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In common bean (Phaseolus vulgaris L.), seed storage protein deficiency is associated with increased total cysteine and methionine concentration. The goal of this study was to generate germplasm lines that combine this characteristic with adaptation to short season conditions in Manitoba, Canada. A recombinant inbred line population was developed by crossing the storage protein deficient genotype, SMARC1N‐PN1 with the cultivar Morden003. Two lines, 2‐37 and 3‐84, with a stable protein profile over 2 years at two locations were identified. Like SMARC1N‐PN1, both lines had a significantly higher cysteine concentration than Morden003, by approximately 35%. Methionine levels were elevated by approximately 15%, while tryptophan levels were also increased by approximately 30%. Line 2‐37 had a significant increase in protein quality, as measured by in vitro protein digestibility corrected amino acid score, by approximately 40%, as compared with Morden003. The increased protein quality for this line is attributable to higher levels of total cysteine and methionine, while having an overall reduction in crude protein concentration. Line 2‐37 had a similar seed yield as SMARC1N‐PN1, with a maturity comparable to Morden003. The results of high‐density single nucleotide polymorphism (SNP) genotyping and quantitative trait locus analysis of recombinant inbred lines indicated that variation in cysteine concentration was determined by the phaseolin locus, while variation in methionine concentration was determined by both the phaseolin and lectin loci. SNP markers that track the introgression of phaseolin and lectin deficiency into the Morden003 background were identified and validated.

Objective: To retrospectively investigate the comparative efficacy, safety and cost-benefits of three nutritional treatment schemes including short peptide jejunal nutrition (SPJN), whole protein jejunal nutrition (WPJN), and partial parenteral nutrition (PPN) in patients underwent esophagectomy for esophageal cancer in our hospital. This study was carried out in accordance with the conceptual framework of nutritional therapy in fast-track rehabilitation surgery.Methods: We retrospectively reviewed 305 patients who were assigned to receive esophagectomy for esophageal cancer. Eligible patients was naturally divided into SPJN group [n = 98 (32.1%)], WPJN group [n = 95 (31.1%)], and PPN group [n = 112 (36.7%)] according to the type of nutritional scheme which was actually prescribed to patients by the attendingphysician in clinical practice. The differences of the serum total protein (TP), albumin (ALB), pre-albumin (PA), hemoglobin (HGB), white blood cells (WBCs), red blood cells (RBCs) and neutrophils were compared among 3 nutritional schemes groups. We also investigated the relationship of the fluid intake, urine output, gastric juice drainage volume and thoracic drainage volume among 3 nutritional groups at 3 days after surgery. Moreover, the differences of cost-benefit indexes, complications, length of hospitalization and hospital expenditure were also compared.Results: The serum TP, ALB, and PA in the SPJN group were all higher than those in the WPJN and PPN groups (p < 0.05). The gastric juice volume of gastrointestinal decompression drainage and fluid volume of thoracic drainage in the SPJN group were all less than that in the WPJN group (p < 0.05). The overall hospital stay and post-operative hospital stay in the SPJN group were all shorter than that in WPJN group (p < 0.05). Moreover, the incidence of post-operative complications including anastomotic leakage, infection, and gastrointestinal reaction was remarkably lower in the SPJN group compared to the WPJN group (p < 0.05). Interesting, hospital expenditure in the PPN group was less than that in the SPJN and the WPJN groups (p < 0.001).Conclusion: Patients may obtain benefits in improving protein level after receiving SPJN scheme at the early stage after esophagectomy. Meanwhile, patients may obtain benefits in improving post-operative complications and hospital stay after receiving SPJN or PPN compared to WPJN protocol. However, the difference between SPJN and PPN requires further study because no difference was detected in terms of clinical outcomes including complications and the length of hospitalization although PPN may achieve a possible decrease of medical expenditure.

Nuclear export signal (NES) motifs function as essential regulators of the subcellular location of proteins by interacting with the major nuclear exporter protein, CRM1. Prediction of NES is of great interest in many aspects of research including cancer, but currently available methods, which are mostly based on the sequence-based approaches, have been suffered from high false positive rates since the NES consensus patterns are quite commonly observed in protein sequences. Therefore, finding a feature that can distinguish real NES motifs from false positives is desired to improve the prediction power, but it is quite challenging when only using the sequence. Here, we provide a comprehensive table for the validated cargo proteins, containing the location of the NES consensus patterns with the disordered propensity plots, known protein domain information, and the predicted secondary structures. It could be useful for determining the most plausible NES region in the context of the whole protein sequence and suggests possibilities for some non-binders of the annotated regions. In addition, using the currently available crystal structures of CRM1 bound to various classes of NES peptides, we adopted, for the first time, the structure-based prediction of the NES motifs bound to the CRM1’s binding groove. Combining sequence-based and structure-based predictions, we suggest a novel and more straight-forward approach to identify CRM1-binding NES sequences by analysis of their structural prerequisites and energetic evaluation of the stability at the CRM1’s binding site.

The intact function of the salivary glands is of utmost importance for oral health. During radiotherapy in patients with head and neck tumors, the salivary glands can be damaged, causing the composition of saliva to change. This leads to xerostomia, which is a primary contributor to oral mucositis. Medications used for protective or palliative treatment often show poor efficacy as radiation-induced changes in the physico-chemical properties of saliva are not well understood. To improve treatment options, this study aimed to carefully examine unstimulated whole saliva of patients receiving radiation therapy and compare it with healthy unstimulated whole saliva. To this end, the pH, osmolality, electrical conductivity, buffer capacity, the whole protein and mucin concentrations, and the viscoelastic and adhesive properties were investigated. Moreover, hyaluronic acid was examined as a potential candidate for a saliva replacement fluid. The results showed that the pH of radiation-induced saliva shifted from neutral to acidic, the osmolality increased and the viscoelastic properties changed due to a disruption of the mucin network and a change in water secretion from the salivary glands. By adopting an aqueous 0.25% hyaluronic acid formulation regarding the lost properties, similar adhesion characteristics as in healthy, unstimulated saliva could be achieved.

BACKGROUND: Sex differences in plasma concentration of arginine and arginase activity of different tissues have been reported in mice. In addition, male but not female C57BL/6 mice have a dietary arginine requirement for growth. OBJECTIVE: The goal of this research was to test the hypothesis that arginase II is a key factor in the sexual dimorphism of arginine metabolism. METHODS: Young adult male and female wild type (WT), and heterozygous and arginase II knockout mice on a C57BL/6 background mice were infused with labeled citrulline, arginine, ornithine, phenylalanine, and tyrosine to determine the rates of appearance and interconversion of these amino acids. Tissue arginase activity was measured in the liver, heart, jejunum, kidney, pancreas, and spleen with an arginine radioisotope. The effect of genotype, sex, and their interaction was tested. RESULTS: Female mice produced ∼36% more citrulline than their male littermates, which translated into a greater arginine endogenous synthesis, flux, and plasma concentration (42, 6, and 27%, respectively; P < 0.001). Female mice also had a greater phenylalanine flux (10%) indicating a greater rate of whole protein breakdown; however, they had a lower protein synthesis rate than males (18%; P < 0.001). The ablation of arginase II reduced the production of citrulline and the de novo synthesis of arginine in females and increased the rate of appearance of arginine and plasma arginine concentration in male mice (16 and 22%, respectively; P < 0.001). No effect of arginase II deletion, however, was observed for whole-body protein kinetics. Arginase II activity was present in the pancreas, kidney, jejunum, and spleen; WT females had a ∼2-fold greater renal arginase activity than their WT counterparts. CONCLUSIONS: A clear sexual dimorphism exists in the endogenous synthesis of arginine and its disposal. Female mice have a greater arginine availability than their male littermates. The ablation of arginase II increases arginine availability in male mice.

The enormous magnitude of scientific research carried out in the field of NSAIDs and cyclooxygenases (COXs) is known. They are crucial in pain management. COX-2 inhibitors have evolved over the years; from traditional NSAIDs to isoform-specific. The present study is aimed to identify a cluster of amino acids in the catalytic site whose energy contribution can better explain COX-2 inhibitory activity accurately than the binding energy of the whole protein. Initially, MD simulations (25 ns) and MM-PBSA calculations were performed for 8 diarylheterocyclic inhibitors. Per-residue energy decomposition studies were carried out to elucidate the energy contribution of each amino acid, and their correlation with COX-2 inhibitory activity was enumerated. A cluster of catalytic amino acids whose free energy sum has a high correlation with biological data was identified. The cluster of Gln178, Ser339, Tyr341, Arg499, Phe504, Val509 and Ala513 showed the correlation of -0.60. Further, the study was extended to a total of 26 COX-2 inhibitors belonging to different classes to validate the applicability of the cluster of amino acids identified. Results clearly suggest that the cluster of amino acids identified provide accurate screening method, and can be applied to predict COX-2 inhibitory activity of small molecules.

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal celebrated for its excellent nutritional quality and potential to improve global food security, especially in marginal environments. However, minimal information is available on how genotype influences seed composition, and thus, nutritional quality. This study aimed to provide a baseline for nutritional quality of Washington grown quinoa and test the hypothesis that these samples contain adequate amounts of essential amino acids to meet daily requirements set by the World Health Organization (WHO). One hundred samples, representing commercial varieties and advanced breeding lines adapted to Washington State, were analyzed for content of 23 amino acids, as well as crude protein, ash, moisture, and crude fat. Mean essential amino acid values for Washington grown quinoa met the daily requirements for all age groups for all essential amino acids, except for the amount of leucine required by infants. We found that only nine genotypes met the leucine requirements for all age groups. A total of 52 and 94 samples met the lysine and tryptophan requirements for all age groups, respectively. Mean values for isoleucine, leucine, lysine, tryptophan, valine, and the sulfur and aromatic amino acids are higher for Washington grown samples than those reported previously reported in the literature. Our results show that not all Washington grown quinoa samples meet daily requirements of essential amino acids, and we identify limiting amino acids for the germplasm and environments investigated. This study provides the first report of leucine as a limiting amino acid in quinoa. Additional research is needed to better understand variation in quinoa nutritional composition, identify varieties that meet daily requirements, and explore how genotype, environment, and management interactions influence nutritional quality.

Approximately two-thirds of those suffering with Alzheimer's disease (AD) are women, however, the biological mechanisms underlying this sex divergence of AD prevalence remain unknown. Previous research has shown sex-specific biochemical differences that bias female mice toward pro-AD signaling on the phosphoproteomic level via corticotropin releasing factor (CRF) receptor 1 activation after CRF overexpression. Here we aimed to determine if chronic stress would induce a similar response in AD mouse models. We stressed 4-month-old APP/PS1 mice using a chronic unpredictable mild stress (CUMS) paradigm for up to 1 month. Following CUMS and behavioral assessments, we quantified whole protein and phosphoprotein levels in the cortex of stressed and non-stressed APP/PS1 mice using mass spectrometry-based proteomics. While there were no statistically significant differences at the total protein and peptide abundance levels, we found 909 and 841 statistically significant phosphopeptides between stressed and unstressed females and males, respectively, using a false discovery rate of 5%. Of these significant phosphopeptides, only 301 were the same in males and females. These results indicate that while both males and females undergo protein phosphorylation changes following stress, the peptides that are phosphorylated differ between sexes. We then used Metacore analysis to determine which biological pathways were affected. We found that several pathways were changed differently between male and female mice including NMDA receptor trafficking, cytoskeleton organization, and tau pathology. The differing biological pathways affected between males and females in response to chronic stress may help us to better understand why women are at a higher risk of AD.

International audience; The sources or types of protein in the diet have long been overlooked regarding their link to cardiometabolic health. The picture is complicated by the fact that animal and plant proteins are consumed along with other nutrients and substances which make up the “protein package” so plant and animal protein come with clear nutrient clusters. This review aimed at deciphering the relation between plant and animal protein and cardiometabolic health by examining different nutritional levels (such as amino acids, protein type, protein foods, protein patterns, and associated overall dietary and nutrient patterns) and varying levels of scientific evidence [basic science, randomized controlled trials (RCTs), observational data]. Plant protein in Western countries is a robust marker of nutrient adequacy of the diet, whereas the contribution of animal protein is highly heterogeneous. Yet recent data from large cohorts have confirmed that total and animal proteins are associated with the risk of cardiovascular disease and diabetes, even when fully adjusting for lifestyle and dietary or nutritional factors. Here again, there is marked variability depending on the type of animal protein. Protein from processed red meat and total red meat on the one hand, and from legumes, nuts, and seeds on the other, are often reported at the extremes of the risk range. RCTs using purified proteins have contributed little to the topic to date, inasmuch as the findings cannot readily be extrapolated to current or near-future diets, but RCTs studying whole protein foods have shown a beneficial effect of pulses. Despite the fact that many of the benefits of plant protein reported in observational or interventional studies may stem from the protein package that they convey and the nutrients that they displace, there are also important indications that protein per se may affect cardiometabolic health via the many amino acids that are present in typically contrasting levels in plant compared with animal proteins.

MotivationIn last three decades, a wide range of protein descriptors/features have been discovered to annotate a protein with high precision. A wide range of features have been integrated in numerous software packages (e.g., PROFEAT, PyBioMed, iFeature, protr, Rcpi, propy) to predict function of a protein. These features are not suitable to predict function of a protein at residue level such as prediction of ligand binding residues, DNA interacting residues, post translational modification etc.ResultsIn order to facilitate scientific community, we have developed a software package that computes more than 50,000 features, important for predicting function of a protein and its residues. It has five major modules for computing; composition-based features, binary profiles, evolutionary information, structure-based features and patterns. The composition-based module allows user to compute; i) simple compositions like amino acid, dipeptide, tripeptide; ii) Properties based compositions; iii) Repeats and distribution of amino acids; iv) Shannon entropy to measure the low complexity regions; iv) Miscellaneous compositions like pseudo amino acid, autocorrelation, conjoint triad, quasi-sequence order. Binary profile of amino acid sequences provides complete information including order of residues or type of residues; specifically, suitable to predict function of a protein at residue level. Pfeature allows one to compute evolutionary information-based features in form of PSSM profile generated using PSIBLAST. Structure based module allows computing structure-based features, specifically suitable to annotate chemically modified peptides/proteins. Pfeature also allows generating overlapping patterns and feature from whole protein or its parts (e.g., N-terminal, C-terminal). In summary, Pfeature comprises of almost all features used till now, for predicting function of a protein/peptide including its residues.AvailabilityIt is available in form of a web server, named as Pfeature (https://webs.iiitd.edu.in/raghava/pfeature/), as well as python library and standalone package (https://github.com/raghavagps/Pfeature) suitable for Windows, Ubuntu, Fedora, MacOS and Centos based operating system.

CRISPR-Cas systems are prevalent in bacterial and archaeal genomes, and these systems provide a powerful adaptive immune system against predation by phages and other mobile genetic elements (MGEs). They also contribute to other functions, such as gene regulation in prokaryotic organisms. Determining Cas proteins and Cas loci can help mine Cas proteins and facilitate the identification of Cas-associated accessory proteins. Therefore, the purpose of this work is to develop a web-based server, CasLocusAnno, to annotate Cas proteins and Cas loci and to classify them according to (sub)type based on a previous study. CasLocusAnno can annotate Cas proteins and Cas loci and assign their (sub)types within ∽28 seconds for whole protein sequence submissions, with protein sequence numbers ranging from ∽30 to ∽10500. Comparison with Makarova et al.’s benchmark data demonstrates that CasLocusAnno can accurately identify Cas loci and (sub)types. In addition, CasLocusAnno can identify Cas proteins with higher accuracy and a lower additional prediction rate (APR) than two excellent software programs, CRISPRCasFinder and MacSyFinder. The domain alignment of a Cas protein can be easily browsed in the annotation results. Our server can be freely accessed at http://cefg.uestc.edu.cn/CasLocusAnno/.

Fortified milk drinks are predominantly manufactured from bovine (cow) sources. Alternative formulations include those prepared with hydrolysed bovine milk proteins or from alternate bovidae species, such as caprine (goat) milk. Currently, there is little data on protein digestive and metabolic responses following ingestion of fortified milk drinks. To examine the digestive and metabolic responses to commercially-available fortified milks, young adults (n = 15 males: 15 females), in a randomised sequence, ingested isonitrogenous quantities of whole cow-protein (WC), whole goat-protein (WG), or partially-hydrolysed whey cow-protein (HC), commercial fortified milks. Plasma amino acid (AA) and hormonal responses were measured at baseline and again at 5 h after ingestion. Paracetamol recovery, breath hydrogen, and subjective digestive responses were also measured. Postprandial plasma AA was similar between WC and WG, while AA appearance was suppressed with HC. Following HC, there was a negative incremental AUC in plasma branched-chain AAs. Further, HC had delayed gastric emptying, increased transit time, and led to exaggerated insulin and GLP-1 responses, in comparison to whole protein formulas. Overall, WC and WG had similar protein and digestive responses with no differences in digestive comfort. Contrastingly, HC led to delayed gastric emptying, attenuated AA appearance, and a heightened circulating insulin response.

βγ-crystallin has emerged as a superfamily of structurally homologous proteins with representatives across all domains of life. A major portion of this superfamily is constituted by microbial members. This superfamily has also been recognized as a novel group of Ca 2+ -binding proteins with a large diversity and variable properties in Ca 2+ binding and stability. We have recently described a new phosphatidylinositol phospholipase C from Lysinibacillus sphaericus (LS-PIPLC) which was shown to efficiently remove phosphatidylinositol from crude vegetable oil. Here, the role of the C-terminal βγ-crystallin domain of LS-PIPLC was analyzed in the context of the whole protein. A truncated protein in which the C-terminal βγ-crystallin domain was deleted (LS-PIPLC ΔCRY ) is catalytically as efficient as the full-length protein (LS-PIPLC). However, the thermal and chemical stability of LS-PIPLC ΔCRY are highly affected, demonstrating a stabilizing role for this domain. It is also shown that the presence of Ca 2+ increases the thermal and chemical stability of the protein both in aqueous media and in oil, making LS-PIPLC an excellent candidate for use in industrial soybean oil degumming. Fil: Cerminati, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Procesos Biotecnológicos y Químicos Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Procesos Biotecnológicos y Químicos Rosario; Argentina Fil: Paoletti, Luciana Elisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Procesos Biotecnológicos y Químicos Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Procesos Biotecnológicos y Químicos Rosario; Argentina Fil: Peirú, Salvador. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Procesos Biotecnológicos y Químicos Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Procesos Biotecnológicos y Químicos Rosario; Argentina Fil: Menzella, Hugo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Procesos Biotecnológicos y Químicos Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Procesos Biotecnológicos y Químicos Rosario; Argentina Fil: Castelli, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Procesos Biotecnológicos y Químicos Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Procesos Biotecnológicos y Químicos Rosario; Argentina

Kai Jia,1 Xin Tong,1 Fang Liang2 1Department of Nutrition, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; 2Department of Hyperbaric Oxygen, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China Objective: To investigate the effects of sequential nutritional support on nutritional status and immune regulation in patients with early severe traumatic brain injury (STBI). Patients and methods: A total of 62 patients diagnosed with STBI enrolled from Chaoyang Hospital (Beijing, China) from February 2015 to October 2016 were divided into two groups. The observational group (n=34) was given sequential nutritional support and the control group (n=28) was given the standard formula of whole protein enteral preparations. The energy supply for the two groups was 30 kcal/kg/d and protein 1.6 g/kg/d, respectively. The albumin (ALB), total protein (TP), high-sensitivity C-reactive protein (Hs-CRP), neuron-specific enolase (NSE), Glasgow Coma Score (GCS), and regulatory T cells before and after nutritional treatment were measured in both groups. Results: At the 14th day, the levels of ALB (41.7±4.2 g/L) and TP (70.6±4.9 g/L) were significantly higher than those in the control group (33.5±2.3 g/L and 62.3±3.9 g/L) (P

There is growing interest in nutrition therapies that deliver a generous amount of protein, but not a toxic amount of energy, to protein-catabolic critically ill patients. Parenteral amino acids can achieve this goal. This article summarizes the biochemical and nutritional principles that guide parenteral amino acid therapy, explains how parenteral amino acid solutions are formulated, and compares the advantages and disadvantages of different parenteral amino acid products with enterally-delivered whole protein products in the context of protein-catabolic critical illness.

Background Previous research has demonstrated the permissive effect of insulin on muscle protein kinetics, and the enhanced insulin sensitizing effect of chromium. In the presence of adequate whole protein and/or essential amino acids (EAA), insulin has a stimulatory effect on muscle protein synthesis, whereas in conditions of lower blood EAA concentrations, insulin has an inhibitory effect on protein breakdown. In this study, we determined the effect of an amylopectin/chromium (ACr) complex on changes in plasma concentrations of EAA, insulin, glucose, and the fractional rate of muscle protein synthesis (FSR). Methods Using a double-blind, cross-over design, ten subjects (six men, four women) consumed 6 g whey protein + 2 g of the amylopectin-chromium complex (WPACr) or 6 g whey protein (WP) after an overnight fast. FSR was measured using a primed, continuous infusion of ring-d5-phenylalanine with serial muscle biopsies performed at 2, 4, and 8 h. Plasma EAA and insulin were assayed by ion-exchange chromatography and ELISA, respectively. After the biopsy at 4 h, subjects ingested their respective supplement, completed eight sets of bilateral isotonic leg extensions at 80% of their estimated 1-RM, and a final biopsy was obtained 4 h later. Results Both trials increased EAA similarly, with peak levels noted 30 min after ingestion. Insulin tended (p = 0.09) to be higher in the WPACr trial. Paired samples t-tests using baseline and 4-h post-ingestion FSR data separately for each group revealed significant increases in the WPACr group (+0.0197%/h, p = 0.0004) and no difference in the WP group (+0.01215%/hr, p = 0.23). Independent t-tests confirmed significant (p = 0.045) differences in post-treatment FSR between trials. Conclusions These data indicate that the addition of ACr to a 6 g dose of whey protein (WPACr) increases the FSR response beyond what is seen with a suboptimal dose of whey protein alone.

The copper-binding features of rat islet amyloid polypeptide (r-IAPP) are herein disclosed through the determination of the stability constants and spectroscopic properties of its copper complex species. To mimic the metal binding sites of the human IAPP (h-IAPP), a soluble, single-point mutated variant of r-IAPP, having a histidine residue in place of Arg18, was synthesized, that is, r-IAPP(1-37; R18H). The peptide IAPP(1-8) was also characterized to have deeper insight into the N-terminus copper(II)-binding features of r-IAPP as well as of its mutated form. A combined experimental (thermodynamic and spectroscopic) and computational approach allowed us to assess the metal loading and the coordination features of the whole IAPP. At physiological pH, the N-terminal amino group is the Cu2+ main binding site both of entire r-IAPP and of its mutated form that mimics h-IAPP. The histidine residue present in this mutated polypeptide accounts for the second Cu2+ binding. We can speculate that the copper driven toxicity of h-IAPP in comparison to that of r-IAPP can be attributed to the different metal loading and the presence of a second metal anchoring site, the His(18), whose role is usually invoked in the process of h-IAPP aggregation.

Physical activity has emerged as a powerful intervention that promotes healthy aging by maintaining the functional capacity of critical organ systems. Here, by combining functional and proteomics analyses, we examined how hepatic phenotypes might respond to exercise treatment in aged rats. 16 male aged (20 months old) SD rats were divided into exercise and parallel control groups at random; the exercise group had 8 weeks of treadmill training with medium intensity. Whole protein samples of the liver were extracted from both groups and separated by two-dimensional gel electrophoresis. Alternatively objective protein spots with >2-fold difference in expression were selected for enzymological extraction and MS/MS identification. Results show increased activity of the manganese superoxide dismutase and elevated glutathione levels in the livers of exercise-treated animals, but malondialdehyde contents obviously decreased in the liver of the exercise group. Proteomics-based identification of differentially expressed proteins provided an integrated view of the metabolic adaptations occurring in the liver proteome during exercise, which significantly altered the expression of several proteins involved in key liver metabolic pathways including mitochondrial sulfur, glycolysis, methionine, and protein metabolism. These findings indicate that exercise may be beneficial to aged rats through modulation of hepatic protein expression profiles.

[This corrects the article DOI: 10.3389/fnut.2020.00126.]., (Copyright © 2020 Craine and Murphy.)

The objective of the present study was to compare the concentrations of acute phase proteins and selected variables of protein metabolism in dairy cows of the Slovak Spotted breed from 4 weeks before parturition to 10 weeks after parturition. Acute phase proteins - haptoglobin (Hp) and serum amyloid A (SAA) - and variables of protein metabolism - total proteins, albumin, urea, creatinine, total immunoglobulins - were evaluated in blood serum. Significant differences were found in average values of the Hp and SAA concentrations in several groups during the monitored period (P < 0.05 and P < 0.001, respectively). The Hp and SAA concentrations in cows during the early postparturient period were significantly higher compared with the later postparturient period. Throughout the monitored time we found differences in mean values of total proteins (P < 0.001), urea (P < 0.001), and total immunoglobulins (P < 0.05). The concentrations of albumin decreased progressively in the postparturient period until 4 weeks after parturition. In the assessment of correlations between the monitored variables in the mentioned period we found significant correlations between Hp and SAA (r = 0.916; P < 0.001), total proteins and urea (r = 0.668; P < 0.05), total proteins and total immunoglobulins (r = 0.827; P < 0.01), and between total immunoglobulins and urea (r = 0.899; P < 0.001). The above mentioned results indicate that in the time around parturition there are significant changes in concentrations of acute phase proteins, as well as in the whole protein metabolism of dairy cows. These facts suggest that the postparturient period is a critical biological phase, throughout which there is the highest incidence of metabolic disorders.

Objective: Protein intake recommendations in phenylketonuria (PKU) are frequently the subject of discussion. For healthy adults, the recommended daily allowance (RDA) is 0.8 g . kg(-1) . d(-1), which is generally lower than that observed in the general Western population. We investigated whether whole-body protein metabolism in patients with PKU is comparable to that of healthy controls at a RDA rate of protein intake.Methods: Six adult patients with well-controlled PKU and six healthy subjects of comparable age, height, and weight were studied using a primed continuous infusion of [1-C-13] -valine for 8 h after an overnight fast before and during frequent meals. Normal protein was given to controls, whereas patients with PKU received a combination of an amino acid mixture and natural protein.Results: No significant differences were observed between patients with PKU and controls in preprandial and prandial rates of valine appearance and oxidation and protein breakdown, protein synthesis, and net protein balance. Feeding resulted in a significant (P Conclusion: Whole-body protein metabolism in adult patients with PKU is fully comparable to that in healthy controls at the RDA level of protein intake. (C) 2007 Elsevier Inc. All rights reserved.

Colliroja, Astyanax fasciatus, is a new aquaculture species, and information on its dietary essential amino acid requirements is lacking. The whole body composition of 120 farmed fish (16.2 ± 8.8 g) was determined to estimate the dietary essential amino acid requirement based on the ideal protein concept ((each essential amino acid/lysine) x100), and the findings were correlated to the whole body essential amino acid content of Nile tilapia Oreochromis niloticus. The dietary essential amino acids, including cysteine and tyrosine, accounted for 5.46, 4.62, 1.16, 3.28, 5.63, 2.01, 2.59, 2.84, 4.66, 3.39, 0.65, and 3.51% of the total protein for lysine, arginine, histidine, isoleucine, leucine, methionine, methionine+tyrosine, phenylalanine, phenylalanine+tyrosine, threonine, tryptophan, and valine, respectively. There were positive linear and high correlations (r = 0.971) between the whole body amino acid profiles of colliroja and Nile tilapia. Thus, the whole body amino acid profile of colliroja might be used to estimate accurately the essential amino acid requirement. Colirroja, Astyanax fasciatus, es una nueva especie de la acuicultura y no hay información sobre sus requerimentos de aminoácidos esenciales en la dieta. Se determinó la composición corporal de 120 peces de cultivo (16,2 ± 8,8 g) para estimar los requirimientos nutricionales de aminoácidos essenciales en la dieta, incluyendo cistina y tirosina, basada en el concepto de proteína ideal ((cada aminoácido essencial/lisina) x 100) y los resultados se correlacionaron con el perfil corporal de la tilapia del Nilo Oreochromis niloticus. El perfil dietético de aminoácidos essenciales explica el 5,46, 4,62, 1,16, 3,28, 5,63, 2,01, 2,59, 2,.84, 4,66, 3,39, 0.65 y 3,51% de la proteína, respectivamente para lisina, arginina, histidina, isoleucina, leucina, metionina, metionina+cistina, fenilalanina, fenilalanina+tirosina, treonina, triptófano y valina. Hubo una alta correlación lineal positiva (r = 0,971) entre el perfil corporal de aminoácidos de colirroja y el de tilapia del Nilo. Por lo tanto, el perfil corporal de los aminoácidos basado en el concepto de proteína ideal podría ser utilizado para estimar con precisión el requisito de aminoácidos essenciales de colirroja.

Heterologous protein production is a key technology for biotechnological, health sciences and many other research fields. Various approaches have been developed for its optimization, but the research emphasis has been on optimization of protein yield rather than protein quality. In this study, we have established a workflow for synthetic gene optimization for heterologous protein expression that combines bioinformatics, laboratory experiments, mass spectrometry and statistical analysis. Two gene primary structure analysis platforms, Anaconda and EuGene, and multivariate optimization methods were employed to re-design the Plasmodium falciparum lysyl-tRNA synthetase gene for optimal expression in Escherichia coli. Synthetic genes were expressed from common vectors, and amino acid mis-incorporations in the expressed proteins were detected and quantified using mass spectrometry. The association between the identified amino acid mis-incorporations and 23 gene variables was then analysed. The synthetic genes yielded significantly higher levels of protein relative to the wild-type gene, but 71 amino acid mis-incorporation sites were observed along the whole protein and across the synthetic genes that were statistically associated with specific codons and protein secondary structures. The optimization method that led to production of the most accurate protein was based on a multivariate approach that combined variables that are known to influence mRNA translation. published

Antifungal proteins produced by molds are generally small, highly basic, and cysteine-rich. The best known effects of these proteins include morphological changes, metabolic inactivation, and membrane perturbation on sensitive fungi. Reactive oxygen species (ROS) generation leads to apoptosis, with G -protein playing a key role in transduction of cell death signals. The antifungal protein PgAFP from Penicillium chrysogenum inhibits growth of some toxigenic molds. Here we analyzed the effect of the antifungal protein PgAFP on the growth of Aspergillus flavus. For this, comparative proteomic analysis was used to identify the whole protein profile and protein change in abundance after PgAFP treatment. PgAFP provoked metabolic changes related to reduced energy metabolism, cell wall integrity alteration, and increased stress response due to higher levels of ROS. The observed changes in protein abundance, favoring a higher glutathione concentration as well as the increased abundance in heat shock proteins, do not seem to be enough to avoid necrosis. The decreased chitin deposition observed in PgAFP-treated A. flavus is attributed to a lower relative quantity of Rho1. The reduced relative abundance of a β subunit of G -protein seems to be the underlying reason for modulation of apoptosis in PgAFP-treated A. flavus hyphae. We propose Rho1 and G -protein subunit β CpcB to be the main factors in the mode of action of PgAFP in A. flavus. Additionally, enzymes essential for the biosynthesis of aflatoxin were no longer detectable in A. flavus hyphae at 24 h, following treatment with PgAFP. This presents a promising effect of PgAFP, which may prevent A. flavus from producing mycotoxins. However, the impact of PgAFP on actual aflatoxin production requires further study.

More than decade ago during systematic search for alternative reading frame derived peptides encoded by influenza A virus recognized by CD8+ T cells, PB1-F2 protein was discovered serendipitously by Chen et al. (2001). Since that time, an increasing body of evidence has continued to highlight the multifunctional meaning of this unusual influenza A protein. After twelve years of intensive research with 56 pubmed records for PB1-F2 in the title there is still a lot yet to explore. Is it a proapoptotic "explosive" protein that suppresses the mechanisms of early innate immune response or does it function as an NS1 antagonist? What is the root of its strain and cell specificity? What is the relationship between PB1-F2 and pathogenicity or secondary bacterial infection? Here we attempt to "take a trip" from the whole protein level through domains and regions to very particular aminoacid residues in correlation with its function in different virus isolates, cell type or animal model.

In a variety of chronic and acute disease states, alterations in protein synthesis, breakdown and protein turnover rates occur that are related to the loss of body protein and skeletal muscle wasting. A key observation is the stimulation of protein breakdown in muscle and the stimulation of protein synthesis in the splanchnic area; mainly liver. An altered splanchnic extraction of amino acids as well as an anabolic resistance to dietary protein, related to stress, disuse and aging play a key role in the pathogenesis of muscle wasting in these conditions. To overcome these factors, specific dietary protein and amino acid diets have been introduced. The main focus of these diets is the quantity and quality of dietary proteins and whether a balanced mixture or solely dietary essential amino acids are required with or without higher intake levels of specific amino acids. Specifically in cancer patients, stimulated muscle protein synthesis has been obtained by increasing the amount of protein in a meal and by providing additional leucine. Also in other chronic diseases such as chronic obstructive pulmonary disease and cystic fibrosis, meals with specific dietary proteins and specific combinations of dietary essential amino acids are able to stimulate anabolism. In acute diseases, a special role for the amino acid arginine and its precursor citrulline as anabolic drivers has been observed. Thus, there is growing evidence that modifying the dietary amino acid composition of a meal will positively influence the net balance between muscle protein synthesis and breakdown, leading to muscle protein anabolism in a variety of chronic and acute disease states. Specific amino acids with anabolic potential are leucine, arginine and citrulline.

A semi automatic flow procedure with photometric detection was developed for the study of meat protein digestion. This system comprised two independent flow pathways, gathered by two compartments. The gastric compartment was simulated by an ultrafiltration cell fitted with a 10 KDa cut off membrane and the intestinal compartment was simulated by a 1 KDa cut off dialysis membrane. The pathways were filled with solutions simulating digestive conditions. The proposed system was employed in digestion studies of whole protein extracts from raw and cooked (100°C) meat. A mathematical modelling for the determination of the digestive kinetic constants was established. The results show that meat cooking leads to an important decrease of protein digestibility by proteases of the digestive tract.

In this study we report the effect of AZT on the whole protein expression profile both in the control and the AZT-treated K562 cells, evidenced by two-dimensional gel electrophoresis and peptide mass fingerprinting analysis. Two-dimensional gels computer digital image analysis showed two spots that appeared up-regulated in AZT-treated cells and one spot present only in the drug exposed samples. Upon extraction and analysis by peptide mass fingerprinting, the first two spots were identified as PDI-A3 and stathmin, while the third one was proved to be NDPK-A. Conversely, two protein spots were present only in the untreated K562 cells, and were identified as SOD1 and HSP-60, respectively.

Amino acid utilization and, therefore, demand differ between the healthy state and various disease states. In the healthy state most circulating amino acids are derived from dietary proteins that are stored and broken down in the gut and released gradually into the portal circulation, and from continuous turnover of body protein. In disease states, the amino acid composition of amino acids derived from periferal protein breakdown and released in the circulation, is different, for example because a substantial part of the branched-chain amino acids is broken down to yield glutamine and alanine, which are released in the circulation. It appears to be advantageous to mimic this continuous autoinfusion in patients, dependent of parenteral of enteral tube feeding. In disease, different endpoints should be used to assess the adequacy of the administered amino acid mix. Maintenance of a positive nitrogen balance and growth is less important than support of wound healing and immune function. Several amino acids such as glutamine, cysteine, and taurine are shown or suggested to be conditionally essential in disease, and to form substrate in the stressed patient for anabolic processes in liver, immune system, and injured sites. Amino acid toxicity is rare, and protein restriction for patients with renal or liver failure is obsolete because this only aggravated malnutrition. A true example of protein toxicity consists of gastrointestinal hemorrhage that precipitates hepatic encephalopathy in liver insufficiency, most likely because hemoglobin is an unbalanced protein because it lacks the essential amino acid isoleucine.

Reductions in dietary protein level and supplementation with certain crystalline amino acids is a well-established method of formulating diets to achieve a more ideal amino acid pattern and to reduce nitrogen excretion. Up to 35% reduction in nitrogen excretion may be achieved by supplementing pig diets with lysine, methionine, threonine, and tryptophan. In broiler nutrition, 41% less N was excreted on feeding diets with 153 g CP per kg supplemented with amino acids

Patients residing in endemic areas for schistosomiasis in Brazil are usually undernourished and when they develop the hepatosplenic clinical form of the disease should usually receive hospital care, many of them being in need of nutritional rehabilitation before specific treatment can be undertaken. In the mouse model, investigations carried out in our laboratory detected a reduced aminoacid uptake in undernourished animals which is aggravated by a superimposed infection with Schistosoma mansoni. However, in well-nourished infected mice no dysfunction occurs. In this study, we tried to improve the absorptive intestinal performance of undernourished mice infected with S. mansoni by feeding them with hydrolysed casein instead of whole casein. The values obtained for the coefficient of protein intestinal absorption (cpia) among well-nourished mice were above 90% (either hydrolysed or whole protein). In undernourished infected mice, however, the cpia improved significantly after feeding them with hydrolysed casein, animals reaching values close to those obtained in well-nourished infected mice.

Free-living species of ciliated Protozoa control their vegetative (mitotic) proliferation and mating (sexual) processes by diffusible, cell type-specific protein signals (pheromones). One of these molecules, designated En-2, was isolated from a species, Euplotes nobilii, living in the stably cold marine waters of Antarctica, and its complete amino acid sequence of 60 residues was determined by automated Edman degradation of the whole protein and peptides generated by trypsin digestion. The proposed sequence is: DIEDFYTSETCPYKNDSQLA20WDTCSGGTGNCGTVCCGQCF40SFPVSQSCAGMADSNDCPNA60. The En-2 structure appears to be characterized by an adaptive insertion of a glycine-rich motif potentially capable to confer more flexibility to a functionally critical region of the molecule.

The most important single factor affecting the efficiency of protein utilization is the profile of digestible essential amino acids entering the small intestine. Assuming a constant ideal amino acid profile of absorbed protein the requirements of all amino acids can be calculated when the requirement of one individual amino acid has been determined. In non-ruminants, the supply will be greatly influenced by the diet, but less so in ruminants due to the rumen microbial degradation of feed protein and synthesis of microbial protein with high biological value. However, the high-producing dairy cow requires a significant amount of rumen escape protein. Thus, the profile of the undegraded feed protein could influence the profile of the amino acids entering the small intestine to a point at which individual amino acids become limiting. For non-ruminants, lysine is usually the first limiting amino acid in feedstuffs. This has led to the general practice of expressing the requirements for all other essential amino acids relative to lysine. Alternatively, the amino acid requirements can be expressed relative to N. Then, dietary N required for synthesis of other N-compounds is also included. Moreover, the requirements of all amino acids can be calculated when the N requirement has been determined. However, this method cannot be used for ruminants, because the N requirement of rumen microbes may be higher than the requirement of the animal. In the future, computerised animal models based on scientifically correct feed evaluation systems offer the opportunity for securing optimal feeding of farm animals in relation to their ideal amino acid profile for all different purposes of production.

The protein digestibility-corrected amino acid score (PDCAAS) has been adopted by FAO/WHO as the preferred method for the measurement of the protein value in human nutrition. The method is based on comparison of the concentration of the first limiting essential amino acid in the test protein with the concentration of that amino acid in a reference (scoring) pattern. This scoring pattern is derived from the essential amino acid requirements of the preschool-age child. The chemical score obtained in this way is corrected for true fecal digestibility of the test protein. PDCAAS values higher than 100% are not accepted as such but are truncated to 100%. Although the principle of the PDCAAS method has been widely accepted, critical questions have been raised in the scientific community about a number of issues. These questions relate to 1) the validity of the preschool-age child amino acid requirement values, 2) the validity of correction for fecal instead of ileal digestibility and 3) the truncation of PDCAAS values to 100%. At the time of the adoption of the PDCAAS method, only a few studies had been performed on the amino acid requirements of the preschool-age child, and there is still a need for validation of the scoring pattern. Also, the scoring pattern does not include conditionally indispensable amino acids. These amino acids also contribute to the nutrition value of a protein. There is strong evidence that ileal, and not fecal, digestibility is the right parameter for correction of the amino acid score. The use of fecal digestibility overestimates the nutritional value of a protein, because amino acid nitrogen entering the colon is lost for protein synthesis in the body and is, at least in part, excreted in urine as ammonia. The truncation of PDCAAS values to 100% can be defended only for the limited number of situations in which the protein is to be used as the sole source of protein in the diet. For evaluation of the nutritional significance of proteins as part of mixed diets, the truncated value should not be used. In those cases, a more detailed evaluation of the contribution of the protein to the amino acid composition of the mixed diet is required. From such an evaluation, it appears that milk proteins are superior to plant proteins in cereal-based diets.

Ideal protein (amino acids) concept focused on broiler ABSTRACT. Accurate estimation of the amino acid requirement is very importance for diet formulation in growing animals such as broiler. Inadequate formulation of dietary amino acids will impair protein utilization and increase the total nitrogen output to the environment. Amino acids requirement of animals changes due to dietary, sex, and genetic and environmental factors. To address all potential combinations of factors with dose-response experiments is almost impossible. Thus the ideal protein concept provides a simple and effective approach to solve this problem. Based on this concept, the requirement of indispensible amino acids can be determined. For this concept, lysine has been used as the reference amino acid to calculate other indispensable amino acids due to several considerations. This paper will review more detailed about protein concept based on amino acid profile by using broiler as sampel review.

To determine if the molecular form of nitrogen intake affects protein metabolism during feeding, 12 normal volunteers received, by continuous nasogastric infusion, a protein or a peptide-based diet. Leucine kinetics (oral [13C]leucine and intravenous [2H3]leucine) were measured during the following three consecutive periods: first carbohydrates and lipids alone, then with either whole casein or oligopeptides in a randomized crossover design, with these two latter periods being isonitrogenous, isocaloric, and of identical amino acid compositions. Leucine concentration, turnover, oxidation, and nonoxidative disposal increased during nitrogen administration (all P < 0.01) and were higher with oligopeptides than with casein (242 +/- 44 vs. 188 +/- 31 mumol/l; 2.75 +/- 0.45 vs. 2.23 +/- 0.31; 1.14 +/- 0.19 vs. 0.82 +/- 0.22 mumol.kg-1.min-1, all P < 0.001; 1.64 +/- 0.32 vs. 1.44 +/- 0.33 mumol.kg-1.min-1, P < 0.05, respectively). Endogenous leucine production was less inhibited by oligopeptides than by casein (0.82 +/- 0.41 vs. 0.38 +/- 0.31 mumol.kg-1.min-1, P < 0.001), whereas splanchnic extractions were similar. Finally, leucine balance was more positive with casein than with oligopeptides (P < 0.001). In conclusion, the response of leucine kinetics to feeding is modified by the molecular form of nitrogen intake, with the oligopeptides inducing a higher oxidation and protein synthesis and a lesser inhibition of protein breakdown.

Given healthy dogs fed abundant iron and protein-free or low protein diets with sustained anemia and hypoproteinemia, we can study the capacity of these animals to produce simultaneously new hemoglobin and plasma protein. Reserve stores of blood protein-building materials are measurably depleted and levels of 6 to 8 gm. per cent for hemoglobin and 4 to 5 gm. per cent for plasma protein can be maintained for weeks or months depending upon the intake of food proteins or amino acid mixtures. These dogs are very susceptible to infection and various poisons. Dogs tire of these diets and loss of appetite terminates many experiments. Under these conditions (double depletion) standard growth mixtures of essential amino acids are tested to show the response in blood protein output and urinary nitrogen balance. As a part of each tabulated experiment one of the essential amino acids is deleted from the complete growth mixture to compare such response with that of the whole mixture. Methionine, threonine, phenylalanine, and tryptophane when singly eliminated from the complete amino acid mixture do effect a sharp rise in urinary nitrogen. This loss of urinary nitrogen is corrected when the individual amino acid is replaced in the mixture. Histidine, lysine, and valine have a moderate influence upon urinary nitrogen balance toward nitrogen conservation. Leucine, isoleucine, and arginine have minimal or no effect upon urinary nitrogen balance when these individual amino acids are deleted from the complete growth mixture of amino acids during 3 to 4 week periods. Tryptophane and to a less extent phenylalanine and threonine when returned to the amino acid mixture are associated with a conspicuous preponderance of plasma protein output over the hemoglobin output (Table 4). Arginine, lysine, and histidine when returned to the amino acid mixture are associated with a large preponderance of hemoglobin output. Various amino acid mixtures under these conditions may give a positive urinary nitrogen balance and a liberal output of blood proteins but there is always weight loss, however we may choose to explain this loss. These experiments touch on the complex problems of parenteral nutrition, experimental and clinical.

Poultry meat and eggs are poised to play a greater role than present, in global food security in the coming years, as the preferred and primary protein source. Efficient production requires precision, of which dietary amino acids are central. As primary poultry breeders continue to provide broiler strains that have improved annual growth, health, and muscle accretion with lower feed intake, nutritionists should continue to assess digestible Lys needs and subsequent ratios of essential amino acids to digestible Lys. This review provides practical experimental design considerations for amino acid researchers and recent work for benchmarking nutrient matrices.

Human kappa-casein was prepared from whole casein by successive hydroxyapatite and thiol-Sepharose chromatographies. The primary structure of its 99-residue N-terminal fragment has been determined by sequencing peptides obtained by tryptic and chymotryptic digestions of the whole protein. This fragment overlaps the known sequence of the 65-residue C-terminal fragment. The 158-residue sequence of human kappa-casein was compared to those of goat, ewe, cow and rat kappa-caseins. Only 22% of the residues are identical in homologous positions. The rate of divergence of the 93-residue N-terminal segment (para-kappa-casein) appears to be higher than that of the rest of the molecule.

An intestinal perfusion technique has been used in normal human subjects to investigate the influence that starter protein composition and hydrolysis procedure have on absorption of amino acid residues from partial enzymic hydrolysates of whole protein. Five starter proteins were studied. Three (egg albumin, casein/soy/lactalbumin, and lactalbumin) were hydrolysed by papain, a second lactalbumin starter protein, and a meat/soy/lactalbumin blend were hydrolysed by a porcine pancreatic enzyme system. Irrespective of starter protein composition or hydrolysis method used, four amino acid residues (threonine, glutamic acid, phenylalanine, and histidine) were absorbed significantly faster from all hydrolysates compared with absorption from their equivalent free amino acid mixtures. In contrast, both starter protein composition and hydrolysis method influenced absorption characteristics of up to nine other amino acid residues.