of GluN1 (residues 841–865) from the NMDA receptor Johannes W. Hell James B. 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Physical Chemistry Chemical Physics Understanding the motional dynamics of the ammonium ion in the mechanism of multiferroicity of cr(v) peroxychromates: a 1h nmr study. Cr(5+)-based peroxychromates, M3Cr(O2)4, with M = NH4 or a mixed NH4-alkali metal are a new class of multiferroics for potential use in molecular memory devices, with the NH4+ being a key element, but the underlying chemical mechanism is not fully understood. The NH4+ ion occupies two different sites but their specific roles are not known. We thus performed detailed 1H NMR spin-relaxation (T1) measurements on (NH4)3Cr(O2)4 over a wide temperature range (120–300 K) to probe the displacive as well as hindered rotational dynamics of the NH4+ ions with the view of understanding their specific roles in the phase transitions. The NH4+ dynamics is seen to consist of at least three different processes with different activation energies. The sharp jump in the T1 at around 250 K is assigned to the change in the displacive motion at one of the two sites, while a kink around 140 K is ascribed to motional slowing at the second site. Interestingly, the slowing down starts around 250 K, well above the structural phase transition at 140 K. Taken together, these results provide a clue to the role of the site and symmetry of the NH4+ ion in the mechanism of solid-solid phase transitions. Article information Download citation, permissions. Understanding the Motional Dynamics of the Ammonium Ion in the Mechanism of Multiferroicity of Cr(V) Peroxychromates: A 1H NMR Study R. samantaray, D. Acharya, A. Priyadarshini, R. Sahu, T. Besara and N. Dalal, Phys. Chem. Chem. Phys. , 2024, Accepted Manuscript , DOI: 10.1039/D4CP02769H To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page . If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given. If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page . Read more about how to correctly acknowledge RSC content . Social activity Search articles by author. This article has not yet been cited. Advertisements Protein NMR A practical guide, introduction. Most books on Protein NMR focus on theoretical aspects and pulse sequences with only little space devoted to resonance assignment and structure calculations. At the same time many software manuals provide detailed information on how to use the software, but assume prior knowledge of the concepts of assignment and structure calculation. This has produced a gap in this area which these webpages aim to bridge by describing the concepts of assignment in detail with the help of many illustrations. Much space and discussion is devoted to practical aspects. The implementation of protein NMR assignment is described using the program CCPNmr Analysis . This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has the advantage (a) that it feeds directly into the CCPN Format Converter thus simplifying the import from and export to other programs, and (b) that as more and more NMR-related programs adopt the CCPN Data Model it is likely to take on a key role in NMR data management – in a similar way to CCP4 for protein X-ray crystallography. CCPNmr Analysis is already one of the best assignment programs available while still being developed and provides excellent support via the CCPN Mailing List (a manual is also available). (Although I now work for the CCPN group, these webpages and my recommendation to use this program far predate this!) Webpages include: description of several resonance assignment strategies simple descriptions and discussions of many multidimensional NMR experiments commonly used in protein NMR basic usage of CCPNmr Analysis (versions 1 and 2 ) how to make publication quality figures using CCPNmr Analysis advice for using CCPNmr Analysis with solid-state MAS NMR data tutorial on protein assignment using solid-state MAS NMR data description of isotopic labelling strategies commonly used in protein NMR links to a large number of protein NMR software packages suggested literature for further reading links to other useful NMR webpages 349 IMAGES SOLUTION: Nmr interpretation guide SOLUTION: 680002 heteronuclear nmr assignment NMR Assignments Solved 1H NMR and 13C NMR Assignment (20 pts) Assign the 1H Solution NMR assignments and structure for the dimeric kinesin neck domain (PDF) Solution NMR backbone assignments of the N-terminal Zα-linker-Zβ VIDEO WileyPLUS: Find Students & Assignments and Edit Student Scores UP Board class 10th Science Adivasi Hair oil honest review NMR Spectroscopy principle NPTEL Swayam Advanced NMR Techniques in Solution and Solid-State Week-1 Assignment Answers| NPTEL Part I. NMR of Paramagnetic substances/complexes COMMENTS Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins The basic solution NMR strategy for protein structure determination has not changed significantly since it was established; ... Marion D: CH 3-specific NMR assignment of alanine, isoleucine, leucine and valine methyl groups in high molecular weight proteins using a single sample. J Biomol NMR 2015, 63:389-402. [Google Scholar] 35. Decoding Atomic Addresses: Solution NMR Resonance Assignment of The goal of this chapter is to provide a comprehensive review of both the currently available experiments and novel methodologies employed for protein resonance assignments in solution NMR. This resource is intended for the biomolecular NMR community, and it assumes that the reader possesses a fundamental understanding of protein NMR. Robust automated backbone triple resonance NMR assignments of ... Automation of the assignment process often remains a bottleneck in the exploitation of solution NMR spectroscopy for the study of protein structure-dynamics-function relationships. Tutorials Solution NMR. Backbone Assignment Tutorial. Learn how to do the semi-automated backbone assignment of a protein using our dedicated tools. DOWNLOAD PDF. ... Learn how to AnalysisAssign to make manual assignments in solid-state NMR spectra, and assign a small protein using [1,3]-13 C and [2]-13 C labelled glycerol samples. Download PDF. Download ... Solution NMR: A powerful tool for structural and functional studies of Solution NMR, a technique limited by a protein's size, is potentially the best tool to study protein dynamics along with its structure. ... (NOE) provides the main source of geometric information utilized for structure determination by NMR and requires the assignment of each proton resonance in a spectrum of the target molecule. Solution NMR resonance assignment strategies for β‐barrel membrane Facilitating loop assignments: temperature. All solution NMR β‐barrel membrane protein structures determined to date have contained relatively short extracellular loops [the longest loop that of OprH containing 29 amino acid; Fig. 1(A)]; thus, spectral overlap and line broadening from loop resonances did not hinder the assignment of the ... Sequence-Specific Solution NMR Assignments of the β-Barrel Insertase Here, we describe ∼70% complete sequence-specific NMR resonance assignments of the transmembrane region of the BamA β-barrel in detergent micelles. On the basis of the assignments, NMR spectra show that the BamA barrel populates a conformational ensemble in slow exchange equilibrium, both in detergent micelles and lipid bilayer nanodiscs. Solution NMR Double Resonance Backbone Assignment. Neighbouring Residues. Directionality. Matching Peaks. Lining Up Strips. Sequence-Specific Assignment. Hints and Tips. Spectrum Descriptions. 1H-15N HSQC. Assignment Practice Initially a more manual method will be described, as this makes it easier to understand the process of assignment for those who are new to protein NMR assignment. This is followed by an outline of the slightly more automated method using the Link Sequential Spin Systems function within CCPNmr Analysis. The assignment is described using Analysis ... Solution NMR backbone assignments of the N-terminal Zα-linker-Zβ Here we present the solution NMR backbone assignment of Zα-Zβ from H. Sapiens ADAR1. The predicted secondary structure of Zα-Zβ based on chemical shifts is in agreement with previously determined structures of Zα and Zβ in isolation, and indicates that the linker is intrinsically disordered. Comparison of the chemical shifts between the ... Rapid protein assignments and structures from raw NMR spectra with the Benchmark dataset. One of the major obstacles for developing deep learning solutions for protein NMR spectroscopy is the lack of a large-scale standardized benchmark dataset of protein NMR spectra. Sequence-Specific Solution NMR Assignments of the beta-Barrel Insertase Hartmann, Jean-Baptiste and Zahn, Michael and Burmann, Irena Matecko and Bibow, Stefan and Hiller, Sebastian. (2018) Sequence-Specific Solution NMR Assignments of the beta-Barrel Insertase BamA to Monitor Its Conformational Ensemble at the Atomic Level. Journal of the American Chemical Society, 140 (36). pp. 11252-11260. Full text not available from this repository. Assignment Theory Large Proteins. Large proteins give worse NMR spectra, because they tumble more slowly. For this reason the CBCANNH and CBCA (CO)NNH spectra of larger proteins (> 150 residues) are often not of sufficient quality to be able to carry out a full assignment. In this case a good option is the use of HNCA, HN (CO)CA, HNCO and HN (CA)CO spectra. I-PINE web server I-PINE accepts, as input, the sequence of the protein plus peak lists (or spin systems) from a variety of NMR experiments and offers automated backbone and sidechain assignments, detection and automated correction of potential referencing problems or inconsistent assignments, secondary structure determination, 3D structure prediction, cysteine oxidation, proline isomerization and hydrophobic ... NMR exercises and their solutions This site provides one dimensional spectra of different nuclei, COSY, HSQC, HMBC and some less common spectra of various compounds for you to interpret, together with worked solutions. Hopefully, these problems will provide a useful resource to help you better understand NMR spectral interpretation. A series of about 50 problems is available in ... Solution-state nuclear magnetic resonance spectroscopy of ... In the case of peak overlap, qualitative assignments can still be performed with the diffusion-edited 1 H NMR experiment and the multiple bond-correlated 2D NMR experiments (Box 1). However, these ... Automatic Assignment AUTOASSIGN. AutoAssign is an artificial intelligence package for automating the analysis of backbone resonance assignments using triple-resonance NMR spectra of proteins. The new AutoAssign distribution automates the assignments of HN, NH, CO, CA, CB, HA, and HB resonances in non-, partially-, and fully-deuterated samples. Home Biomolecular NMR Assignments is a dedicated forum for publishing sequence-specific resonance assignments for proteins and nucleic acids. Provides an avenue for depositing these data into a public database at BioMagResBank. Assignment Notes are published in biannual editions in June and December. No page charges or fees for online color images. Protein NMR assignment by isotope pattern recognition A further recent innovation is to make NMR signal shapes differ between amino acids by supplying isotopically patterned pyruvate during protein expression in genetically engineered bacteria ().Because biosynthesis paths differ for the 20 natural amino acids (), so do the isotope patterns in their NMR spectra.This radically simplifies signal assignment but still requires a human to look at the ... CHEMICAL PHYSICS copyright © 2024 the Protein NMR assignment by isotope Protein NMR assignment by isotope pattern recognition Uluk Rasulov1, Harrison K. Wang2,3, Thibault Viennet 4, Maxim A. Droemer5, ... we offer a solution to this problem. We pro-pose polyadic decompositions to store millions of simulated three-dimensional NMR spectra, on-the- fly generation of artifacts during training, a probabilistic way to ... Triple Resonance Backbone Assignment Triple Resonance Backbone Assignment. Standard triple resonance backbone assignment of proteins is based on the CBCANNH and CBCA (CO)NNH spectra. The idea is that the CBCANNH correlates each NH group with the Cα and Cβ chemical shifts of its own residue (strongly) and of the residue preceding (weakly). The CBCA (CO)NNH only correlates the NH ... Understanding the Motional Dynamics of the Ammonium Ion in the We thus performed detailed 1H NMR spin-relaxation (T1) measurements on (NH4)3Cr(O2)4 over a wide temperature range (120-300 K) to probe the displacive as well as hindered rotational dynamics of the NH4+ ions with the view of understanding their specific roles in the phase transitions. The NH4+ dynamics is seen to consist of at least three ... Protein NMR Much space and discussion is devoted to practical aspects. The implementation of protein NMR assignment is described using the program CCPNmr Analysis. This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has the advantage (a ... assignment essay homework paper phd report resume review speech thesis