Chemical Shift Assignments Research Articles

Backbone and Ile, Leu, Val methyl group resonance assignment of CoV-Y domain of SARS-CoV-2 non-structural protein 3.

The worldwide COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonstructural protein 3 (nsp3) has 1945 residues and is the largest protein encoded by SARS-CoV-2. It comprises more than a dozen independent domains with various functions. Many of these domains were studied in the closely-related virus SARS-CoV following an earlier outbreak. Nonetheless structural and functional information on the C-terminal region of nsp3 containing two transmembrane and three extra-membrane domains remains incomplete. This part of the protein appears to be involved in initiation of double membrane vesicle (DMV) formation, membranous organelles the virus builds to hide its replication-transcription complex from host immune defenses. Here we present the near-complete backbone and Ile, Leu, and Val methyl group chemical shift assignments of the most C-terminal domain of nsp3, CoV-Y. As the exact function and binding partners of CoV-Y remain unknown, our data provide a basis for future NMR studies of protein–protein interactions to elucidate the molecular mechanism of DMV formation.

NMR chemical shifts of carbon atoms and characteristic shift ranges in the oil sample

Application of high resolution 13C nuclear magnetic resonance (NMR) spectroscopy to characterize crude oil was demonstrated. The chemical shifts of 13C NMR functional groups that determine the composition of the oil sample were determined. Molar fractions of primary, secondary, quaternary, tertiary, aromatic groups, aromatic factor and average hydrocarbon chain length of aliphatic hydrocarbons of the oil sample according to 13C NMR spectra were determined. Detailed description of the 13C NMR spectra of the oil sample using a single consideration of three NMR spectra: 13C, 13C Attached Proton Test (APT), 13C with Gated Decoupling (GD) was performed. The different contribution of the studied oil sample in the aliphatic (10–75 ppm) and aromatic (115–165 ppm) areas of the 13C NMR spectra was determined. The presence of all major hydrocarbon components in the studied oil sample was established on the quantitative level, the aromaticity factor and the mean length of the hydrocarbon chain were evaluated. Quantitative fractions of aromatic molecules and functional groups constituting oil hydrocarbons were determined. In this work we demonstrate that the attached proton test and gated decoupling 13C NMR spectroscopy can afford all information to complete the chemical shift assignment of an oil sample, especially for determination of long range 1H–13C coupling constants and 13C multiplicity.

NMR assignments and characterization of the DNA-binding domain of Arabidopsis transcription factor WRKY11

The WRKY proteins are a family of plant-specific transcription factors (TFs) that are widely involved in plant development and anti-stress responses. Arabidopsis WRKY11 (AtWRKY11) functions in regulating plant defense against abiotic stress and belongs to the IId subgroup of WRKY TFs. We herein report the expression, purification and preliminary structural characterization of AtWRKY11 DNA-binding domain (DBD) using solution NMR. Almost complete backbone chemical shift assignments of AtWRKY11-DBD have been obtained. Chemical shift-based secondary structure analysis suggests that AtWRKY11-DBD may exhibit local conformational differences from the X-ray structure of the C-terminal WRKY domain of AtWRKY1, particularly in the β1 and β5 strands. Our current study provides the basis for further structural and interactional studies.

Molecular models of three ω-3 fatty acids based on NMR and DFT calculations of 1H NMR chemical shifts

Structures of low-energy conformers of α-linolenic acid (ALA;18:3-cis-9,12,15 ω-3), eicosapentaenoic acid (EPA;20:5-cis 5,8,11,14,17 ω-3) and docosahexaenoic acid (DHA;22:6-cis 4,7,10,13,16,19 ω-3) in the liquid state, based on NMR and density functional theory calculations of 1H NMR chemical shifts, are provided. A critical discussion of the J. Mol. Liq. 314 (2020) 113,376 article is also presented on a number of issues related to: (i) the method of assignment of 1H and 13C chemical shifts of ALA, EPA and DHA; (ii) attribution of NMR signals of impurities to those of EPA and (iii) the conclusion of an unusually strong electron 13C and 1H shielding of HCCH2CH protons and carbons, due to an asymmetry in a twist between the two ends, which results in torque at the methylene site near the geometric center. The present data demonstrate that the folding effects of the chain as a function of the fragment number (CHCHCH2)n, were n = 3, 5 and 6 for ALA, EPA and DHA, do not result in unusually strong electron 1H and 13C shielding.

Solid-State NMR Studies of the Succinate-Acetate Permease from Citrobacter Koseri in Liposomes and Native Nanodiscs

The succinate-acetate permease (SatP) is an anion channel with six transmembrane domains. It forms different oligomers, especially hexamers in the detergent as well as in the membrane. Solid-state NMR studies of SatP were carried out successfully on SatP complexes by reconstructing the protein into liposomes or retaining the protein in the native membrane of E. coli., where it was expressed. The comparison of 13C-13C 2D correlation spectra between the two samples showed great similarity, opening the possibility to further study the acetate transport mechanism of SatP in its native membrane environment. Solid-state NMR studies also revealed small chemical shift differences of SatP in the two different membrane systems, indicating the importance of the lipid environment in determining the membrane protein structures and dynamics. Combining different 2D SSNMR spectra, chemical shift assignments were made on some sites, consistent with the helical structures in the transmembrane domains. In the end, we pointed out the limitation in the sensitivity for membrane proteins with such a size, and also indicated possible ways to overcome it.

1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

Backbone and nearly complete side-chain chemical shift assignments of the human Uncharacterized protein CXorf51A

Backbone and nearly complete side-chain chemical shift assignments of the human Uncharacterized protein CXorf51A

NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database.

RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the Biological Magnetic Resonance Data Bank (BMRB) to identify sequences that had no (or limited) chemical shift information. Here, we report the chemical shift assignments for 12 RNA hairpins designed specifically to help populate the BMRB.

Resonance assignment of coiled-coil 3 (CC3) domain of human STIM1

The protein stromal interaction molecule 1 (STIM1) plays a pivotal role in mediating store-operated calcium entry (SOCE) into cells, which is essential for adaptive immunity. It acts as a calcium sensor in the endoplasmic reticulum (ER) and extends into the cytosol, where it changes from an inactive (tight) to an active (extended) oligomeric form upon calcium store depletion. NMR studies of this protein are challenging due to its membrane-spanning and aggregation properties. Therefore follow the divide-and-conquer approach, focusing on individual domains first is in order. The cytosolic part is predicted to have a large content of coiled-coil (CC) structure. We report the 1H, 13C, 15N chemical shift assignments of the CC3 domain. This domain is crucial for the stabilisation of the tight quiescent form of STIM1 as well as for activating the ORAI calcium channel by direct contact, in the extended active form.

Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered

Even though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these “unknown” proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the ^1H, ^{13}C, ^{15}N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.

1H, 15N and 13C resonance assignments of the C-terminal domain of PulL, a component of the Klebsiella oxytoca type II secretion system.

Type II secretion systems (T2SS) allow Gram-negative bacteria to transport toxins and enzymes from the periplasm to the external milieu, and are thus important for the pathogenicity of bacteria. To drive secretion, T2SS assemble filaments called pseudopili closely related to bacterial type IV pili. These filaments are non-covalent polymers of proteins that are assembled by an inner membrane complex called the assembly platform connected to a cytoplasmic ATPase motor. In the Klebsiella oxytoca T2SS, the PulL protein from the assembly platform is essential for pseudopilus assembly and protein secretion. However, its role in these processes is not well understood. To decipher the molecular basis of PulL function, we used solution NMR to study its structure and interactions with other components of the machinery. Here as a first step, we report the 1H, 15N and 13C backbone and side-chain chemical shift assignments of the C-terminal periplasmic domain of PulL and its secondary structure based on NMR data.

Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam.

Backbone chemical shift assignments for the Toho-1 β-lactamase (263 amino acids, 28.9kDa) are reported based on triple resonance solution-state NMR experiments performed on a uniformly 2H,13C,15N-labeled sample. These assignments allow for subsequent site-specific characterization at the chemical, structural, and dynamical levels. At the chemical level, titration with the non-β-lactam β-lactamase inhibitor avibactam is found to give chemical shift perturbations indicative of tight covalent binding that allow for mapping of the inhibitor binding site. At the structural level, protein secondary structure is predicted based on the backbone chemical shifts and protein residue sequence using TALOS-N and found to agree well with structural characterization from X-ray crystallography. At the dynamical level, model-free analysis of 15N relaxation data at a single field of 16.4T reveals well-ordered structures for the ligand-free and avibactam-bound enzymes with generalized order parameters of ~ 0.85. Complementary relaxation dispersion experiments indicate that there is an escalation in motions on the millisecond timescale in the vicinity of the active site upon substrate binding. The combination of high rigidity on short timescales and active site flexibility on longer timescales is consistent with hypotheses for achieving both high catalytic efficiency and broad substrate specificity: the induced active site dynamics allows variously sized substrates to be accommodated and increases the probability that the optimal conformation for catalysis will be sampled.

NMR backbone chemical shift assignments of the mitochondrial membrane protein MPV17 labeled with MMTS in DPC micelles

NMR backbone chemical shift assignments of the mitochondrial membrane protein MPV17 labeled with MMTS in DPC micelles

NMR backbone resonance assignment of Japanese encephalitis virus capsid protein.

Japanese encephalitis virus (JEV) is a flavivirus in the same family as West Nile virus (WNV), dengue virus (DENV) and yellow fever virus (YFV), which are transmitted by mosquitoes. About 68 thousand people are infected with JEV every year. In many Asian countries, JEV is the main cause of viral encephalitis. There are no specific antiviral drugs for Japanese encephalitis. Capsid protein C is the core protein of virus particles. Many studies have revealed that capsid protein C plays an important role in the life cycle of flaviviruses. Although the structure of JEV capsid protein (JEVC) has been determined by X-ray crystallography, the mechanism of how it assembles into an inner core to encapsulate the virus genome remains elusive. What's more, the disordered N-terminal region that is reported to affect its assembly is absent in the crystal structure. NMR spectroscopy has distinct advantages over other technologies in the characterization of conformational dynamics. Here we report the backbone 1H, 13C and 15N chemical shift assignments of JEVC by heteronuclear multidimensional spectroscopy and predict its secondary structure in solution using TALOS+.

Backbone resonance assignment of PDI b'xa' domain construct.

Human protein disulfide isomerase (PDI), a protein containing 4 domains a, b, b', a', disordered x linker and C-terminus, plays critical roles in disulfide bond reactions and proper protein folding in the endoplasmic reticulum. The bb' domain contributes to client binding, the a, a' domain catalyse the rearrangement of the disulfide bonds. The x linker and a' domain were the main dynamics region for full-length PDI and the b'xa' construct has the minimum functional domain within full-length PDI. Herein, we report a new preparation strategy with 1, 6-hexandiol and backbone NMR chemical shift assignments for the monomer b'xa' domain.

Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment.

An automated NMR chemical shift assignment algorithm was developed using multi-objective optimization techniques. The problem is modeled as a combinatorial optimization problem and its objective parameters are defined separately in different score functions. Some of the heuristic approaches of evolutionary optimization are employed in this problem model. Both, a conventional genetic algorithm and multi-objective methods, i.e., the non-dominated sorting genetic algorithms II and III (NSGA2 and NSGA3), are applied to the problem. The multi-objective approaches consider each objective parameter separately, whereas the genetic algorithm followed a conventional way, where all objectives are combined in one score function. Several improvement steps and repetitions on these algorithms are performed and their combinations are also created as a hyper-heuristic approach to the problem. Additionally, a hill-climbing algorithm is also applied after the evolutionary algorithm steps. The algorithms are tested on several different datasets with a set of 11 commonly used spectra. The test results showed that our algorithm could assign both sidechain and backbone atoms fully automatically without any manual interactions. Our approaches could provide around a 65% success rate and could assign some of the atoms that could not be assigned by other methods.

Structure of Nanobody Nb23.

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

Side chain 1H, 13C, 15N chemical shift assignments of lysine residues in delta+PHS/V66K staphylococcal nuclease selectively labeled with SAIL Lysine

Side chain 1H, 13C, 15N chemical shift assignments of lysine residues in delta+PHS/V66K staphylococcal nuclease selectively labeled with SAIL Lysine

Synthesis, Physicochemical Characteristics and Plausible Mechanism of Action of an Immunosuppressive Isoxazolo[5,4-e]-1,2,4-Triazepine Derivative (RM33).

Previous studies demonstrated strong anti-inflammatory properties of isoxazolo[5,4-e]-1,2,4-triazepine (RM33) in vivo. The aim of this investigation was to describe synthesis, determine physicochemical characteristics, evaluate biological activities in murine and human in vitro models, as well as to propose mechanism of action of the compound. The compound was devoid of cell toxicity up to 100 μg/mL against a reference A549 cell line. Likewise, RM33 did not induce apoptosis in these cells. The compound stimulated concanavalin A (ConA)-induced splenocyte proliferation but did not change the secondary humoral immune response in vitro to sheep erythrocytes. Nevertheless, a low suppressive effect was registered on lipopolysaccharide (LPS)-induced splenocyte proliferation and a stronger one on tumor necrosis factor alpha (TNFα) production by rat peritoneal cells. The analysis of signaling pathways elicited by RM33 in nonstimulated resident cells and cell lines revealed changes associated with cell activation. Most importantly, we demonstrated that RM33 enhanced production of cyclooxygenase 2 in LPS-stimulated splenocytes. Based on the previous and herein presented results, we conclude that RM33 is an efficient, nontoxic immune suppressor with prevailing anti-inflammatory action. Additionally, structural studies were carried out with the use of appropriate spectral techniques in order to unequivocally confirm the structure of the RM33 molecule. Unambiguous assignment of NMR chemical shifts of carbon atoms of RM33 was conducted thanks to full detailed analysis of 1H, 13C NMR spectra and their two-dimensional (2D) variants. Comparison between theoretically predicted chemical shifts and experimental ones was also carried out. Additionally, N-deuterated isotopologue of RM33 was synthesized to eliminate potentially disturbing frequencies (such as NH, NH2 deformation vibrations) in the carbonyl region of the IR (infrared) spectrum to confirm the presence of the carbonyl group.

Backbone and methyl resonances assignment of the 87 kDa prefoldin from Pyrococcus horikoshii.

Prefoldin is a heterohexameric protein assembly which acts as a co-chaperonin for the well conserved Hsp60 chaperonin, present in archaebacteria and the eukaryotic cell cytosol. Prefoldin is a holdase, capturing client proteins and subsequently transferring them to the Hsp60 chamber for refolding. The chaperonin family is implicated in the early stages of protein folding and plays an important role in proteostasis in the cytosol. Here, we report the assignment of 1HN, 15N, 13C', 13Cα, 13Cβ, 1Hmethyl, and 13Cmethyl chemical shifts of the 87 kDa prefoldin from the hyperthermophilic archaeon Pyrococcus horikoshii, consisting of two α and four β subunits. 100% of the [13C, 1H]-resonances of Aβ, Iδ1, Iδ2, Tγ2, Vγ2 methyl groups were successfully assigned for both subunits. For the β subunit, showing partial peak doubling, 80% of the backbone resonances were assigned. In the α subunit, large stretches of backbone resonances were not detectable due to slow (μs-ms) time scale dynamics. This conformational exchange limited the backbone sequential assignment of the α subunit to 57% of residues, which corresponds to 84% of visible NMR signals.