15N-labeled Protein Research Articles

Absolute quantitation of human serum cystatin C: candidate reference method by 15N-labeled recombinant protein isotope dilution UPLC-MS/MS.

Serum cystatin C (CysC) is a reliable and ideal endogenous marker for accurately assessing early changes in glomerular filtration rate (GFR), surpassing the limitations of creatinine-based estimated GFR. To improve the precision of GFR calculation, the development of strategies for accurately measuring serum CysC is crucial. In this study, the full-length CysC pure product and fully recombinant 15N-labeled CysC internal standard were subjected to protein cleavage. Subsequently, an LC-MS/MS method was developed for the absolute quantification ofserum CysC. The traceability of the method was assigned calibrator using the amino acid reference measurement procedure (RMP). It involved calibrating the instrument using an amino acid reference material with known amino acid concentrations for calibration and comparison purposes. The total imprecision of the method was determined to be≤8.2 %, and a lower functional limit of quantification (LLoQ) was achieved. The recoveries ranged from 97.36 to 103.26 %. The relative bias between this candidate RMP for measurement of ERM-DA471-IFCC and the target value was 1.74 %. The linearity response was observed within the concentration range of 0.21-10.13 mg/L, with a high R2 value of 0.999. The results obtained using our method was consistent with those obtained using other certified RMPs. With the establishment of this highly selective and accurate serum CysC measurement method, it is now possible to assess the correlation between immunoassay results of serum CysC and the intended target when discrepancies are suspected in the clinical setting.

Effects of gastric bypass on the digestibility and postprandial metabolic fate of 15N dietary protein in rats.

Roux-en-Y Gastric Bypass may be associated with an alteration of protein bioavailability in relation to intestinal remodeling. Our study aimed to test this hypothesis by Roux-en-Y Gastric Bypass. Diet-induced obese rats underwent Roux-en-Y Gastric Bypass surgery (RYGB rats) while a Sham-operated control group was used. All rats received a 15N-labeled protein meal 1 or 3 months after surgery and were euthanized 6h later. Protein digestibility, 15N recovered in organs and urea pool, fractional protein synthesis rate, and intestinal morphometry were assessed. Protein digestibility was similar in all groups (94.2±0.3%). The small intestine was hypertrophied in RYGB rats 1 month after surgery, weighing 9.1±0.2g vs. 7.0±0.3g in Sham rats (P = 0.003). Villus height and crypt depth were increased in the alimentary limb and ileum of RYGB rats. However, Roux-en-Y Gastric Bypass had no impact on the fractional synthesis rate. In the gastrointestinal tract, 15N retention only differed in the ileal mucosa and was higher in RYGB rats at 1 month (0.48±0.2% vs. 0.3±0.09%, P = 0.03). 15N recovery from the liver, muscle, and skin was lower in RYGB rats at 1 month. 15N recovery from urinary and plasma urea was higher in RYGB rats at both times, resulting in increased total deamination (13.2±0.9% vs. 10.1±0.5%, P<0.01). This study showed that Roux-en-Y Gastric Bypass did not affect protein digestibility. Dietary nitrogen sequestration was transitorily and moderately diminished in several organs. This was associated with a sustained elevation of postprandial deamination after Roux-en-Y Gastric Bypass, whose mechanisms merit further studies.

1Hβ chemical shift-based phase modulated NMR methods for fast identification of amino acid types in proteins

Here we report two phase modulated NMR experiments: PM-2D HN(CACBHB) and PM-2D HN(HB), that use 1Hβ chemical shifts to rapidly identify amino acid type in proteins. The magnetization on the 1Hβ spins during the experiments is allowed to evolve for a fixed evolution period that results in phase modulation (positive or negative) of the cross peaks corresponding to various amino acid residues on their 2D HN projections, resembling a typical 2D [1H–15N]-HSQC spectrum. All amino acids except glycine can be categorized into three discernible groups based on their 1Hβ chemical shifts, resulting in unique phase patterns at different fixed evolution periods for 1Hβ, thus facilitating their identification. Remarkably, the PM-2D HN(HB) stands out among all amino acid type identification NMR techniques for its applicability with cost-effective and most routinely employed 15N-labeled protein samples for NMR studies. Furthermore, when combined effectively with the 13Cβ chemical shift-based phase modulated NMR method (PM-2D HN(CACB)), these methods resolved the identification of large groups of amino acids into relatively smaller groups. Moreover, these techniques can accelerate the sequence-specific sequential resonance assignment (SSRA) process and would help in fast tracking of assigned NMR signals exhibiting chemical shift perturbation on the 2D [1H–15N]-HSQC spectrum of proteins during various experiments (e.g., temperature change, pH change, and protein or ligand or cofactor binding) as well as in site-directed mutagenesis.

Backbone 1H, 13C and 15N resonance assignment of the ubiquitin specific protease 7 catalytic domain (residues 208-554) in complex with a small molecule ligand.

The backbone 1H, 13C and 15N resonance assignment of Ubiquitin Specific Protease 7 catalytic domain (residues 208-554) was performed in its complex with a small molecule ligand and in its apo form as a reference. The amide 1H-15N signal intensities were boosted by an amide hydrogen exchange protocol, where expressed 2H, 13C, 15N-labeled protein was unfolded and re-folded to ensure exchange of amide deuterons to protons. The resonance assignments were used to determine chemical shift perturbations on ligand binding, which are consistent with the binding site observed by crystallography.

Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest.

Ostrinia nubilalis, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The Ostrinia nubilalis pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a 13C, 15N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.

The use of 15N-labelled protein to account for the endogenous nitrogen contribution to in vitro protein digestibility measurement

Protein digestibility, a key indicator of dietary protein quality for human nutrition, can be estimated using an in vitro digestion model, however its definition and determination remain variable across studies. The present study aimed to determine the contribution of the endogenous nitrogen (N) to the plant and animal protein digestibility values obtained in vitro. 15N-labelled gluten and caseins (4, 8 and 16 % of the model meal) were used to differentiate dietary and endogenous N and were digested using the INFOGEST in vitro digestion model with no oral phase. The dietary and endogenous N were measured before and during digestion after centrifugation and 10 kDa ultrafiltration. The proteolysis degree was measured by the OPA method. The endogenous and dietary N were determined by elemental analyser coupled with isotopic ratio mass spectrometry. Apparent and true digestibility were determined and values of 135, 92 and 71 % for apparent vs. 78, 69, 60 % for true digestibility were obtained for 4, 8 and 16 % dietary protein level, respectively, with a significant effect of protein level. Differences between apparent and true digestibility pointed out the important contribution of the endogenous nitrogen. Our results showed that 40 % of the N below 10 kDa, i.e., the digestible fraction, were from endogenous origin (i.e. from the pancreatin) and was even present before digestion. An average value of 27 % for pancreatin N autolysis was estimated independently of the protein levels or sources. The use of 15N-labelled protein to evaluate in vitro protein digestibility highlighted the important contribution of the endogenous N, in particular when low dietary protein solution (4 %) are digested. This gives new keys to overcome drawbacks of in vitro models for determining protein digestibility.

Differential effects of milk proteins on amino acid digestibility, post-prandial nitrogen utilization and intestinal peptide profiles in rats

ObjectiveThe aim of this study was to analyze the protein digestibility and postprandial metabolism in rats of milk protein matrices obtained by different industrial processes. Material and methodsThe study was conducted on Wistar rats that consumed a meal containing different 15N-labeled milk proteins. Four milk matrices were tested: native micellar caseins (C1), caseins low in calcium (C2 low Ca2+), a matrix containing a ratio 63:37 of caseins and whey proteins (CW2) and whey proteins alone (W). Blood and urine were collected during the postprandial period and rats were euthanized 6 h after meal intake to collect digestive contents and organs. ResultsOrocaecal digestibility values of amino acids ranged between 96.0 ± 0.2% and 96.6 ± 0.4% for C1-, C2 low Ca2+- and W-matrices, while this value was significantly lower for CW2 matrix (92.4 ± 0.5%). More dietary nitrogen was sequestered in the splanchnic area (intestinal mucosa and liver) as well as in plasma proteins after ingestion of W matrix, especially compared to the C1- and C2 low Ca2+-matrices. Peptidomic analysis showed that more milk protein-derived peptides were identified in the caecum of rats after the ingestion of the matrices containing caseins compared to W matrix. ConclusionWe found that demineralization of micellar caseins did not modify its digestibility and postprandial metabolism. The low digestibility of the modified casein-to-whey ratio matrix may be ascribed to a lower accessibility of the protein to digestive enzymes due to changes in the protein structure, while the higher nitrogen splanchnic retention after ingestion of whey was probably due to the fast assimilation of its protein content. Finally, our results showed that industrial processes that modify the structure and/or composition of milk proteins influence protein digestion and utilization.

Resonance Raman Studies on Heme Ligand Stretching Modes in Methionine80-Depleted Cytochrome c: Fe-His, Fe-O2, and O-O Stretching Modes.

The peroxidase activity of cytochrome (cyt) c increases when Met80 dissociates from the heme iron, which is related to the initial cyt c membrane permeation step of apoptosis. Met80-dissociated cyt c can form an oxygenated species. Herein, resonance Raman spectra of Met80-depleted horse cyt c (M80A cyt c) were analyzed to elucidate the heme ligand properties of Met80-dissociated cyt c. The Fe-His stretching (νFe-His) mode of ferrous M80A cyt c was observed at 236 cm-1, and this frequency decreased by 1.5 cm-1 for the 15N-labeled protein. The higher νFe-His frequency of M80A cyt c than of other His-ligated heme proteins indicates strong heme coordination and the imidazolate character of His18. Peaks attributed to the Fe-O2 stretching (νFe-O2) and O-O stretching (νO-O) modes of the oxygenated species of M80A cyt c were observed at 576 and 1148 cm-1, respectively, under an 16O2 atmosphere, whereas the frequencies decreased to 544 and 1077 cm-1, respectively, under an 18O2 atmosphere. The νFe-O2 mode of Hydrogenobacter thermophilus (HT) M59A cyt c552 was observed at 580 cm-1 under an 16O2 atmosphere, whereas the frequency decreased to 553 cm-1 under an 18O2 atmosphere, indicating that relatively high νFe-O2 frequencies are characteristic of c-type cyt proteins. By comparison of the simultaneously observed νFe-O2 and νO-O frequencies of oxygenated cyt c and other oxygenated His-ligated heme proteins, the frequencies tend to have a positive linear relationship; the νFe-O2 frequency increases when the νO-O frequency increases. The imidazolate character of the heme-coordinated His and strong Fe-O and O-O bonds are characteristic of cyt c and apparently related to the peroxidase activity when Met80 dissociates from the heme iron.

NMR Titration Studies in Z-DNA Dynamics.

Chemical shift perturbation (CSP) is a simple NMR technique for studying the DNA binding of proteins. Titration of the unlabeled DNA into the 15N-labeled protein is monitored by acquiring a two-dimensional (2D) heteronuclear single-quantum correlation (HSQC) spectrum at each step of the titration. CSP can also provide information on the DNA-binding dynamics of proteins, as well as protein-induced conformational changes in DNA. Here, we describe the titration of DNA for the 15N-labeled Z-DNA-binding protein, monitored via 2D HSQC spectra. NMR titration data can be analyzed with the active B-Z transition model to provide the protein-induced B-Z transition dynamics of DNA.

Effect of Gastric Bypass on Dietary Protein Digestibility and Dietary Nitrogen Sequestration in the Splanchnic Bed in Rats

Abstract Objectives Roux-en-Y Gastric Bypass (RYGB) decreases the stomach size and bypasses a part of the small intestine. RYGB has been often associated with protein malnutrition but in the light of previous studies, this was not ascribed to protein malabsorption. We hypothesized that dietary amino acids are more sequestered by the small intestine mucosa due to adaptative hypertrophy after RYGB. Our study aimed to quantify the sequestration of dietary nitrogen (N) in the small intestine after RYGB at different times of the post-surgery recovery. Methods Diet-induced obese Wistar rats were operated for RYGB. The control group was composed of pair-fed sham-operated rats. One month (RYGB: n = 9, Sham: n = 8) or three months (RYGB: n = 7, Sham: n = 8) after surgery, rats were fed a test meal including 15N-labeled protein. Protein digestibility and dietary N sequestration in the intestine were assessed by determination of 15N recovery in the digesta and gastrointestinal tract (GIT) tissues 6 h after the meal. Results One month after surgery, protein digestibility in Sham and RYGB rats was 94.0 ± 0.8% and 94.2 ± 1.8% (NS), respectively. Digestibility was similar 3 months after surgery, whatever the group. The GIT was hypertrophied in RYGB after 1 month, an effect that disappeared after 3 months. Dietary N sequestration in the splanchnic bed differed depending on the segment. In the stomach wall as well as the duodenum + jejunum mucosa, N retention was lower in RYGB than in Sham at 1 month, this difference being aggravated at 3 months. In contrast, in the ileum mucosa, there was more N in RYGB than in Sham at 1 month (0.48 ± 0.18% vs 0.3 ± 0.09% of ingested N respectively), these values being similar at 3 months. In the caecum, dietary N was higher in RYGB at 1 month compared to Sham but lower in the colon. No differences between groups were observed in these two segments at 3 months. Conclusions RYGB did not improved protein digestibility, in contrast to the findings of our previous study. Our hypothesis of a higher sequestration in the intestinal wall was confirmed in the ileum and colon only, an effect that tended to be attenuated over time. Funding Sources This study was funded by the doctoral school ABIES.

Silkworm Pupae Function as Efficient Producers of Recombinant Glycoproteins with Stable-Isotope Labeling.

Baculovirus-infected silkworms are promising bioreactors for producing recombinant glycoproteins, including antibodies. Previously, we developed a method for isotope labeling of glycoproteins for nuclear magnetic resonance (NMR) studies using silkworm larvae reared on an artificial diet containing 15N-labeled yeast crude protein extract. Here, we further develop this method by introducing a technique for the expression of isotope-labeled glycoproteins by silkworm pupae, which has several potential advantages relative to larvae-based techniques in terms of production yield, ease of handling, and storage. Here, we fed fifth instar larvae an artificial diet with an optimized composition containing [methyl-13C]methionine, leading to pupation. Nine-day-old pupae were then injected with recombinant Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid for expression of recombinant human immunoglobulin G (IgG). From the whole-body homogenates of pupae, 0.35 mg/pupa of IgG was harvested, which is a yield that is five times higher than can be obtained from larvae. Recombinant IgG, thus prepared, exhibited mainly three kinds of pauci-mannose-type oligosaccharides and had a 13C-enrichment ratio of approximately 80%. This enabled selective observation of NMR signals originating from the methionyl methyl group of IgG, confirming its conformational integrity. These data demonstrate the utility of silkworm pupae as factories for producing recombinant glycoproteins with amino-acid-selective isotope labeling.

Blood 15N:13C Enrichment Ratios Are Proportional to the Ingested Quantity of Protein with the Dual-Tracer Approach for Determining Amino Acid Bioavailability in Humans

ABSTRACTBackgroundAssessment of amino acid bioavailability is of key importance for the evaluation of protein quality; however, measuring ileal digestibility of dietary proteins in humans is challenging. Therefore, a less-invasive dual stable isotope tracer approach was developed.ObjectiveWe aimed to test the assumption that the 15N:13C enrichment ratio in the blood increases proportionally to the quantity ingested by applying different quantities of 15N test protein.MethodsIn a crossover design, 10 healthy adults were given a semi-liquid mixed meal containing 25 g (low protein) or 50 g (high protein) of 15N-labeled milk protein concentrate simultaneous with 0.4 g of highly 13C–enriched spirulina. The meal was distributed over multiple small portions, frequently provided every 20 min during a period of 160 min. For several amino acids, the blood 15N- related to 13C-isotopic enrichment ratio was determined at t = 0, 30, 60, 90, 120, 180, 240, 300, and 360 min and differences between the 2 meals were compared using paired analyses.ResultsNo differences in 13C AUC for each of the measured amino acids in serum was observed when ingesting a low- or high-protein meal, whereas 15N AUC of amino acids was ∼2 times larger on the high-protein meal (P < 0.001). Doubling the intake of 15N-labeled amino acids increased the 15N:13C ratio by a factor of 2.04 ± 0.445 for lysine and a factor between 1.8 and 2.2 for other analyzed amino acids, with only phenylalanine (2.26), methionine (2.48), and tryptophan (3.02) outside this range.ConclusionsThe amino acid 15N:13C enrichment ratio in the peripheral circulation increased proportionally to the quantity of 15N-labeled milk protein ingested, especially for lysine, in healthy adults. However, when using 15N-labeled protein, correction for, e.g., α-carbon 15N atom transamination is advised for determination of bioavailability of individual amino acids. This trial was registered at www.clinicaltrials.gov as NCT02966704.

Influence of Hyperfine Coupling Strain on Two-Dimensional ESEEM Spectra from I = 1/2 Nuclei

HYSCORE, a variant of two-dimensional ESEEM spectroscopy, is currently one of the most effective tools in high-resolution solid-state EPR spectroscopy. Our systematic studies of hydrogen bonds with semiquinones in 15N-labeled proteins have previously provided us with an extensive collection of 15N HYSCORE spectra produced by N–H…O nitrogen donors. Examination of these spectra has indicated in several cases lineshape distortions not described by available theoretical models. We were able to explain all observed artificial phenomena in the 15N spectra of semiquinones considering a single mechanism—strain of the isotropic hyperfine interaction. In this review article, we introduce the HYSCORE experiment and the theoretical background for spectra of I = 1/2 nuclei in orientation-disordered samples. We then present a description of the observed lineshape distortions and an explanation of the hyperfine strain’s influence on the experimental spectra. In the final part of the article, we discuss (i) similar lineshape distortions found in previously published spectra from 15N, 29Si, 31P, and 57Fe nuclei that can be explained using the approach applied for the analysis of the 15N spectra of semiquinones, and (ii) a recently published analysis of 31P spectra with a different type of lineshape distortion based on a more sophisticated method, where the strength of anisotropic coupling is correlated with the sign and value of the isotropic constant in different conformations of a Cu(II) complex.

Fragment screening targeting Ebola virus nucleoprotein C-terminal domain identifies lead candidates

The Ebola Virus is a causative agent of viral hemorrhagic fever outbreaks and a potential global health risk. The outbreak in West Africa (2013–2016) led to 11,000+ deaths and 30,000+ Ebola infected individuals. The current outbreak in the Democratic Republic of Congo (DRC) with 3000+ confirmed cases and 2000+ deaths attributed to Ebola virus infections provides a reminder that innovative countermeasures are still needed. Ebola virus encodes 7 open reading frames (ORFs). Of these, the nucleocapsid protein (eNP) encoded by the first ORF plays many significant roles, including a role in viral RNA synthesis. Here we describe efforts to target the C-terminal domain of eNP (eNP-CTD) that contains highly conserved residues 641–739 as a pan-Ebola antiviral target. Interactions of eNP-CTD with Ebola Viral Protein 30 (eVP30) and Viral Protein 40 (eVP40) have been shown to be crucial for viral RNA synthesis, virion formation, and virion transport. We used nuclear magnetic response (NMR)-based methods to screened the eNP-CTD against a fragment library. Perturbations of 1D 1H NMR spectra identified of 48 of the 439 compounds screened as potential eNP CTD interactors. Subsequent analysis of these compounds to measure chemical shift perturbations in 2D 1H,15N NMR spectra of 15N-labeled protein identified six with low millimolar affinities. All six perturbed an area consisting mainly of residues at or near the extreme C-terminus that we named “Site 1” while three other sites were perturbed by other compounds. Our findings here demonstrate the potential utility of eNP as a target, several fragment hits, and provide an experimental pipeline to validate viral-viral interactions as potential panfiloviral inhibitor targets.

α-Actinin-1 promotes activity of the L-type Ca2+ channel Cav 1.2.

The L-type Ca2+ channel CaV 1.2 governs gene expression, cardiac contraction, and neuronal activity. Binding of α-actinin to the IQ motif of CaV 1.2 supports its surface localization and postsynaptic targeting in neurons. We report a bi-functional mechanism that restricts CaV 1.2 activity to its target sites. We solved separate NMR structures of the IQ motif (residues 1,646-1,664) bound to α-actinin-1 and to apo-calmodulin (apoCaM). The CaV 1.2 K1647A and Y1649A mutations, which impair α-actinin-1 but not apoCaM binding, but not the F1658A and K1662E mutations, which impair apoCaM but not α-actinin-1 binding, decreased single-channel open probability, gating charge movement, and its coupling to channel opening. Thus, α-actinin recruits CaV 1.2 to defined surface regions and simultaneously boosts its open probability so that CaV 1.2 is mostly active when appropriately localized.

1H, 13C, and 15N resonance assignment and secondary structure of the pheromone-binding protein2 from the agricultural pest Ostrinia furnacalis (OfurPBP2).

Ostrinia furnacalis, a lepidopteran moth, is an invasive pest found in Asia, Australia, Africa, and parts of the United States. The O. furnacalis pheromone-binding protein2 (OfurPBP2), present in the male moth antenna, plays a role in the detection of female-secreted pheromone in a process that leads to mating. To understand the structural mechanism of pheromone binding and release in this pest, we have initiated characterization of OfurPBP2 by solution NMR. Here, we report the backbone resonance assignments and the secondary structural elements of OfurPBP2 at pH 6.5 using uniformly 13C, 15N-labeled protein with various triple resonance NMR experiments. The assignments are 97% completed for backbone and 88% completed for side-chain resonances. The secondary structure of OfurPBP2, based on backbone chemical shifts, consists of eight α-helices, including a well-structured C-terminal helix.

Protein resonance assignment by BSH-CP-based 3D solid-state NMR experiments: A practical guide.

Solid-state NMR (ssNMR) spectroscopy has evolved into a powerful method to obtain structural information and to study the dynamics of proteins at atomic resolution and under physiological conditions. The method is especially well suited to investigate insoluble and noncrystalline proteins that cannot be investigated easily by X-ray crystallography or solution NMR. To allow for detailed analysis of ssNMR data, the assignment of resonances to the protein atoms is essential. For this purpose, a set of three-dimensional (3D) spectra needs to be acquired. Band-selective homo-nuclear cross-polarization (BSH-CP) is an effective method for magnetization transfer between carbonyl carbon (CO) and alpha carbon (CA) atoms, which is an important transfer step in multidimensional ssNMR experiments. This tutorial describes the detailed procedure for the chemical shift assignment of the backbone atoms of 13 C-15 N-labeled proteins by BSH-CP-based 13 C-detected ssNMR experiments. A set of six 3D experiments is used for unambiguous assignment of the protein backbone as well as certain side-chain resonances. The tutorial especially addresses scientists with little experience in the field of ssNMR and provides all the necessary information for protein assignment in an efficient, time-saving approach.

Measuring translational diffusion of 15N-enriched biomolecules in complex solutions with a simplified 1H-15N HMQC-filtered BEST sequence.

Pulsed-field gradient nuclear magnetic resonance has seen an increase in applications spanning a broad range of disciplines where molecular translational diffusion properties are of interest. The current study introduces and experimentally evaluates the measurement of translational diffusion coefficients of 15N-enriched biomolecules using a 1H-15N HMQC-filtered band-selective excitation short transient (BEST) sequence as an alternative to the previously described SOFAST-XSTE sequence. The results demonstrate that accurate translational diffusion coefficients of 15N-labelled peptides and proteins can be obtained using this alternative 1H-15N HMQC-filtered BEST sequence which is implementable on NMR spectrometers equipped with probes fitted with a single-axis field gradient, including most cryoprobes dedicated to bio-NMR. The sequence is of potential use for direct quantification of protein or peptide translational diffusion within complex systems, such as in mixtures of macromolecules, crowded solutions, membrane-mimicking media and in bicontinuous cubic phases, where conventional sequences may not be readily applicable due to the presence of intense signals arising from sources other than the protein or peptide under investigation.

Chemical shift assignments of RHE_RS02845, a NTF2-like domain-containing protein from Rhizobium etli.

The nuclear transport factor 2 (NTF2) like superfamily includes members of the NTF2 family, delta-5-3-ketosteroid isomerases, and the beta subunit of ring hydroxygenases. This family plays important roles in both eukaryotic and prokaryotic cells, and is taken as a classic example of divergent evolution because proteins in this family exhibit diverse biological functions, although share common structural features. We cloned the gene RHE_RS02845 encoding a predicted NTF2-like domain-containing protein in Rhizobium etli, and prepared U-13C/15N-labeled protein samples for its three-dimensional NMR structural determination. Here, chemical shift assignments for both backbone and side-chain atoms are reported, which is prerequisite for further structural calculation and functional research using NMR spectroscopy.

Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring-Mass Spectrometry.

Saliva is an attractive sample source for the biomarker-based testing of several diseases, especially oral cancer. Here, we sought to apply multiplexed LC-MRM-MS to precisely quantify 90 disease-related proteins and assess their intra- and interindividual variability in saliva samples from healthy donors. We developed two multiplexed LC-MRM-MS assays for 122 surrogate peptides representing a set of disease-related proteins. Saliva samples were collected from 10 healthy volunteers at three different time points (Day 1 morning and afternoon, and Day 2 morning). Each sample was spiked with a constant amount of a 15 N-labeled protein and analyzed by MRM-MS in triplicate. Quantitative results from LC-MRM-MS were calculated by single-point quantification with reference to a known amount of internal standard (heavy peptide). The CVs for assay reproducibility and technical variation were 13 and 11%, respectively. The average concentrations of the 99 successfully quantified proteins ranged from 0.28±0.58ng mL-1 for profilin-2 (PFN2) to 8.55±8.96 μg mL-1 for calprotectin (S100A8). For the 90 proteins detectable in >50% of samples, the average CVs for intraday, interday, intraindividual, and interindividual samples were 38%, 43%, 45%, and 69%, respectively. The fluctuations of most target proteins in individual subjects were found to be within±twofold. Our study elucidated the intra- and interindividual variability of 90 disease-related proteins in saliva samples from healthy donors. The findings may facilitate the further development of salivary biomarkers for oral and systemic diseases.