Amino Acids

Published by Springer Nature
Online ISSN: 1438-2199
Learn more about this page
Recent publications
Schematic diagram of the main functions of Fascin. a Fascin bundles two actin filaments in parallel, with two surfaces attached to one F-actin and one independent surface bound to the other. Four β-trefoil domains of Fascin are shown in different colors, with 3 actin-binding surfaces roughly illustrated. b Fascin is a major actin bundling protein involved in the formation of filopodia. c Filopodia formation is essential in the promotion of cancer-related cellular properties, including migration, invasion, and metastasis
Fascin PTMs. The major sites of Fascin modifications, including phosphorylation, ubiquitination, sumoylation, acetylation, malonylation, and glutathionylation, are plotted in the figure. Different colors are used to represent different modification types. The functions of some modifications have been illustrated
Examples of conserved sites within Fascin as revealed by alignment of multiple amino acid sequences. Examples of conserved Fascin PTMs are indicated in the figure. Phosphorylation sites, ubiquitination sites, and acetylation sites are highlighted in the red, black, and blue boxes, respectively
Article
  • Nan-LiNan-Li
  • Zhi-Da ZhangZhi-Da Zhang
  • Rong-Rong LiRong-Rong Li
  • [...]
  • En-Min LiEn-Min Li
The post-translational modifications (PTMs), which are crucial in the regulation of protein functions, have great potential as biomarkers of cancer status. Fascin (Fascin actin-bundling protein 1, FSCN1), a key protein in the formation of filopodia that is structurally based on actin filaments (F-actin), is significantly associated with tumor invasion and metastasis. Studies have revealed various regulatory mechanisms of human Fascin, including PTMs. Although a number of Fascin PTM sites have been identified, their exact functions and clinical significance are much less explored. This review explores studies on the functions of Fascin and briefly discusses the regulatory mechanisms of Fascin. Next, to review the role of Fascin PTMs in cell biology and their associations with metastatic disease, we discuss the advances in the characterization of Fascin PTMs, including phosphorylation, ubiquitination, sumoylation, and acetylation, and the main regulatory mechanisms are discussed. Fascin PTMs may be potential targets for therapy for metastatic disease.
 
Article
Methylmalonic acidemia is a neurometabolic disorder biochemically characterized by the accumulation of methylmalonic acid (MMA) in different tissues, including the central nervous system (CNS). In this sense, it has been shown that high levels of this organic acid have a key role in the progressive neurological deterioration in patients. Astroglial cells actively participate in a wide range of CNS functions, such as antioxidant defenses and inflammatory response. Considering the role of these cells to maintain brain homeostasis, in the present study, we investigated the effects of MMA on glial parameters, focusing on redox homeostasis and inflammatory process, as well as putative mediators of these events in C6 astroglial cells. MMA decreased cell viability, glutathione levels, and antioxidant enzyme activities, increased inflammatory response, and changed the expression of nuclear factor erythroid 2-related factor 2 (Nrf2), nuclear factor kappa B (NFκB), peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), inducible nitric oxide synthase (iNOS), cyclooxygenase 2 (COX-2), and adenosine receptors, suggesting that these transcriptional factors and proteins may underlie the glial responses induced by MMA. Moreover, we also demonstrated the protective roles of melatonin and resveratrol against MMA-induced inflammation and decrease in glutathione levels. In summary, our findings support the hypothesis that astroglial changes are associated with pathogenesis of methylmalonic acidemia. In addition, we showed that these cells might be potential targets for preventive/therapeutic strategies by using molecules, such as melatonin and resveratrol, which mediated glioprotection in this inborn error of metabolism.
 
Article
The peptide segment S6 is known to form the inner lining of the voltage-gated K⁺ channel KvAP (potassium channel of archaea-bacterium, Aeropyrum pernix). In our previous work, it has been demonstrated that S6 itself can form an ion channel on a bilayer lipid membrane (BLM). In the present work, the role of a specific amino acid sequence ‘LIG’ in determining the secondary structure of S6 has been investigated. For this purpose, 22-residue synthetic peptides named S6-Wild (S6W) and S6-Mutant (S6M) were used. Sequences of these peptides are similar except that the two amino acids isoleucine and glycine of the wild peptide interchanged in the mutant peptide. Channel forming capabilities of both the peptides were checked electro-physiologically on BLM composed of DPhPC and cholesterol. Bilayer electrophysiological experiments showed that the conductance of S6M is higher than that of S6W. Significant differences in the current versus voltage (I–V) plot, open probability, and gating characteristics were observed. Interestingly, two sub-types of channels, S6M Type 1 and Type 2, were identified in S6M differing in conductances and open probability patterns. Circular dichroism (CD) spectroscopy indicated that the secondary structures of the two peptides are different in phosphatidyl choline/asolectin liposomes and 1% SDS detergent. Reduced helicity of S6M was also noticed in membrane mimetic liposomes and 1% SDS detergent micelles. These results are interpreted in view of the difference in hydrophobicity of the two amino acids, isoleucine and glycine. It is concluded that the ‘LIG’ stretch regulates the structure and pore-forming ability of the S6 peptide.
 
Article
A novel intramolecular cyclization of isothiocyanyl amino acids/peptide is reported to arrive at unnatural thioxoimidazolidinyl (TOI)/thioxooxazolidinyl (TOO) amino acids for the first time. Interestingly, analogous isothiocyanyl amines under a similar reaction condition either follow 5-endo-dig cyclization to offer 5-membered thiourea or acyclic diethylaminyl thiourea derivative instead of 6-membered cyclic thiourea.
 
Article
The emergence of antimicrobial peptides (AMPs) as a potential alternative to conventional antibiotics has led to the development of efficient computational methods for predicting AMPs. Among all organisms, the presence of multiple genes encoding AMPs in plants demands the development of a plant-based prediction tool. To this end, we developed models based on multiple peptide features like amino acid composition, dipeptide composition, and physicochemical attributes for predicting plant-derived AMPs. The selected compositional models are integrated into a web server termed PTPAMP. The designed web server is capable of classifying a query peptide sequence into four functional activities, i.e., antimicrobial (AMP), antibacterial (ABP), antifungal (AFP), and antiviral (AVP). Our models achieved an average area under the curve of 0.95, 0.91, 0.85, and 0.88 for AMP, ABP, AFP, and AVP, respectively, on benchmark datasets, which were ~ 6.75% higher than the state-of-the-art methods. Moreover, our analysis indicates the abundance of cysteine residues in plant-derived AMPs and the distribution of other residues like G, S, K, and R, which differ as per the peptide structural family. Finally, we have developed a user-friendly web server, available at the URL: http://www.nipgr.ac.in/PTPAMP/. We expect the substantial input of this predictor for high-throughput identification of plant-derived AMPs followed by additional insights into their functions.
 
Article
Bacteria from the genus Paenibacillus make a variety of antimicrobial compounds, including lipopeptides produced by a non-ribosomal synthesis mechanism (NRPS). In the present study, we show the genomic and phenotypical characterization of Paenibacillus elgii AC13 which makes three groups of small molecules: the antimicrobial pelgipeptins and two other families of peptides that have not been described in P. elgii. A family of lipopeptides with [M + H]⁺ 1664, 1678, 1702, and 1717 m/z was purified from the culture cell fraction. Partial characterization revealed that they are similar to tridecaptin from P. terrae. However, they present amino acid chain modifications in positions 3, 7, and 10. These new variants were named tridecaptin G1, G2, G3, and G4. Furthermore, a gene cluster was identified in P. elgii AC13 genome, revealing high similarity to the tridecaptin-NRPS gene cluster from P. terrae. Tridecaptin G1 and G2 showed in vitro antimicrobial activity against Escherichia coli, Klebsiella pneumonia (including a multidrug-resistant strain), Staphylococcus aureus, and Candida albicans. Tri G3 did not show antimicrobial activity against S. aureus and C. albicans at all tested concentrations. An intriguing feature of this family of lipopeptides is that it was only observed in the cell fraction of the P. elgii AC13 culture, which could be a result of the amino acid sequence modifications presented in these variants.
 
Amino acid sequences of the BR-1GHa, temporin A and the designed peptides (BR-1GHa-1-5). BR-1GHa is a 24 amino acid long peptide whereas temporin A is a 13 amino acid long peptide. All the new BR-1GHa-1-5 analogues were obtained after truncation of the last 11 residues at the C-terminus of BR-1GHa and are 13 amino acids long as temporins. * indicates the amidated C-terminus
The helical wheel projections (upper panel) and the predicted 3D models (lower panel) of peptides with higher C-scores. The predicted 3D models were prepared with MOLMOL (Koradi et al. 1996)
The percentage of hemolytic activity of the synthetic BR-1GHa and the new analogues against RBCs. Synthetic version of the native BR-1GHa peptide has the highest % hemolysis value compared to the new analogues. BR-1GHa-1 has no hemolytic activity and BR-1GHa-4 peptide showed hemolytic activity only at 128 µM peptide concentration. Triton X-100 and PBS were used as positive and negative controls, respectively, and the % hemolysis values are given as mean ± standard deviation (some % hemolysis values below zero for lower concentrations were set to zero)
Article
Naturally occurring frog skin peptides are one of largest sources of antimicrobial peptides that have many advantages including high potency, broad spectrum of targets and low susceptibility to multiple drug-resistance bacteria. However, they also have disadvantages such as hemolytic activity, low stability and high production costs. For these reasons, various strategies have been applied to overcome these drawbacks restricting their use in clinical trials. Previously reported brevinin-1GHa (BR-1GHa) is a 24 amino acid long antimicrobial peptide isolated from Hylarana guentheri with hemolytic activity. To enhance the antimicrobial activity of this peptide and to reduce its hemolytic activity, we designed five new temporin like analogues and examined their bioactivities. Temporins are another class of frog skin peptides without hemolytic activity and shorter than brevinins. When the antimicrobial activities of new analogues were examined against a panel of microorganisms , BR-1GHa-3, in which two alanine residues in the truncated version of BR-1GHa were replaced with leucine, exhibited significantly improved antimicrobial activity against Gram-positive bacterial strains (e.g., S. aureus ATCC 29213 and E. casseliflavus ATCC 700327) with lower hemolytic activity compared to the BR-1GHa peptide. Furthermore, BR-1GHa-4 analogue, in which Gly3 was replaced with Pro, did not show any hemolytic activity except for highest (128 µM) concentration tested and have a strong antimicrobial effect on Gram-positive bacteria (e.g., E. faecalis ATCC 51299 and B. cereus ATCC 13061).
 
Article
Research has demonstrated that tryptophan (Trp) regulated the composition and metabolism of the gut microbiota. However, the detailed mode of action of Trp on the metabolism of intestinal commensal lactobacilli has not been well characterized. This study aimed to compare the effects of Trp concentration (0.2, 0.4, 0.6 mmol/L) in the media on the metabolism of Lactobacillus amylovorus and Limosilactobacillus mucosae isolated from the small intestine of piglets in vitro by high-performance liquid chromatography and metabolomics study. Results showed that increased Trp concentration increased (P < 0.05) net utilization of lysine, methionine, tryptophan, asparagine/aspartate, glutamine/glutamate, however, increased net production of glycine and taurine in Lac. amylovorus. In contrast, increased Trp concentration decreased (P < 0.05) net utilization of leucine, phenylalanine, and serine and increased (P < 0.05) net utilization of arginine and net production of ornithine and glycine in Lim. mucosae. Targeted metabolomics analysis showed that increased Trp concentration promoted (P < 0.05) the production of indole-3-lactic acid and 3-indoleacetic acid in the two lactobacilli strains. Increased concentration of Trp increased (P < 0.01) glycochenodeoxycholic acid metabolism in Lim. mucosae and glycocholic acid and taurocholic acid metabolism in Lac. amylovorus. Untargeted metabolomics analysis showed that metabolic pathways related to phenylalanine and tryptophan metabolism, and nicotinate and nicotinamide metabolism were regulated by Trp in Lim. mucosae. These findings will help develop new biomarkers and dietary strategies to maintain the functionality of the gut microbiota aiming at improving the nutrition and health of both humans and animals.
 
A Plasma MDA concentrations in the arginine (ARG) and placebo (PLA) groups at day 1 and day 90 upon oral administration of L-arginine or placebo to patients with peripheral arterial occlusive disease (PAOD). B Difference in the plasma MDA concentrations in the ARG and PLA groups at day 1 and day 90th upon oral administration of L-arginine or placebo to patients with PAOD (each n = 20). Statistical analysis was performed using unpaired t test. Numbers on the top are mean ± standard error of the mean of MDA concentrations and differences. The Figure was constructed with the data of Table 2 of a previously reported work (Tsikas 2017). d day
Time course of the concentration of total 15(S)-8-iso-prostaglandin F2α (free acid and esterified to lipids) in aliquoted (1 ml) and at − 80 °C stored human plasma samples serving as the quality control (QC) sample over 153 days. 15(S)-8-iso-prostaglandin F2α was determined by GC–MS/MS after immunoaffinity chromatography (IAC) column extraction and derivatization (Tsikas and Suchy 2016). n = 2 for day 1, day 10, day 18, and day 74; n = 3 for day 86; n = 5 for day 96; n = 1 each for days 149, 151 and 153, thus simulating a long-term clinical study. Unpaired t test was performed between three groups in the periods 1 to 18 days, 74–96 days, and 149–160 days, as indicated by the frames. Numbers on the top are mean ± standard error of the mean. d day
Article
N -Acetyl-L-cysteine (NAC) is an endogenous cysteine metabolite. The drug is widely used in chronic obstructive pulmonary disease (COPD) and as antidote in acetaminophen (paracetamol) intoxication. Currently, the utility of NAC is investigated in rheumatoid arthritis (RA), which is generally considered associated with inflammation and oxidative stress. Besides clinical laboratory parameters, the effects of NAC are evaluated by measuring in plasma or serum nitrite, nitrate or their sum (NOx) as measures of nitric oxide (NO) synthesis. Malondialdehyde (MDA) and relatives such as 4-hydroxy-nonenal and 15( S )-8- iso -prostaglandin F 2α serve as measures of oxidative stress, notably lipid peroxidation. In this work, we review recent clinico-pharmacological studies on NAC in rheumatoid arthritis. We discuss analytical, pre-analytical and clinical issues and their potential impact on the studies outcome. Major issues include analytical inaccuracy due to interfering endogenous substances and artefactual formation of MDA and relatives during storage in long-term studies. Differences in the placebo and NAC groups at baseline with respect to these biomarkers are also a serious concern. Modern applied sciences are based on data generated using commercially available instrumental physico-chemical and immunological technologies and assays. The publication process of scientific work rarely undergoes rigorous peer review of the analytical approaches used in the study in terms of accuracy/trueness. There is pressing need of considering previously reported reference concentration ranges and intervals as well as specific critical issues such as artefactual formation of particular biomarkers during sample storage. The latter especially applies to surrogate biomarkers of oxidative stress, notably MDA and relatives. Reported data on NO, MDA and clinical parameters, including C-reactive protein, interleukins and tumour necrosis factor α, are contradictory in the literature. Furthermore, reported studies do not allow any valid conclusion about utility of NAC in RA. Administration of NAC patients with rheumatoid arthritis is not recommended in current European and American guidelines.
 
Article
Loss of cognitive function is a typical consequence of aging in humans and rodents. The extent of decline in spatial memory performance of rats, assessed by a hole-board test, reaches from unimpaired and comparable to young individuals to severely memory impaired. Recently, proteomics identified peroxiredoxin 6, an enzyme important for detoxification of oxidized phospholipids, as one of several synaptosomal proteins discriminating between aged impaired and aged unimpaired rats. In this study, we investigated several components of the epilipidome (modifications of phospholipids) of the prefrontal cortex of young, aged memory impaired (AI) and aged unimpaired (AU) rats. We observed an age-related increase in phospholipid hydroperoxides and products of phospholipid peroxidation, including reactive aldehydophospholipids. This increase went in hand with cortical lipofuscin autofluorescence. The memory impairment, however, was paralleled by additional specific changes in the aged rat brain epilipidome. There was a profound increase in phosphocholine hydroxides, and a significant decrease in phosphocholine-esterified azelaic acid. As phospholipid-esterified fatty acid hydroxides, and especially those deriving from arachidonic acid are both markers and effectors of inflammation, the findings suggest that in addition to age-related reactive oxygen species (ROS) accumulation, age-related impairment of spatial memory performance has an additional and distinct (neuro-) inflammatory component.
 
Trunk fat and odds ratios of having abdominal obesity according to circulating glutamate quintiles. Left panels: abdominal fat for each circulating amino acid quintile. The lower, middle, and top borders of the boxplot represent the second quantile, median, and third quantile, respectively. Right panel: Odds ratios of having abdominal obesity of the second, third, fourth, and fifth circulating glutamate quintiles, compared to the first. Error bars represent the 95% confidence interval. Abdominal obesity was defined as having 37.7% of fat or more in the trunk region. Odds ratios were obtained for mixed logistic regression models, adjusted for age, sex, metabolomic batch, and twin-pair clustering. This figure and all others were created using ggplot2 (Wickham 2016)
Difference in circulating glutamate between heavier and leaner twins from monozygotic pairs discordant for trunk fat percentage (n = 108, 54 pairs). Twin pairs were considered discordant if the intra-pair trunk fat difference was greater or equal to the 95th percentile of intra-pair trunk fat percentage difference for monozygotic twins. In each discordant pair, we identified the leaner and heavier (in terms of trunk fat) individual. Left panel shows circulating glutamate level of all individuals, according to whether they are the leaner of heavier twin of the pair. The right panel shows the circulating glutamate difference between the heavier and leaner twin. P values are from two-tailed and paired Student’s t tests
Article
Circulating levels of the amino acid glutamate are associated with central fat accumulation, yet the pathophysiology of this relationship remains unknown. We aimed to (i) refine and validate the association between circulating glutamate and abdominal obesity in a large twin cohort, and (ii) investigate whether transcriptomic profiles in adipose tissue could provide insight into the biological mechanisms underlying the association. First, in a cohort of 4665 individuals from the TwinsUK resource, we identified individuals with abdominal obesity and compared prevalence of the latter across circulating glutamate quintiles. Second, we used transcriptomic signatures generated from adipose tissue, both subcutaneous and visceral, to investigate associations with circulating glutamate levels. Individuals in the top circulating glutamate quintile had a sevenfold higher prevalence of abdominal obesity compared to those in the bottom quintile. The adipose tissue transcriptomic analyses identified GLUL, encoding Glutamate-Ammonia Ligase, as being associated with circulating glutamate and abdominal obesity, with pronounced signatures in the visceral depot. In conclusion, circulating glutamate is positively associated with the prevalence of abdominal obesity which relates to dysregulated GLUL expression specifically in visceral adipose tissue.
 
Amygdala and surrounding structures on anatomical MRI. a A high-resolution (1 mm isotropic) 3D T2-weighted MRI acquired on a 3 T GE scanner with an 8 channel head coil from a pediatric subject who suffered a severe TBI (7 days after injury). The red cross-hair visible in each plane (sagittal, coronal, axial) colocalizes the same voxel location (superior aspect of the anterior hippocampus). b Same background slices as in panel A are labelled according to Freesurfer segmentation and parcellation methods (https://surfer.nmr.mgh.harvard.edu). Radiological convention is used for display
Mean diffusivity maps displaying range of mean diffusivity (MD) values in same post-TBI subject at 1 and 12 months after TBI. a 1 month post-injury b 12 months post-injury. Radiological convention is used for display. c Graph depicts average MD values of amygdala (integrated across the entire structure) in each hemisphere at each time point
Model of TBI-induced hyperexcitability and anxiety in the BLA. a Cartoon of a pyramidal neuron with excitatory and inhibitory synapses along a dendrite and inhibitory neuronal synapses on the soma and α2-containing GABAA receptors along the axon initial segment (AIS) of a glutamatergic axon that activate the central amygdala. Also note the GABAergic neurons co-expressing NPY (orange GABAergic neuron synapsing on soma) where release of NPY would activate the NPYR1 receptor to enhance inhibition and reduce excitability. Under this condition, one would expect a higher mature BDNF to pro-BDNF ratio that would increase GABAA receptors on the cell surface. b In the setting of a mild TBI, there is significant loss of GABAergic neurons (brown X at dendrite) including possibly those that co-express NPY (Brown X on orange GABAergic neuron at soma), and reduced cell surface expression of GABAA receptors that may include loss of α2-containing GABAA receptors at the AIS (brown X) leading to hyperexcitability (yellow lightning bolt) of the central amygdala and an anxiety-like phenotype. Under this condition, an increased pro-BDNF/mature BDNF ratio may be present along with a possible increase in specific phosphatases and decreased synthesis of GABAA receptors
Article
Traumatic brain injury (TBI) has reached epidemic proportions around the world and is a major public health concern in the United States. Approximately 2.8 million individuals sustain a traumatic brain injury and are treated in an Emergency Department yearly in the U.S., and about 50,000 of them die. Persistent symptoms develop in 10–15% of the cases including neuropsychiatric disorders. Anxiety is the second most common neuropsychiatric disorder that develops in those with persistent neuropsychiatric symptoms after TBI. Abnormalities or atrophy in the temporal lobe has been shown in the overwhelming number of TBI cases. The basolateral amygdala (BLA), a temporal lobe structure that consolidates, stores and generates fear and anxiety-based behavioral outputs, is a critical brain region in the anxiety circuitry. In this review, we sought to capture studies that characterized the relationship between human post-traumatic anxiety and structural/functional alterations in the amygdala. We compared the human findings with results obtained with a reproducible mild TBI animal model that demonstrated a direct relationship between the alterations in the BLA and an anxiety-like phenotype. From this analysis, both preliminary insights, and gaps in knowledge, have emerged which may open new directions for the development of rational and more efficacious treatments.
 
Article
The emergence of multidrug-resistant (MDR) bacteria is a major challenge for antimicrobial chemotherapy. Concerning this issue, antimicrobial peptides (AMPs) have been presented as novel promising antibiotics. Our previous de novo designed melittin-derived peptides (MDP1 and MDP2) indicated their potential as peptide drug leads. Accordingly, this study was aimed to evaluate the kinetics of activity, toxicity, and stability of MDP1 and MDP2 as well as determination of their structures. The killing kinetics of MDP1 and MDP2 demonstrate that all bacterial strains were rapidly killed. MDP1 and MDP2 were ca. 100- and 26.6-fold less hemolytic than melittin and found to be respectively 72.9- and 41.6-fold less cytotoxic than melittin on the HEK293 cell line. MDP1 and MDP2 showed 252- and 132-fold improvement in their therapeutic index in comparison to melittin. MDP1 and MDP2 sustained their activities in the presence of human plasma and were found to be ca. four to eightfold more stable than melittin. Spectropolarimetry analysis of MDP1 and MDP2 indicates that the peptides adopt an alpha-helical structure predominantly. According to the fast killing kinetics, significant therapeutic index, and high stability of MDP1, it could be considered as a drug lead in a mouse model of septicemia infections.
 
The design of study. pAHF persistent/late AHF more than 48 h after admission, pLVEF preserved left-ventricular ejection fraction, STEMI ST-elevation myocardial infarction
ROC curve of plasma glycine level for prediction of pAHF in patients with STEMI and pLVEF (n = 69) (AUC 0.84 ± SE 0.05 [95% CI 0.73–0.92], p < 0.0001). AUC area under curve, CI confidence interval, pAHF persistent/late AHF more than 48 h after admission, pLVEF preserved left-ventricular ejection fraction, ROC receiver-operator characteristic, SE standard error, STEMI ST-elevation myocardial infarction
Article
Nowadays, the problem of preventing acute heart failure (AHF) in patients with ST-elevation myocardial infarction (STEMI) and preserved left-ventricular ejection fraction (pLVEF) is still not completely resolved, especially in late-presented patients. The purpose of study was: (1) assessment of free plasma amino acid (PAA) alterations in STEMI patients [not receiving reperfusion therapy (RT)], depending on sex and LVEF; (2) analysis of development of late/persistent AHF more than 48 h after admission (pAHF) in STEMI patients with pLVEF depending on PAA levels. This prospective cohort study included 92 STEMI patients (33 women and 59 men), not receiving RT. The free PAA were investigated by ion-exchange liquid-column chromatography. The women had significantly higher PAA levels than men in general cohort and cohort with pLVEF (n = 69). There were associations between female sex and pAHF in general cohort (OR 3.7, p = 0.004) and cohort with pLVEF (OR 11.4, p = 0.0001) by logistic regression. The association between pAHF and glycine level [OR 2.5, p < 0.0001; AUC 0.84, p < 0.0001; 86.7% sensitivity and 77.8% specificity for > 2.6 mg/dL] was revealed in cohort with pLVEF (including female and male). Glycine remained a predictor of pAHF with pLVEF by multivariable logistic regression adjusting for comorbidities, demographic and clinical variables. Higher rate of pAHF in female than in male STEMI patients with pLVEF is associated with higher plasma glycine in women. The glycine level may be genetically determinated by female sex. The plasma glycine > 2.6 mg/dL is a predictor of pAHF in STEMI with pLVEF (including female and male).
 
Article
Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of ¹H-¹⁵N and ¹⁹F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive ¹⁹F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed ¹⁹F-NMR.
 
Article
Hypertension is a major risk factor for kidney and cardiovascular disease. The treatment of hypertensive individuals by selected ACE inhibitors and certain di-and tripeptides halts the progression of renal deterioration and extends life-span. Renal reabsorption of these low molecular weight substrates are mediated by the PEPT1 and PEPT2 cotransporters. This study aims to investigate whether hypertension and ageing affects renal PEPT cotransporters at gene, protein expression and distribution as well as function in the superficial cortex and the outer medulla of the kidney. Membrane vesicles from the brush border (BBMV) and outer medulla (OMMV) were isolated from the kidneys of young Wistar Kyoto (Y-WKY), young spontaneously hypertensive (Y-SHR), and middle aged SHR (M-SHR) rats. Transport activity was measured using the substrate, β-Ala-Lys (AMCA). Gene expression levels of PEPT genes were assessed with qRT-PCR while renal localisation of PEPT cotransporters was examined by immunohistochemistry with Western Blot validation. The Km and Vmax of renal PEPT1 were decreased significantly in SHR compared to WKY BBMV, whilst the Vmax of PEPT2 showed differences between SHR and WKY. By contrast to the reported cortical distribution of PEPT1, PEPT1-staining was detected in the outer medulla, whilst PEPT2 was expressed primarily in the cortex of all SHR; PEPT1 was significantly upregulated in the cortex of Y-SHR. These outcomes are indicative of a redistribution of PEPT1 and PEPT2 in the kidney proximal tubule under hypertensive conditions that has potential repercussions for nutrient handling and the therapeutic use of ACE inhibitors in hypertensive individuals.
 
Overview of the study design
Effects of BCAA supplementation on serum amino acid levels and protein status in dams fed a low-protein diet. A Serum BCAA levels and B EAA and NEAA levels. C Serum amino acid levels, which were significantly different among the groups. D Serum total protein, albumin and BUN levels. E Hepatic total protein levels. Data are presented as the mean ± SEM (n = 3–4). Bars without a common superscript significantly differ (one-way ANOVA followed by Duncan’s multiple range test, p < 0.05)
Effects of BCAA supplementation on hepatic protein synthesis in dams fed a low-protein diet. Protein levels of A p-S6, total S6, p-mTOR and total mTOR and B p-eIF2α and total eIF2α were determined by immunoblotting. HSC70 was used as an endogenous control to normalize the band. Data are presented as the mean ± SEM (n = 3). Bars without a common superscript significantly differ (one-way ANOVA followed by Duncan’s multiple range test, p < 0.05)
Effects of maternal BCAA supplementation on body growth and biochemical parameters in PND21 offspring from dams fed a low-protein diet. A Body weight change. B Organ weight. C Serum and D hepatic biochemical parameters. Data are the mean ± SEM (n = 11–12). Bars without a common superscript significantly differ (one-way ANOVA followed by Duncan’s multiple range test, p < 0.05). E Heatmap of Pearson correlation coefficients between the significantly altered anthropometric and biochemical parameters of dams and their offspring. Asterisks indicate that the correlation is significant (p < 0.05)
Effects of maternal BCAA supplementation on liver development in PND21 offspring from dams fed a low-protein diet. A Relative protein levels of PCNA were determined by immunoblotting. HSC70 was used as an endogenous control to normalize the band. B Representative images of H&E staining of liver sections (bar size = 50 μm) and relative area of hepatic vessel system. C Correlation between offspring hepatic vessel system area, and maternal serum and hepatic total protein levels. Pearson correlation coefficient, r and p value are indicated. D Relative mRNA levels of hepatic growth factor and sinusoidal development markers, were analyzed by qRT–PCR. The expression of Actb gene was used as the internal control to normalize the data. Data are expressed as the mean ± SEM (n = 3–4). Bars without a common superscript significantly differ (one-way ANOVA followed by Duncan’s multiple range test, p < 0.05)
Article
A considerable number of studies have reported that maternal protein restriction may disturb fetal growth and organ development due to a lower availability of amino acids. Leucine, one of branched-chain amino acid (BCAA) promotes protein synthesis through mechanistic target of rapamycin signaling. Here, we investigated the effects of BCAA supplementation in the dams fed a low-protein diet on serum and hepatic biochemical parameters of protein metabolism of dams and their offspring. Female ICR mice were fed a control (20% casein), a low-protein (10% casein), a low-protein with 2% BCAAs or a low-protein with 2% alanine diet for 2 weeks before mating and then throughout pregnancy and lactation. Alanine was used as an amino nitrogen control for the BCAA. Dams and their male offspring were sacrificed at postnatal day 21. There were no changes in body weight and fat mass in low-protein fed dams; however, BCAA supplementation significantly increased fat mass and serum leptin levels. Low-protein diet consumption reduced maternal protein synthesis based on biochemical analysis of serum albumin and hepatic protein levels and immunoblotting of S6 protein, which were increased by BCAA and alanine supplementation. Offspring from dams fed a low-protein diet exhibited lower body and organ weights. Body weight and hepatic protein levels of the offspring were increased by alanine supplementation. However, the decreased serum biochemical parameters, including glucose, triglyceride, total protein and albumin levels in the low-protein offspring group were not changed in response to BCAA or alanine supplementation. A reduced density of the hepatic vessel system in the offspring from dams fed a low-protein diet was restored in the offspring from dams fed either BCAA and alanine-supplemented diet. These results suggest that supplementation of amino nitrogen per se may be responsible for inducing hepatic protein synthesis in the dams fed a low-protein diet and alleviating the distorted growth and liver development of their offspring.
 
Article
Using 3,4-dihalo-2(5H)-furanones and easily available hemostatic drugs, such as tranexamic acid (TA), 4-aminomethylbenzoic acid (ABA), aminocaproic acid (AA) as starting materials, serial multi-functional molecules 2(5H)-furanonyl amino acids are designed by the combination of different pharmacophores, and successfully synthesized by a transition metal-free Michael addition-elimination reaction. The reaction is carried out under mild conditions with ethanol-dichloromethane as solvent and only stirring at room temperature for 24 h, and the yield can be up to 91%. All products are well characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), high-resolution mass spectra (HRMS). Ten typical target compounds among them are selected out for the experiments of hemostasis performance by the evaluation of in vitro clot formation model and liver hemorrhage model. The test results show that, their hemostasis effect is better than the original drugs. Especially the target compound G, a TA derivative from 5-borneoloxy-3,4-dibromo-2(5H)-furanone, has the best hemostasis effect among all the tested compounds. These obtained target molecules are expected to be used as multi-functional hemostatic drugs.
 
Article
Sepsis-induced fulminant hepatitis (FH) is a fatal syndrome that has a worse prognosis in clinical practice. Hence, seeking effective agents for sepsis-induced FH treatment is urgently needed. Fibroblast growth factors (FGFs) are vital for tissue homeostasis and damage repair in various organs including the liver. Our study aims to investigate the protective effects and potential mechanisms of FGF9 on lipopolysaccharide (LPS)/D-galactosamine (D-Gal)-induced FH in mice. We found that pre-treatment with FGF9 exhibited remarkable hepaprotective effects on liver damage caused by LPS/D-Gal, as manifested by the concomitant decrease in mortality and serum aminotransferase activities, and the attenuation of hepatocellular apoptosis and hepatic histopathological abnormalities in LPS/D-Gal-intoxicated mice. We further found that FGF9 alleviated the infiltration of neutrophils into the liver, and decreased the serum levels of pro‐inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) in LPS/D-Gal-challenged mice. These effects can be explained at least in part by the inhibition of NF-κB signaling pathway. Meanwhile, FGF9 enhanced the antioxidative defense system in mice livers by upregulating the expression of NRF-2-related antioxidative enzymes, including glutamate-cysteine ligase catalytic subunit (GCLC), NAD(P)H: quinone oxidoreductase 1 (NQO-1), and heme oxygenase-1 (HO-1). These data indicate that FGF9 represents a promising therapeutic drug for ameliorating sepsis-induced FH via its anti-apoptotic and anti-inflammatory capacities.
 
Article
Carnosine and other histidine-containing dipeptides are expected to be important anti-oxidants in vertebrates based on various in vitro and in vivo studies with exogenously administered carnosine or its precursor β-alanine. To examine a possible anti-oxidant role of endogenous carnosine, mice lacking carnosine synthase (Carns1−/−) had been generated and were examined further in the present study. Protein carbonylation increased significantly between old (18 months) and aged (24 months) mice in brain and kidney but this was independent of the Carns1 genotype. Lipoxidation end products were not increased in 18-month-old Carns1−/− mice compared to controls. We also found no evidence for compensatory increase of anti-oxidant enzymes in Carns1−/− mice. To explore the effect of carnosine deficiency in a mouse model known to suffer from increased oxidative stress, Carns1 also was deleted in the type II diabetes model Leprdb/db mouse. In line with previous studies, malondialdehyde adducts were elevated in Leprdb/db mouse kidney, but there was no further increase by additional deficiency in Carns1. Furthermore, Leprdb/db mice lacking Carns1 were indistinguishable from conventional Leprdb/db mice with respect to fasting blood glucose and insulin levels. Taken together, Carns1 deficiency appears not to reinforce oxidative stress in old mice and there was no evidence for a compensatory upregulation of anti-oxidant enzymes. We conclude that the significance of the anti-oxidant activity of endogenously synthesized HCDs is limited in mice, suggesting that other functions of HCDs play a more important role.
 
Article
Enterocytes of young pigs are known to use glutamine, glutamate, and glucose as major metabolic fuels. However, little is known about the roles of aspartate, alanine, and fatty acids as energy sources for these cells. Therefore, this study simultaneously determined the oxidation of the amino acids and glucose as well as short- and long-chain fatty acids in enterocytes of developing pigs. Jejunal enterocytes were isolated from 0-, 7-, 14- and 21-day-old piglets, and incubated at 37 °C for 30 min in Krebs–Henseleit bicarbonate buffer (pH 7.4) containing 5 mM d-glucose and one of the following: d-[U-¹⁴C]glucose, 0.5–5 mM l-[U-¹⁴C]glutamate, 0.5–5 mM l-[U-¹⁴C]glutamine, 0.5–5 mM l-[U-¹⁴C]aspartate, 0.5–5 mM l-[U-¹⁴C]alanine, 0.5–2 mM l-[U-¹⁴C]palmitate, 0.5–5 mM [U-¹⁴C]propionate, and 0.5–5 mM [1-¹⁴C]butyrate. At the end of the incubation, ¹⁴CO2 produced from each ¹⁴C-labeled substrate was collected. Rates of oxidation of each substrate by enterocytes from all age groups of piglets increased (P < 0.05) gradually with increasing its extracellular concentrations. The rates of oxidation of glutamate, glutamine, aspartate, and glucose by enterocytes from 0- to 21-day-old pigs and of alanine from newborn pigs were much greater (P < 0.05) than those for the same concentrations of palmitate, propionate, and butyrate. Compared with 0-day-old pigs, the rates of oxidation of glutamate, aspartate, glutamine, alanine, and glucose by enterocytes from 21-day-old pigs decreased (P < 0.05) markedly, without changes in palmitate oxidation. Oxidation of alanine, propionate, butyrate and palmitate by enterocytes of pigs was limited during their postnatal growth. At each postnatal age, the oxidation of glutamate, glutamine, aspartate, and glucose produced much more ATP than alanine, propionate, butyrate and palmitate. The degradation of glutamate was initiated primarily by glutamate-pyruvate and glutamate-oxaloacetate transaminases. Our results indicated that amino acids (glutamate plus glutamine plus aspartate) are the major metabolic fuels in enterocytes of 0- to 21-day-old pigs.
 
Article
This study was conducted to test the hypothesis that increasing dietary content of glutamate through addition of monosodium glutamate (MSG) enhances milk production by lactating sows and the growth of their offspring. Thirty multiparous sows (Landrace × Large White) were assigned randomly into one of three dietary groups: control (a corn- and soybean meal-based diet), the basal diet + 1% MSG, and the basal diet + 2% MSG. Diets were made isonitrogenous by the addition of appropriate amounts of l-alanine. Lactating sows had free access to drinking water and were fed twice daily their respective diets. The number of live-born piglets was standardized to 9 per sow at day 0 of lactation (the day of farrowing). On days 3, 15, and 29 of lactation, body weight and milk consumption of piglets were measured, and blood samples obtained from sows and piglets at 2 h and 1 h after feeding, respectively. Feed intake of sows did not differ (P > 0.05) among the three groups of sows. Concentrations of aspartate, glutamine, citrulline, arginine, tryptophan, proline, branched-chain amino acids, and glutamate were greater (P < 0.05) in the plasma of MSG-supplemented sows and their piglets than for controls. When compared with the control, dietary supplementation with 1–2% MSG increased (P < 0.05): concentrations of many free amino acids (including glutamate plus glutamine) and all protein-bound amino acids in milk; the milk intake of piglets by 14–25%; and daily weight gains of piglets by 23–44%. These results indicate that dietary supplementation with 1–2% MSG to lactating sows enhances milk production to support the growth of sow-reared piglets.
 
Article
Hypusination is a unique two-step enzymatic post-translational modification of the N ε -amino group of lysine-50 of the eukaryotic initiation factor 5A (eIF5A). We developed a specific and sensitive gas chromatography–mass spectrometry (GC–MS) method for the measurement of biological hypusine (Hyp), i.e., N ε -(4-amino-2-hydroxybutyl)lysine. The method includes a two-step derivatization of Hyp: first esterification with 2 M HCl in CH 3 OH (60 min, 80 °C) to the methyl ester (Me) and then acylation with penta-fluoro-propionic (PFP) anhydride in ethyl acetate (30 min, 65 °C). Esterification with 2 M HCl in CD 3 OD was used to prepare the internal standard. The major derivatization product was identified as the un-labelled (d 0 Me) and the deuterium-labelled methyl esters (d 3 Me) derivatives: d 0 Me-Hyp-(PFP) 5 and d 3 Me-Hyp-(PFP) 5 , respectively. Negative-ion chemical ionization generated the most intense ions with m / z 811 for d 0 Me-Hyp-(PFP) 5 and m / z 814 for the internal standard d 3 Me-Hyp-(PFP) 5 . Selected-ion monitoring of m / z 811 and m / z 814 was used in quantitative analyses. Free Hyp was found in spot urine samples (10 µL) of two healthy subjects at 0.60 µM (0.29 µmol Hyp/mmol creatinine) in the female and 1.80 µM (0.19 µmol Hyp/mmol creatinine) in the male subject. The mean accuracy of the method in these urine samples spiked with 1–5 µM Hyp was 91–94%. The limit of detection (LOD) of the method is 1.4 fmol Hyp. The method was applied to measure the urinary excretion rates of Hyp in healthy black ( n = 38, age 7.8 ± 0.7 years) and white ( n = 41, age 7.7 ± 1.0 years) boys of the Arterial Stiffness in Offspring Study (ASOS). The Hyp concentrations were 3.55 [2.68–5.31] µM (range 0.54–9.84 µM) in the black boys and 3.87 [2.95–5.06] µM (range 1.0–11.7 µM) in the white boys ( P = 0.64). The creatinine-corrected excretion rates were 0.25 [0.20–0.29] µmol/mmol (range 0.11–0.36 µmol/mmol) in the black boys and 0.26 [0.21–0.30] µmol/mmol (range 0.10–0.45 µmol/mmol) in the white boys ( P = 0.82). These results suggest that there is no ethnic-related difference in the ASOS population in the eIF5A modification. Remarkable differences were found between black and white boys with respect to correlations of urinary Hyp with amino acids and advanced glycation end-products of Lys, Arg and Cys. Deoxyhypusine, formally the direct precursor of Hyp, seems not to be excreted in the urine by healthy subjects.
 
A representative chromatogram showing signals and retention time of four analytes in human serum
Differences in serum analyte levels between PE patients and controls (CTL) in the same period. Data were expressed from minimum to maximum. *P < 0.05, **P < 0.01, ***P < 0.001, when compared to CTL in the same period
Differences in serum analyte levels among MPE, SPE and controls (CTL) in the same period. Data were expressed from minimum to maximum, showing all points. *P < 0.05, **P < 0.01, ***P < 0.001, when compared with each other in the same period
ROC curve analysis of the single serum analyte and combination panels predicting MPE a and all PE b before the 20th week. hARG + ADMA represents the combination panels of the serum hARG and ADMA levels. hARG + ADMA + SDMA represents the combination panels of the serum hARG, ADMA and SDMA levels
Article
l-homoarginine (hARG) is involved in nitric oxide biosynthesis, but its role and concentration in preeclampsia (PE) have not been fully revealed. The purpose of this study was to develop and validate a feasible clinical assay to quantify serum hARG, arginine (ARG), asymmetric (ADMA) and symmetric dimethylarginines (SDMA) levels by LC–MS/MS and investigate their differences at different stages of pregnancy with or without preeclampsia. Serum samples were collected from 84 pregnant women without complications (controls), 84 with mild preeclampsia (MPE), and 81 with severe preeclampsia (SPE) at various gestation stages (before the 20th week, during the 20th–28th week or after the 28th week of gestation). No significant difference in ARG levels was observed between PE and controls at any stage (P > 0.05). The serum hARG levels and hARG/ADMA ratios of MPE before the 20th week were higher than those of controls (P < 0.001). ADMA levels of MPE were higher than those of controls during the 20th–28th week (P < 0.01). SDMA levels of SPE were higher than those of MPE (P < 0.01) and controls (P < 0.05) after the 28th week. Elevated serum hARG before the 20th week was identified as an independent predictor for PE (OR = 1.478, 95% CI 1.120–1.950). ROC curve analysis showed serum hARG before the 20th week had a good potential to predict MPE (AUC = 0.875, 95% CI 0.759–0.948). In conclusion, our study indicated that elevated serum hARG and dimethylarginine levels detected by LC–MS/MS might serve as potential biomarkers for the early prediction of PE.
 
Article
Oxidative stress may cause extended tyrosine posttranslational modifications of peptides and proteins. The 3-nitro-L-tyrosine (Nit), which is typically formed, affects protein behavior during neurodegenerative processes, such as Alzheimer’s and Parkinson’s diseases. Such metabolic products may be conveniently detected at very low concentrations by surface enhanced Raman spectroscopy (SERS). Previously, we have explored the SERS detection of the Nit NO2 bending vibrational bands in a presence of hydrogen chloride (Niederhafner et al., Amino Acids 53:517–532, 2021, ibid). In this article, we describe performance of a new SERS substrate, “pink silver”, synthesized photochemically. It provides SERS even without the HCl induction, and the acid further decreases the detection limit about 9 times. Strong SERS bands were observed in the asymmetric (1550–1475 cm⁻¹) and symmetric (1360–1290 cm⁻¹) NO stretching in the NO2 group. The bending vibration was relatively weak, but appeared stronger when HCl was added. The band assignments were supported by density functional theory modeling.
 
Article
Vanadium carbide MXene (V2C) acts as a new type of two-dimensional (2D) graphene-like transition metal material that has attracted research interest. V2C has been widely used in various fields due to its excellent physical and chemical properties. Herein, the self-assembled V2C@gold nanoparticles (V2C@AuNPs) are prepared by water bath process at 80 °C. With the addition of glutathione (GSH), the absorbance (Abs.) at 550 nm of V2C@AuNPs was decreased. Therefore, an optical sensor is developed to detect GSH based on the properties of V2C@AuNPs. Under the optimal conditions, the detection range is 1–32 µM and the detection limit is 0.099 µM. Furthermore, the proposed GSH sensor exhibits high sensitivity, high selectivity, strong stability, and excellent recovery. The work will expand the application of V2C in biosensing.
 
Article
Amino acids are the essential building blocks of both synthetic and natural peptides, which are crucial for biological functions and also important as biological probes for mapping the complex protein–protein interactions (PPIs) in both prokaryotic and eukaryotic systems. Mapping the PPIs through the chemical biology approach provides pharmacologically relevant peptides, which can have agonistic or antagonistic effects on the targeted biological systems. It is evidenced that ≥ 60 peptide-based drugs have been approved by the US-FDA so far, and the number will improve further in the foreseeable future, as ≥ 140 peptides are currently in clinical trials. However, natural peptides often require fine-tuning of their pharmacological properties by strategically replacing the αL-amino acids of the peptides with non-coded amino acids (NCAA), for which codons are absent in the genetic code for biosynthesis of proteins, prior to their applications as therapeutics. Considering the diverse repertoire of the NCAAs, the conformational space of many NCAAs is yet to be explored systematically in the context of the rational design of therapeutic peptides. The current study deciphers the conformational landscape of a few such Cα-substituted aromatic NCAAs (Ing: 2-indanyl-l-Glycine; Bpa: 4-benzoyl-l-phenylalanine; Aic: 2-aminoindane-2-carboxylic acid) both in the context of tripeptides and model synthetic peptide sequences, using alanine (Ala) and proline (Pro) as the reference. The combined data obtained from the computational and biophysical studies indicate the general success of this approach, which can be exploited further to rationally design optimized peptide sequences of unusual architecture with potent antimicrobial, antiviral, gluco-regulatory, immunomodulatory, and anti-inflammatory activities.
 
Article
Moderate oxidative stress induces temporal impairment in mitochondrial ATP production. As glutathione (GSH) content is reduced to eliminate oxidative stress by oxidation–reduction reaction, intracellular GSH content is crucial for maintaining mitochondrial function under oxidative stress. GSH precursors such as N-acetyl cysteine (NAC) and cysteine are known to suppress oxidative stress based on the supply of cysteine residues being rate-limiting for GSH synthesis. However, it remains unclear whether cystine (Cys2) can suppress mitochondrial dysfunction under oxidative stress conditions. Therefore, we examined whether Cys2 could attenuate mitochondrial dysfunction under moderate oxidative stress without scavenging reactive oxygen species (ROS) in the medium. C2C12 myotubes were incubated for 120 min in a Cys2-supplemented medium and subsequently exposed to hydrogen peroxide (H 2 O 2 ). Heme oxygenase-1 (HO-1) gene expression, intracellular cysteine and GSH content, intracellular ATP level, and maximal mitochondrial respiration were assessed. Cys2 treatment significantly increased GSH content in a dose-dependent manner under oxidative stress. Cys2 treatment significantly decreased HO-1 expression induced by H 2 O 2 exposure. In addition, maximal mitochondrial respiration rate was decreased by H 2 O 2 exposure, but improved by Cys2 treatment. In conclusion, Cys2 treatment mitigates oxidative stress-induced mitochondrial dysfunction by maintaining GSH content under moderate oxidative stress without scavenging ROS in the medium.
 
A In cyclic voltammetry, the scan rate was 100 mVs⁻¹ for 0.1 M NH4H2PO4 at the concentration ranges of 10, 20, 30, 40, 50, 60, 70, 80, and 90 ugL⁻¹ of insulin. B Square-wave anodic stripping voltammetry with pH ranges of 2.9, 3.5, 3.9, 4.5, 4.6, 5.2, 5.8, 6.4, and 7.1 at 3.5 mgL⁻¹ insulin, a deposition potential of − 1.6 V, a frequency of 450 Hz, an amplitude of 0.2 V, and a potential step of 25 mV. The other experimental parameters were the same as those in Fig. 2
A The peak current on the accumulation time variations from 20 to 400 s. B Accumulation potential variations from − 1.8 to − 1.2 V. C SW amplitude variations from 0.5 to 0.1 V at 3 mgL⁻¹ added insulin. The other experimental parameters were the same as those in Fig. 3
The calibration curve and raw voltammogram obtained from 0.01–0.10 ngL⁻¹ and 1–10 ngL⁻¹ insulin at a pH of 4.5, an initial potential of − 1.6 V, a final potential of 1.1 V, a square-wave frequency of 450 Hz, an amplitude of 0.2 V, an incremental potential of 25 mV, and an accumulation time of 100 s
The complete sequence of insulin DNA
Metal and insulin-like ionic interference effects
Article
This paper describes the development of a voltammetric assay of insulin using a DNA immobilized onto a carbon nanotube paste electrode (CNPE), the peak potential of which was 0.2 V, vs. Ag/AgCl on the CNPE. The cyclic voltammetry (CV) and square-wave (SW) stripping voltammetry parameters of the optimized conditions were determined. Low analytical working ranges of 10–80 ugL−1 CV and 0.01–0.1 ngL−1 SW were attained. The precision of the insulin concentration of 0.01 ugL−1 was 0.14 (n = 15) RSD using the optimum conditions, in which the detection limit was 0.004 ngL−1 (6.9 × 10–12 M) (S/N = 3) using only an accumulation time of 400 s. The developed method was applied to determine insulin in a pharmacy drug from analytical-grade chemicals (from Aldrich).
 
Article
Human microtubule-associated protein Tau (τ) is abundant in the axons of neurons where it stabilizes microtubule bundles; abnormally hyperphosphorylated τ is a hallmark of Alzheimer’s disease (AD) and related tauopathies. The hyperphosphorylation events can be recognized by phosphotyrosine-recognition domain SH2 (Src homology 2) to elicit downstream τ signaling in AD pathology. In this study, a comprehensive binary interaction map (CBIM) of all the 6 τ phosphotyrosine sites with 120 SH2 domains in the human genome was systematically created at structural level using computational analyses and binding assays, from which we were able to identify those of strong and moderate binding pairs of sites to domains. It is found that the SH2-recognition specificity of different τ phosphotyrosine sites has been evolutionally optimized to become roughly orthogonal to each other, and thus these site phosphorylations would regulate different but probably partially overlapped biological functions in τ signaling. Some SH2 groups such as SRC, RIN, PLCG, SOCS and SH2D were revealed to have effective binding potency as compared to others; they could be regarded as potential τ-associated proteins to transduce the downstream signaling. We further determined the systematic binding affinities of 6 τ-phosphopeptides to the 11 SH2 domains in SRC group, from which the FYN-τ¹⁸ and YES-τ²⁹ pairs were identified as strong binders. Subsequently, rational molecular design was performed on τ¹⁸ and τ²⁹ to derive a number of τ-phosphopeptide mutants with increased affinity; they are self-inhibitory candidates to competitively target τ hyperphosphorylation events in AD. In addition, it is revealed that the primary anchor pY0 and secondary anchor X+3 of τ-phosphopeptides play an important role in SRC-group SH2 recognition, which confer stability and specificity to the SH2–phosphopeptide binding, respectively.
 
Visual predictive check stratified on baseline (a), single dose (b) and dose in steady state (c) for the final kinetic model. Observed homoarginine concentrations (points) and observed median (dot dashed line) with 5th to 95th percentile (dotted lines) compared to predicted median (solid line) with 5th to 95th percentile (dashed lines) and 95% confidence interval (shaded areas)
Conditionally weighted residuals (CWRES) versus individual population predictions (a) and time after dose (b) with LOESS smoothing curve (dashed line). Normalized prediction distribution errors (NPDE) versus individual population predictions (c) and time (d) with LOESS smoothing curve (dashed line)
Percentage of time in target within one dosing interval in steady state [dosing interval: 24 h, for the dose from 1.25 to 50 mg and reference 125 mg weekly, i.e., 168 h (right apart)] for the older (a) and young population (b). The population median is given by the solid line and variability is illustrated by shaded areas as 5th to 95th percentile in 10-percentile steps
Article
Homoarginine is an endogenous amino acid whose levels are reduced in patients with renal, cardio- and cerebrovascular disease. Moreover, low homoarginine concentrations independently predict morbidity and mortality in these patients. Besides endogenous synthesis, homoarginine is also a constituent of the human diet. The objective of the present study was to analyze the kinetics of orally supplemented homoarginine in human plasma by means of a pharmacometric approach. We developed a pharmacometric model to evaluate different dosing regimens, especially the regimen of 125 mg once weekly, based on a previous clinical study ( n = 20). The model was adapted to account for differences in baseline homoarginine plasma concentrations between healthy and diseased individuals. A novel dosing regimen of 25 mg once daily led to higher attainment of homoarginine reference concentrations using clinical trial simulations. With 25 mg/day, the trough concentration of only 6% of the older and 3.8% of the younger population was predicted to be below the target concentration of 2.0–4.1 µmol/L. In synopsis, the new dosing regimen recapitulates the kinetics of homoarginine in healthy individuals optimally.
 
Correlations between KP metabolites and inflammatory markers and disease activity in patients with BD. CRP C-reactive protein, ESR erythrocyte sedimentation rate, 3HAA hydroxyanthranilic acid, KYN kynurenine, KYNA kynurenic acid, NLR neutrophil-to-lymphocyte ratio, PCT plateletcrit, PLR platelet–lymphocyte ratio, QUIN quinolinic acid, TRP tryptophan
Article
Behçet disease (BD) is an inflammatory, multisystemic vasculitis of unknown etiopathogenesis. However, innate and adaptive immune system involvement and immune-mediated networks play a vital role in the inflammatory cascade. Indoleamine 2,3-dioxygenase 1 (IDO1) is activated in chronic inflammatory states and catalyzes the first and rate-limiting step of tryptophan (TRP) metabolism along the kynurenine pathway (KP). The study aimed to measure KP metabolites levels in patients with BD and investigate the relationship between disease activity and clinical findings with these metabolites. The study included 120 patients with BD and 120 healthy volunteers. Serum TRP, kynurenine (KYN), kynurenic acid (KYNA), 3-hydroxyanthranilic acid (3HAA), 3-hydroxykynurenine (3HK), and quinolinic acid (QUIN) levels were measured with the tandem mass spectrometric method. Demographic data, clinical manifestations, and disease activity score (BDCAF) were recorded. Serum KYN, KYNA, 3HK, 3HAA, QUIN levels, and KYN/TRP ratio were higher (p < 0.05) in patients with BD compared to the control group, while TRP levels were lower (p < 0.05). KYN/TRP ratio and QUIN levels were significantly higher in the presence of neuro-Behçet, while serum KYN levels were significantly higher in the presence of arthritis (p < 0.05). In addition, serum QUIN levels were significantly higher in the presence of thrombosis (p < 0.05). BDCAF score positively correlated with KYN/TRP ratio. Our findings showed that serum KP metabolite levels were elevated in patients with BD, and there is a relationship between these metabolites with disease activity, clinical findings, and inflammatory burden.
 
Article
The simple and facilitated transfer of tripeptide glutathione across the water/2-nitrophenyl octhyl ether interface was studied via cyclic voltammetry at interface between two immiscible electrolyte solutions (ITIES). The micro-perforated membrane prepared with a laser with a femtosecond pulse was used for mechanical stabilization of the interface. The method of cyclic voltammetry was used to study the passive and facilitated interfacial transfer of glutathione and its complex with the crown ether dibenzo-18-crown-6 (DB18C6).The glutathione mass transfer mechanism was established and substantiated, the diffusion coefficients, thermodynamic characteristics of interphase transfer and the constant of complexation of the glutathione by DB18C6 were determined. Square wave voltammetry based on facilitated transfer was used for more accurate and sensitive determination of glutathione low detection limit (0.8 μM) with wide linear dynamic range (from 3.0 to 80 μM) was reached. The influence of various potentially interfering ions on the voltammetric determination of glutathione has also been investigated. The method developed was applied to determine glutathione in aqueous solutions and malt extract.
 
Article
The Alzheimer’s disease leads to neurodegenerative processes and affecting negatively million people worldwide. The treatment of the disease is still difficult and incomplete in practice. Galanthamine is one of the most commonly used drugs against the illness. The main aim of this work is design and synthesis of new derivatives of galanthamine comprising peptide moiety as well as study of their β-secretase inhibitory activity and the anti-aggregating effect. All new derivatives of galanthamine containing analogues of Leu-Val-Phe-Phe (Aβ17-Aβ20) were synthesized in solution using fragment and consecutive condensation approaches. The new derivatives were characterized by melting points, NMR, and HPLC/MS. They were tested in vitro for β-secretase inhibition activity by means of fluorescent method and were investigated in vitro for anti-aggregation activity on sheep platelet-rich plasma. Although the new compounds do not contain a structural element responsible for the β-secretase inhibition, five of them show high or good β-secretase inhibitory activity between 19.98 and 51.19% with IC50 between 1.95 and 5.26 nM. Four of the new molecules were able to inhibit platelet aggregation between 55.0 and 90.0% with IC50 between 0.69 and 1.36 µM. Four of the compounds were able to inhibit platelet aggregation and two of them have high anti-aggregating effects.
 
Panel (a) Domain Mimicry Pair (DMPs) and Motif Mimicry Pairs in Host–pathogen protein–protein interactions and Host–host interaction network: a pathogen protein(red) interacts with many host proteins(blue) that in turn interacts with many other host proteins (yellow). The pathogen protein(red) and host first interactor protein(yellow) with a common interacting host protein (blue) are compared for similar domains (green) and motifs (purple) to determine DMPs and MMPs respectively. Panel (b) A Schematic of individual DMP: a host first interactor protein (yellow) and pathogen protein (red) that interacts with the same host protein (blue) share the same domain ‘A’ (green). B Schematic of individual MMP: a host first interactor protein (yellow) and pathogen protein (red) that interacts with the same host protein (blue) share the same motif ‘A’ (purple)
a Schematic of DMP through allosteric binding: a host first interactor protein (yellow) and pathogen protein (red) that interact with the same host protein (blue) share the same domain ‘A’ (green). Here, the pathogen protein and host first interactor protein bind to the same host through the mimicked domain but at different sites i.e., allosterically, thus leading to a change in shape of the host protein binding site. b Schematic of MMP through allosteric binding: a host first interactor protein (yellow) and pathogen protein (red) that interacts with the same host protein (blue) share the same motif ‘A’ (purple). Here, the pathogen protein and host first interactor protein bind to the same host through the mimicked motif but at different sites, i.e., allosterically thus leading to a change in shape of the host protein binding site
Database schematic: the basic pipeline for search options is represented on the left and the basic workflow as well as the count of entities in the database are shown on the right
a The ImitateDB web interface: expanded view of the search panel of the web interface showing the steps to query the ImitateDB database. b Receive large result files by email: expanded view of the mailer popped up on the ImitateDB interface
Article
Molecular mimicry of host proteins by pathogens constitutes a strategy to hijack the host pathways. At present, there is no dedicated resource for mimicked domains and motifs in the host–pathogen interactome. In this work, the experimental host–pathogen (HP) and host–host (HH) protein–protein interactions (PPIs) were collated. The domains and motifs of these proteins were annotated using CD Search and ScanProsite, respectively. Host and pathogen proteins with a shared host interactor and similar domain/motif constitute a mimicry pair exhibiting global structural similarity (domain mimicry pair; DMP) or local sequence motif similarity (motif mimicry pair; MMP). Mimicry pairs are likely to be co-expressed and co-localized. 1,97,607 DMPs and 32,67,568 MMPs were identified in 49,265 experimental HP-PPIs and organized in a web-based resource, ImitateDB (http://imitatedb.sblab-nsit.net) that can be easily queried. The results are externally integrated using hyperlinked domain PSSM ID, motif ID, protein ID and PubMed ID. Kinase, UL36, Smc and DEXDc were frequent DMP domains whereas protein kinase C phosphorylation, casein kinase 2 phosphorylation, glycosylation and myristoylation sites were frequent MMP motifs. Novel DMP domains SANT, Tudor, PhoX and MMP motif microbody C-terminal targeting signal, cornichon signature and lipocalin signature were proposed. ImitateDB is a novel resource for identifying mimicry in interacting host and pathogen proteins.
 
Article
Recently, we reviewed the important role of carbohydrates and lipids metabolism in different clinical aspects of multiple sclerosis (MS) disease. In the current paper, we aimed to review the contribution of amino acids and their major derivatives to different clinical outcomes of the disease, including etiology, pathogenesis, diagnosis, prognosis, and treatment. In this line, Thr (threonine), Phe (phenylalanine), Glu (glutamate), Trp (tryptophan), and Sero (serotonin) are the main examples of biomolecules that have been suggested for MS therapy. It has been concluded that different amino acids and their derivatives might be considered prominent tools for the clinical management of MS disease.
 
Article
The recent paleoproteomic studies, including paleo-metaproteomic analyses, improved our understanding of the dietary of ancient populations, the characterization of past human diseases, the reconstruction of the habitat of ancient species, but also provided new insights into the phylogenetic relationships between extant and extinct species. In this respect, the present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 30,000 years old. In particular, proteins were extracted by applying EVA (Ethylene–Vinyl Acetate studded with hydrophilic and hydrophobic resins) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: (i) an indirect description of the habitat of these two mammoths, and (ii) an improved characterization of the collagen type I, alpha-1 and alpha-2 chains (col1a1 and col1a2). Sequence characterization of the col1a1 and col1a2 highlighted some differences between M. primigenius and other Proboscidea together with the identification of three (two for col1a1, and one for col1a2) potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius with respect to the other two genera of elephantids (i.e., Elephas and Loxodonta), and the extinct American mastodon (i.e., Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. The data have been deposited to the ProteomeXchange with identifier < PXD029558 > .
 
Article
The ability of amino acid “ customizable units ” to generate structural diversity is illustrated by the conversion of 4-hydroxyproline (Hyp) units into a variety of nitrogen heterocycles. After a first common step, where the unit underwent a one-pot decarboxylation–alkylation reaction to afford 2-alkylpyrrolidines with high stereoselectivity, a divergent step was carried out. Thus, the deprotected 4-hydroxy group was used either to initiate a radical scission that afforded aliphatic β-amino aldehydes, or to carry out an elimination reaction, to give 2-alkyl-2,5-dihydro-1H-pyrroles. In the first case, the amines underwent a tandem reductive amination–cyclization to afford β-amino-δ-lactams, an efficient rigidifying unit in peptides. Different lactam N-substituents, such as alkylamines, peptides, and alkenyl chains suitable for olefin metathesis were introduced this way. In the second case, the pyrrole derivatives were efficiently converted into alkaloid and iminosugar derivatives in good global yields and with excellent stereoselectivity.
 
Simplified schematic of the arginine:glycine amidinotransferase (AGAT)-catalyzed biosynthesis of (1) L-homoarginine (hArg) from L-arginine (Arg) and L-lysine (Lys), and (2) of guanidinoacetate (GAA) from Arg and glycine (Gly), with L-ornithine (Orn) being the second common reaction product. Arginase hydrolyzes hArg to Lys and urea. GAA is methylated by guanidinoacetate N-methyltransferase (GAMT) to creatine using S-adenosylmethionine (SAM) as the methyl (Me) group donor. Creatine cyclizes to creatinine. The arrow below the structure of Arg indicates the C atom that is involved in the catalytic process. The width and thickness of the arrows indicates roughly the extent of the reactions
Partial correlation network between all targeted metabolites across all timepoints. The thicker the curve the stronger the correlation between two nodes. Red color means positive associations and blue color means negative associations
Changes in standardized estimates of coefficients of each predictor entered in the stepwise models (upper panel) and improvement in the SBC criteria (lower panel) when entering further metabolites
Calculated yield values for hArg from Lys in the rats of the study at baseline (T0; n = 95 rats), after 2 months (T2; n = 81 rats) and after 4 months (T4; n = 77 rats). One-way ANOVA and Tukey's multiple comparisons test were performed. There was no difference between T2 and T4 (P = 0.98). Date on the top are the median [interquartile range] values of the yield (%)
Article
L-Lysine (Lys) and L-arginine (Arg), but not L-homoarginine (hArg), are proteinogenic amino acids. In healthy humans, oral administration of hArg increased the plasma concentration of Lys, suggesting Lys as a metabolite of hArg. In humans and animals, hArg is biosynthesized from Arg and Lys by arginine:glycine amidinotransferase (AGAT). In vitro, recombinant human arginase and bovine liver arginase I hydrolyzed hArg to Lys, suggesting Lys as a metabolite of hArg. The aim of the present study was to investigate whether changes in blood concentrations of hArg and Lys in old rats fed for 4 months with varied controlled experimental diets could suggest interconversion of these amino acids. Blood samples (n = 253) were taken before (T0) and after 2 months (T2) and 4 months (T4) of the experiment. Plasma concentrations of Lys and hArg were determined by gas chromatography–mass spectrometry. The plasma hArg concentration markedly correlated with the plasma Lys concentration at all timepoints (r ≥ 0.7, P < 0.0001). Further analysis demonstrated that hArg and Lys are closely and specifically associated independently of experimental time/rat age and diet, suggesting that hArg and Lys are mutual metabolites in old rats. Based on the plasma concentration changes, the median yield of hArg from Lys was determined to be 0.17% at T0 and each 0.27% at T2 and T4. With a circulating concentration of about 3 µM, hArg a major metabolite of Lys in healthy humans. hArg supplementation is currently investigated as a cardioprotective means to improve impaired hArg synthesis. Present knowledge suggests that Lys rather than hArg supplementation may be even more favorable.
 
Article
Granular activated sludge has been described as a promising tool in treating wastewater. However, the effect of high concentrations of sulphur amino acids, cysteine and methionine, in the evolution, development and stability of AGS-SBRs (aerobic granular sludge in sequential batch reactors) and their microbial communities is not well-established. Therefore, this study aimed to evaluate microbial communities' size, structure and dynamics in two AGS-SBRs fed with two different concentrations of amino acids (50 and 100 mg L⁻¹ of both amino acids). In addition, the impact of the higher level of amino acids was also determined under an acclimatization or shock strategy. While N removal efficiency decreased with amino acids, the removal of the organic matter was generally satisfactory. Moreover, the abrupt presence of both amino acids reduced even further the removal performance of N, whereas under progressive adaptation, the removal yield was higher. Besides, excellent removal rates of cysteine and methionine elimination were found, in all stages below 80% of the influent values. Generally considered, the addition of amino acids weakly impacts the microbial communities' total abundances. On the contrary, the presence of amino acids sharply modulated the dominant bacterial structures. Furthermore, the highest amino acid concentration under the shock strategy resulted in a severe change in the structure of the microbial community. Acidovorax, Flavobacterium, Methylophilus, Stenotrophomonas and Thauera stood out as the prominent bacteria to cope with the high presence of cysteine and methionine. Hence, the AGS-SBR technology is valuable for treating influents enriched in sulphur Aa inclusively when a shock strategy was used.
 
Article
We studied the effect of feeding a single probiotic Limosilactobacillus reuteri DSM 17938 (LR 17938) on the luminal and plasma levels of amino acids and their derivatives in the suckling newborn mouse, using gas chromatography and high-performance liquid chromatography. We found that LR 17938 increased the relative abundance of many amino acids and their derivatives in stool, while it simultaneously significantly reduced the plasma levels of three amino acids (serine, citrulline, and taurine). Many peptides and dipeptides were increased in stool and plasma, notably gamma-glutamyl derivatives of amino acids, following ingestion of the LR 17938. Gamma-glutamyl transformation of amino acids facilitates their absorption. LR 17938 significantly upregulated N-acetylated amino acids, the levels of which could be useful biomarkers in plasma and warrant further investigation. Specific fecal microbiota were associated with higher levels of fecal amino acids and their derivatives. Changes in luminal and circulating levels of amino acid derivatives, polyamines, and tryptophan metabolites may be mechanistically related to probiotic efficacy.
 
Article
Chief cells are the predominant cells in parathyroid glands of healthy adults; however, parathyroid oxyphil cells, whose function is unknown, increase dramatically in patients with secondary hyperparathyroidism (SHPT). Calcitriol and calcimimetics are the most powerful treatments for SHPT, while the mechanisms leading to calcitriol or calcimimetic resistance in oxyphil cell–predominant SHPT are unknown. Here we used transcriptomic and proteomic techniques to characterize oxyphil cells by comparing the differences between chief and oxyphil cell nodules of parathyroid glands in uremic patients. Compared to chief cell nodules, the most marked expression increases in oxyphil cell nodules were for mitochondrion-associated proteins. The mitochondria number and mitochondrial DNA content were also significantly increased in oxyphil cell nodules. Moreover, oxyphil cell nodules expressed parathyroid-specific factors, and exhibited lower levels of proliferation-related proteins but higher synthesis and secretion level of parathyroid hormone (PTH). The protein expression of SHPT-regulating factors, including vitamin-D receptor, calcium-sensing receptor and Klotho, were significantly downregulated in oxyphil cell nodules. Therefore, oxyphil cells characterized by enrich mitochondria in uremic patients showed higher synthesis and secretion of PTH but lower expression of SHPT regulators than chief cells, which may contribute to the pathophysiology of SHPT and the treatment resistance to calcitriol and calcimimetics.
 
The whole framework of ATGPred-FL for autophagy protein identification
Feature selection of the 52-dimensional probability feature. A The ranking orders of the top 20 features based on the classification importance score. B ten-fold cross-validation accuracy and MCC on the SVM classifier with a varied feature number
Comparison of our optimal feature with the class feature and individual feature descriptors. A–E The t-SNE distribution of DDE, QSOrder, ASDC, F41_c and F14_p feature, respectively. F The ROC curves of DDE, QSOrder, ASDC, F41_c and F14_p feature on the training set
Performance comparison of ATGPred-FL with three traditional ensemble methods on the training set (A) and independent test set (B)
A False positive rate of ATGPred-FL on fibrinogen, cytoplasmic and lectin proteins. B Predictive results of ATGPred-FL on unreviewed ATGs sequences
Article
Autophagy plays an important role in biological evolution and is regulated by many autophagy proteins. Accurate identification of autophagy proteins is crucially important to reveal their biological functions. Due to the expense and labor cost of experimental methods, it is urgent to develop automated, accurate and reliable sequence-based computational tools to enable the identification of novel autophagy proteins among numerous proteins and peptides. For this purpose, a new predictor named ATGPred-FL was proposed for the efficient identification of autophagy proteins. We investigated various sequence-based feature descriptors and adopted the feature learning method to generate corresponding, more informative probability features. Then, a two-step feature selection strategy based on accuracy was utilized to remove irrelevant and redundant features, leading to the most discriminative 14-dimensional feature set. The final predictor was built using a support vector machine classifier, which performed favorably on both the training and testing sets with accuracy values of 94.40% and 90.50%, respectively. ATGPred-FL is the first ATG machine learning predictor based on protein primary sequences. We envision that ATGPred-FL will be an effective and useful tool for autophagy protein identification, and it is available for free at http://lab.malab.cn/~acy/ATGPred-FL, the source code and datasets are accessible at https://github.com/jiaoshihu/ATGPred.
 
Article
Bombesin mediates several biological activities in the gastrointestinal (GI) tract and central nervous system in mammals, including smooth muscle contraction, secretion of GI hormones and regulation of homeostatic mechanisms. Here, we report a novel bombesin-like peptide isolated from Boana raniceps. Its amino acid sequence, GGNQWAIGHFM-NH2, was identified and structurally confirmed by HPLC, MS/MS and 454-pyrosequencing; the peptide was named BR-bombesin. The effect of BR-bombesin on smooth muscle contraction was assessed in ileum and esophagus, and its anti-secretory activity was investigated in the stomach. BR-bombesin exerted significant contractile activity with a concentration–response curve similar to that of commercially available bombesin in ileum strips of Wistar rats. In esophageal strips, BR-bombesin acted as an agonist, as many other bombesin-related peptides act, although with different behavior compared to the muscarinic agonist carbachol. Moreover, BR-bombesin inhibited stomach secretion by approximately 50% compared to the untreated control group. This novel peptide has 80% and 70% similarity with the 10-residue C-terminal domain of human neuromedin B (NMB) and human gastrin releasing peptide (GRP10), respectively. Molecular docking analysis revealed that the GRP receptor had a binding energy equal to − 7.3 kcal.mol⁻¹ and − 8.5 kcal.mol⁻¹ when interacting with bombesin and BR-bombesin, respectively. Taken together, our data open an avenue to investigate BR-bombesin in disorders that involve gastrointestinal tract motility and acid gastric secretion.
 
Article
Serine hydroxymethyltransferase 2 (SHMT2) converts serine into glycine in the mitochondrial matrix, transferring a methyl group to tetrahydrofolate. SHMT2 plays an important role in the maintenance of one-carbon metabolism. Previously, we found a negative correlation between the serine concentration and the progression of fatty liver disease (FLD). However, little is known about the role of SHMT2 in hepatic lipid metabolism. We established SHMT2 knockdown (KD) mouse primary hepatocytes using RNA interference to investigate the role of SHMT2 in lipid metabolism. SHMT2 KD hepatocytes showed decreased lipid accumulation with reduced glycine levels compared to the scramble cells, which was restored upon reintroducing SHMT2. SHMT2 KD hepatocytes showed downregulation of the mTOR/PPARɣ pathway with decreased gene expression related to lipogenesis and fatty acid uptake. Pharmacological activation of mTOR or PPARɣ overexpression blocked the inhibitory effect of SHMT2 KD on lipid accumulation. We also showed that glycine activated mTOR/PPARɣ signaling and identified glycine as a mediator of SHMT2-responsive lipid accumulation in hepatocytes. In conclusion, silencing SHMT2 in hepatocytes ameliorates lipid accumulation via the glycine-mediated mTOR/PPARɣ pathway. Our findings underscore the possibility of SHMT2 as a therapeutic target of FLD.
 
Kinetics of ¹⁵N (A) and ²H (B) goat milk enrichment during the five-day labeling protocol. For ¹⁵N labeling, the four goats received 5 g of ¹⁵N ammonium salt for 4 consecutive days (from day 1 to day 4). For ²H labeling, goats 1 and 3 received 80 and 160 mL of deuterated water, respectively, on one day (day 1) and goats 2 and 4 received 80 and 160 mL of deuterated water, respectively, for three consecutive days (from day 1 to day 3). Data are presented as mean of the 4 goats ± SD for ¹⁵N. AP atom percent
¹⁵N (A) and ²H (B) enrichment in individual amino acids of goat milk used to extract doubly labelled whey protein for the animal study. The dotted lines represent the natural abundance of ¹⁵N (0.367) and ²H (0.016). Data are presented as mean  ± SD for ¹⁵N. AP atom percent, IAA indispensable amino acid, DAA dispensable amino acid
²H goat milk enrichment in individual amino acids on day 5 of the five-day labeling protocol in each goat (A) and kinetics of ²H goat milk enrichment in individual amino acids during the five-day labeling protocol for goat 4 (B). Goats 1 and 3 received 80 and 160 mL of deuterated water, respectively, on one day (day 1) and goats 2 and 4 received 80 and 160 mL of deuterated water, respectively, for three consecutive days (from day 1 to day 3). AP atom percent
Recovery of dietary nitrogen (A) and hydrogen (B) in the different segments of the gastrointestinal tract 6 h after meal ingestion. Data are presented as mean + SD. n = 6 rats/group. * Significantly (P < 0.05) different from the dietary nitrogen within the same gastrointestinal segment and time
Article
Measurement of ileal amino acids (AA) bioavailability is recommended to evaluate protein quality. A dual isotope tracer method, based on plasma isotopic enrichment ratios, has been proposed to determine true digestibility in humans. In a pilot study, we aimed to evaluate whether this method could be implemented in rats to determine AA bioavailability based on isotopic enrichment ratios measured in cecal digesta or plasma samples. Goat milk proteins were intrinsically labeled with ¹⁵N and ²H. Wistar rats were fed a meal containing the doubly labeled goat whey proteins and a tracer dose of ¹³C-spirulina. Blood samples were collected 0, 1 h and 3 h after meal ingestion from the tail vein. The rats were euthanized 4 h (n = 6) or 6 h (n = 6) after meal to collect plasma and intestinal contents. True orocecal protein digestibility and AA bioavailability were assessed by means of ¹⁵N and ²H enrichment in cecum content and compared with absorption indexes determined at the plasma or cecum level using isotopic ratios. Plasma kinetics of isotopic enrichment could not be completed due to the limited quantity of plasma obtained with sequential blood collection. However, the absorption indexes determined from cecal ¹⁵N or ²H/¹³C ratios gave coherent values with true orocecal AA bioavailability. This dual isotope approach with measurements of isotopic ratios in digestive content could be an interesting strategy to determine true AA bioavailability in ileal digesta of rats.
 
Chemical structures of the secondary amino acids discussed in this review
Biosynthesis and racemization of proline and hydroxyprolines, adapted according to (Ogata et al. 1999; Konig et al. 2018)
Biosynthesis of pipecolic acid and N-hydroxy pipecolic acid, adapted according to (Takagi et al. 2001; Fujii et al. 2002; Velíšek et al. 2006; Leandro and Houten 2020; Ogata et al. 1999; Hartmann and Zeier 2018)
Chromatograms of eight cyclic secondary amino acid enantiomer separation on the capillary Chirasil-L-Val column after heptafluorobutyl chloroformate and methylamine derivatization (Opekar et al. 2021)
Article
Naturally occurring secondary amino acids, with proline as the main representative, contain an alpha-imino group in a cycle that is typically four-, five-, and six-membered. The unique ring structure exhibits exceptional properties—conformational rigidity, chemical stability, and specific roles in protein structure and folding. Many proline analogues have been used as valuable compounds for the study of metabolism of both prokaryotic and eukaryotic cells and for the synthesis of compounds with desired biological, pharmaceutical, or industrial properties. The d-forms of secondary amino acids play different roles in living organisms than the l-forms. They have different metabolic pathways, biological, physiological, and pharmacological effects, they can be indicators of changes and also serve as biomarkers of diseases. In the scientific literature, the number of articles examining d-amino acids in biological samples is increasing. The review summarises information on the occurrence and importance of d- and l-secondary amino acids—azetidic acid, proline, hydroxyprolines, pipecolic, nipecotic, hydroxypipecolic acids and related peptides containing these d-AAs, as well as the main analytical methods (mostly chromatographic) used for their enantiomeric determination in different matrices (biological samples, plants, food, water, and soil).
 
Alignment of the primary structure of Lm-SCL. The colors in the primary structures indicate the character of sidechain of amino acid residues and specific amino acids as follows: : hydrophobic, : cationic, : anionic, : polar, : G, : P, : H and Y. Jnetpred: the consensus prediction. Helices are marked as red tubes, and sheets are marked as light green arrows. JNETCONF: the confidence estimates for the prediction. High values mean high confidence. JNETHMM: the HMM profile-based prediction. Helices are marked as red tubes, and sheets are marked as light green arrows. JNETPSSM: the PSSM profile-based prediction. Helices are marked as red tubes, and sheets are marked as light green arrows. JNETJURY: An asterisk in this annotation indicates that JNETJURY was invoked to rationalize significantly different primary predictions. Jnet Burial: prediction of solvent accessibility
Molecular models of the substrate in the active center of Lm-SCL. The binding modes for Lm-SCL and l-selenocysteine (A) and l-cysteine (B) calculated by AutoDock Vina were visualized using PyMOL software. Carbon atoms of chains A and B of Lm-SCL, PLP molecules bound to K222 of chain A, and ligand molecules are shown in blue, green, yellow, and orange, respectively. Flexible residues during the simulation are shown in magenta. The binding affinities calculated from this simulation are noted below each image
Spectroscopic analysis of Lm-SCL and its mutated enzymes. A Absorption spectra of holo, apo, and reduced forms of Lm-SCL. Blue line, holo form; Green line, apo form; Red line, reduced form. The protein concentration was as follows: holo form, 0.44 mg/mL; apo form, 0.36 mg/mL; reduced form 0.37 mg/mL. The buffer used was 50 mM KPB (pH 7.0). B Comparison of the absorption spectrum of the holo-form of Lm-SCLwith that of Lm-SCL-H119A, C362A, R377A, and H119A/C362A. Blue line, Lm-SCL; Green line, Lm-SCL-C362A; Red line, Lm-SCL-H119A; Pale blue, Lm-SCL-R377A, Yellow, Lm-SCL-H119A/C362A. The protein concentration was as follows: Lm-SCL, 0.59 mg/mL; Lm-SCL-C362A, 0.54 mg/mL; Lm-SCL-H119A, 0.49 mg/mL; Lm-SCL-R377A, 0.51 mg/mL; Lm-SCL-H119A/C362A, 0.51 mg/mL. The buffer used was 50 mM KPB (pH 7.0)
Phylogenetic analysis of Lm-SCL. The phylogenetic analysis was carried out using the following sequences (accession no; identity for Lm-SCL): Leuconostoc miyukkimuchii (WP_220740652.1; 91.7%), Leuconostoc suionicum (WP_211636978.1; 82.8%), Leuconostoc litchii (WP_148606558.1; 82.4%), Leuconostoc pseudomesenteroides (TOZ08121.1; 80.6%), Leuconostoc falkenbergense (WP_188356479.1; 80.6%), Leuconostoc gelidum (WP_060391196.1; 77.5%), Leuconostoc inhae. (WP_220734553.1; 77.6%), Leuconostoc rapi (WP_204769388.1; 72.5%), Leuconostoc carnosum (WP_150280309.1; 74.0%), Leuconostoc holzapfelii (WP_168676043.1; 70.2%), Leuconostoc palmae (WP_220741874.1; 65.9%), Agrilactobacillus composti (WP_057002295.1; 63.8%), Companilactobacillus halodurans (WP_153522285.1; 64.3%), Enterococcus hulanensis (WP_206916504.1; 63.8%), Enterococcus faecalis (EGO6530340.1; 63.3%), Enterococcus gilvus (WP_221676086.1; 63.8%), Companilactobacillus heilongjiangensis (WP_041499075.1; 65.0%), Enterococcus phoeniculicola ATCC BAA-412 (EOL41599.1; 62.8%), Agrilactobacillus yilanensis (WP_125713532.1; 62.5%), Companilactobacillus huachuanensis (WP_137611559.1; 63.5%), Lentilactobacillus hilgardii (WP_003557453.1; 63.4%), and Enterococcus pseudoavium (WP_115872699.1; 64.8%)
Proposed reaction mechanism of Lm-SCL. A Without nucleophilic attack by Cys362. B With nucleophilic attack by Cys362
Article
We succeeded in expressing selenocysteine β-lyase (SCL) from a lactic acid bacterium, Leuconostoc mesenteroides LK-151 (Lm-SCL), in the soluble fractions of Escherichia coli Rosetta (DE3) using a novel expression vector of pET21malb constructed by ourselves that has both maltose binding protein (MBP)- and 6 × His-tag. Lm-SCL acted on l-selenocysteine, l-cysteine, and l-cysteine sulfinic acid but showed a high preference for l-selenocysteine. The kcat and kcat/Km values of Lm-SCL were determined to be 108 (min−1) and 42.0 (min−1・mM−1), respectively, and this was enough catalytic efficiency to suggest that Lm-SCL might also be involved in supplying elemental selenium from l-selenocysteine to selenoproteins like other SCLs. The optimum temperature and optimum pH of Lm-SCL were determined to be 37 °C and pH 6.5, respectively. Lm-SCL was stable at 37–45 °C and pH 6.5–7.5. Lm-SCL was completely inhibited by the addition of hydroxylamine, semicarbazide, and iodoacetic acid. The enzyme activity of Lm-SCL was decreased in the presence of various metal ions, especially Cu2+. The quaternary structure of Lm-SCL is a homodimer with a subunit molecular mass of 47.5 kDa. The similarity of the primary structure of Lm-SCL to other SCLs from Citrobacter freundii, Escherichia coli, humans, or mouse was calculated to be 47.0, 48.0, 12.5, or 24.0%, respectively. Unlike Ec-SCL, our mutational and molecular docking simulation studies revealed that C362 of Lm-SCL might also catalyze the deselenation of l-selenocysteine in addition to the desulfuration of l-cysteine.
 
Multilevel linear regression analysis of plasma amino acid levels according to metabolic status using (0: metabolic stability, 1: decompensation with ketosis, 2: decompensation with hyperammonemia)
Interorgan relationship of metabolic pathways implicated in PA. P5CS Δ¹-pyrroline-5-carboxylate synthetase, G-ase glutaminase, GS, glutamine synthetase, NAGN-acetyl-l-glutamate, NAGS NAG synthase, OAT ornithine ω-aminotransferase, OTC ornithine transcarbamylase, P5CS pyrroline-5-carboxylate synthetase, PYCR1,2 pyrroline-5-carboxylate reductase isoforms 1 and 2, TCA cycle tricarboxylic acids cycle, CPS1 carbamoyl phosphate synthetase 1, GSA Glutamate-5-semialdehyde, PCC propionyl-CoA carboxylase, MUT methyl malonyl- CoA mutase, Ile isoleucine, Val valine, AST aspartate aminotransferase, ALT alanine aminotransferase, BCAT1 branched-chain amino acid aminotransferase 1, Glu glutamate, Ala alanine, OAA oxaloacetate, PDH: pyruvate dehydrogenase
Article
Background Propionic acidemia is an inborn error of metabolism caused by a deficiency in the mitochondrial enzyme propionyl-CoA carboxylase that converts the propionyl CoA to methyl malonyl CoA. This leads to profound changes in distinct metabolic pathways, including the urea cycle, with consequences in ammonia detoxification. The implication of the tricarboxylic acid cycle is less well known, but its repercussions could explain both some of the acute and long-term symptoms of this disease. Materials and methods The present observational study investigates the amino acid profiles of patients with propionic acidemia being monitored at the Hospital Ramón y Cajal (Madrid, Spain), between January 2015 and September 2017, comparing periods of metabolic stability with those of decompensation with ketosis and/or hyperammonemia. Results The concentrations of 19 amino acids were determined in 188 samples provided by 10 patients. We identified 40 metabolic decompensation episodes (22 only with ketosis and 18 with hyperammonemia). Plasma glutamine and alanine levels were reduced during these metabolic crises, probably indicating deficiency of anaplerosis ( p < 0.001 for both alanine and glutamine). Hypocitrulllinemia and hypoprolinemia were also detected during hyperammonemia ( p < 0.001 and 0.03, respectively). Conclusions The amino acid profile detected during decompensation episodes suggests deficient anaplerosis from propionyl-CoA and its precursors, with implications in other metabolic pathways like synthesis of urea cycle amino acids and ammonia detoxification.
 
Article
Protein hot spot residues are functional sites in protein–protein interactions. Biological experimental methods are traditionally used to identify hot spot residues, which is laborious and time-consuming. Thus a variety of computational methods were widely used in recent years. Despite the success of computational methods in hot spot identification, most of them are impractical in reality because they can recognize hot spot residues only from known protein–protein interface residues. Therefore, identifying hot spots from whole protein sequence is a meaningful and interesting issue. However, it will bring extreme imbalance between positive and negative samples. Hot spot residues only account for about 1–2% of whole protein sequences. To address the issue, this paper proposes a two-step ensemble model for identifying hot spot residues from extremely unbalanced data set. The model is composed of 134 classifiers constructed by base KNN and SVM. Compared to the previous methods, our model yields good performance with an F1 score of 0.593 on the BID test set. Furthermore, to validate the robustness of our model, it was tested on other three independent test sets and also achieved good predictions. More importantly, the performance of our model tested on unbalanced data set is comparable with other methods tested on balanced hot spot data set.
 
Top-cited authors
Guoyao Wu
  • China Agricultural University
Yulong Yin
  • Chinese Academy of Sciences
Peng Li
  • Texas A&M University
Xilong Li
  • Chinese Academy of Agricultural Sciences
Junjun Wang
  • China Agricultural University