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The decrease of whole protein in synovial fluid, nitrites, uric and lactic acids against the background of the increase of glucose level and C-reactive protein is observed in patients with osteoarthrosis of second synovitis of knee joints (control group), at that, the degree of activity and roentgenological stage of the disease, presence of digital arteritis and the impairment of endocardium influence the integral surfactant condition of the synovial fluid, and the content of whole protein and β2-microglobulin depend accordingly on the indices of its severity and disease progressing, but dynamic interfacial tension, viscous, elastic and viscoelastic adsorption-rheological properties of articular liquor are closely connected with active surface properties., По сравнению с больными остеоартрозом со вторичным синовитом коленных суставов (контрольная группа) при ревматоидном гоните наблюдается уменьшение содержания в синовиальной жидкости общего белка, нитритов, мочевой и молочной кислоты на фоне повышения уровней глюкозы и С-реактивного протеина, причем на интегральное сурфактантное состояние синовии влияют степень активности и рентгенологическая стадия заболевания, наличие дигитального артериита и поражения эндокарда. Кроме того содержание общего белка и β2-микроглобулина зависит соответственно от индексов тяжести течения и прогрессирования заболевания, а с поверхностно-активными веществами тесно связаны динамическое межфазное натяжение, вязкие, упругие и вязкоэластичные адсорб­ционно-реологические свойства суставного ликвора., Порівняно із хворими на остеоартроз із вторинним синовітом колінних суглобів (контрольна група) при ревматоїдному гоніті спостерігається зменшення вмісту в синовіальній рідині загального білка, нітритів, сечової й молочної кислоти на тлі підвищення рівнів глюкози та С-реактивного протеїну, причому на інтегральний сурфактантний стан синовії впливають ступінь активності та рентгенологічна стадія захворювання, наявність дигітального артеріїту й ураження ендокарда, до того ж вміст загального білка та β2-мікроглобуліну залежить відповідно від індексів тяжкості перебігу та прогресування захворювання, а з поверхнево-активними речовинами щільно пов’язані динамічний міжфазний натяг, в’язкі, пружні й вязкоеластичні адсорбційно-реологічні властивості суглобового ліквору.

The nucleocapsid protein N from SARS-CoV-2 is one of the most highly expressed proteins by the virus and plays a number of important roles in the transcription and assembly of the virion within the infected host cell. It is expected to be characterized by a highly dynamic and heterogeneous structure as can be inferred by bioinformatics analyses as well as from the data available for the homologous protein from SARS-CoV. The two globular domains of the protein (NTD and CTD) have been investigated while no high-resolution information is available yet for the flexible regions of the protein. We focus here on the 1–248 construct which comprises two disordered fragments (IDR1 and IDR2) in addition to the N-terminal globular domain (NTD) and report the sequence-specific assignment of the two disordered regions, a step forward towards the complete characterization of the whole protein.

Background This work evaluated the performances of protein-based bioplastics obtained from black soldier fly (Hermetia illucens) prepupae. Protein films were synthesized by film casting, using both the whole proteins and their soluble fraction at pH = 10. The effects of glycerol as a plasticizer and of citric acid as a mild crosslinker on film properties were also evaluated. Results Films obtained using the soluble protein fraction were the strongest, as well as the most homogeneous and transparent ones. Protein mild crosslinking improved film tensile properties, especially in films obtained with the whole protein fraction. Non-crosslinked samples had a high affinity with water while crosslinking almost eliminated the ability of films to absorb water. All protein-based films proved to be effective barriers to red light (transmittance less than 2%). Conclusions Bioplastics derived from black soldier fly prepupae may find applications in the agricultural sector (biodegradable pots, mulching films, utensils) and deserve to be tested for food and non-food packaging. © 2021 Society of Chemical Industry.

Cataract, the major cause of blindness worldwide occurs due to the misfolding and aggregation of the protein crystallin, which constitute a major portion of the lens protein. Other than the whole protein crystallin, the peptide sequences generated from crystallin as a result of covalent protein damage have also been shown to possess and foster protein aggregation, which can be established as crystallin aggregation models. Thus, the disaggregation or inhibition of these protein aggregates could be a viable approach to combat cataract and preserve lens proteostasis. Herein, we tried to explore the disruption as well as inhibition of the intact α-crystallin protein and α-crystallin derived model peptide aggregates by l-3,4-dihydroxyphenylalanine (levodopa) coated gold (Au) nano/micro-roses as modulators. Thioflavin T fluorescence enhancement assay, and electron microscopic analysis were being employed to probe the anti-aggregation behavior of the Au nano/micro-roses towards the aggregating α-crystallin peptides/protein. Further, computational studies were performed to reveal the nature of molecular interactions between the levodopa molecule and the α-crystallin derived model peptides. Interestingly, both levodopa coated Au nano/micro-roses were found to be capable of inhibiting as well as preventing the aggregation of the intact α-crystallin protein and other model peptides derived from it.

The ethanolic extract of leaves of Phyllanthus distichus results maximum yield value than that of petroleum ether extract, chloroform extract through successive extraction process. The ethanolic extract of leaves of Phyllanthus distichus showed maximum control in blood sugar in hyperglycemic wistar rats than other experimental extracts. The test extract also reduces the blood sugar level to a maximum extent in case of normal animals. Among the study of effects of alcoholic extracts of leaves of Phyllanthus distichus in both normoglycemic and hyperglycemic model through oral route. Toxicological study revealed that the alcoholic extracts Phyllanthus distichus leaves were safe and does not alter normal physiological and behavioral effect even at a higher dose level of 3000 mg/kg body weight. Administration of alcoholic extracts Phyllanthus distichus significantly reduces the elevated glucose level in alloxan induced diabetic rats confirms its anti-diabetic activity. This also reduces normal glucose level, which reveals the hypoglycemic property. The whole protein, whole cholesterol, ASAT, ALAT, ALP enzyme activity of alloxan administered rats showed significantly higher than normal rats, the test extract treated rats significantly reduced the elevated levels. The results of the present investigation indicate that the alcoholic extracts Phyllanthus Distichus leaves may have a place in the therapy of Diabetes Mellitus as anti-diabetic and/or hypoglycemic agent. The hypoglycemic and/or anti-diabetic effect of the test extract may be due to the influence on glycogenesis, glycogenolysis metabolic activity property of one or more of its constituents. Ethanolic extract of leaves of Phyllanthus Distichus is beneficial in lowering the blood sugar concentration and in the management of other diabetic complications without any doubt. Keywords: Alcoholic Extract of Phyllanthus Distichus (AEPD), Antigen (Ag), Alanine Amino Transferase (ALAT) Alkaline Phosphate (ALP), Asparatate

Summary: Background: Patients with gastrointestinal dysfunction have a reduced ability to digest and absorb nutrients and are often unable to tolerate oral nutritional supplements (ONS) containing whole protein. Peptide-based formulas have been shown to be more efficacious and better tolerated compared with whole protein formulas in malnourished patients. Compliance to ONS is essential to maximizing outcomes. We evaluated compliance to twice-daily use of a peptide-based ONS (220 mL Vital® 1.5, Abbott Nutrition, Columbus, Ohio, USA) in adult patients with chronic malabsorption or maldigestion, over a 16-day treatment period. Results: 25 evaluable participants (of 35 participants enrolled) were compliant to the study product for 97% of the 16-day treatment period, with the number of days compliant being 15.52, and the average daily percentage of the prescribed product consumed being 98.31%. A significant increase in mean body weight gain, mean body mass index and serum prealbumin of 0.90 Kg (p = 0.0035), 0.32 (p = 0.005) and 1.87 mg/dL respectively, was also observed. There were no significant changes in the total energy, protein, carbohydrate and fat intake from food alone before and during the study product intake. No safety concerns were observed. Conclusion: Oral supplementation with the peptide-based ONS (Vital® 1.5, Abbott Nutrition, Columbus, Ohio, USA) in adults with chronic malabsorption or maldigestion is safe and effective in improving nutritional status. Keywords: Peptide-based oral nutritional supplement, Compliance, Malnutrition, Malabsorption, Maldigestion

The use of plant protein in food products is increasing. Potato protein gelation is scarcely documented, therefore potato protein gel properties were tested for two whole protein isolates (freeze dried or spray dried) and the purified sub-fractions, protease inhibitors and patatins. The effects of protein concentrations, 8 or 15% (w/w), pH-range of 3.0–7.5, and 2 different levels of ionic strength; low (15 mM NaCl) or high (200 mM NaCl) on heat induced gel properties was studied by oscillatory rheology and by uniaxial compression. Spray drying did not impair gel properties of the whole protein isolates, with the spray dried isolate actually showing higher gel strength at most conditions. For whole protein isolates, gel strength expressed as the storage modulus (G′) had a minimum at pH 4.7 at both high and low salt. The isolated patatin fraction showed a similar trend at low salt, but at high salt the gel strength was very low at pH 3, with progressively higher values at pH 5 and pH 7.5. The protease inhibitor fraction gelled best at low salt and pH values below pH 3.3, while higher pH resulted in very weak gels with a 10-fold decrease in G’. Gel appearance was affected by protein sample, pH, and ionic strength. Both whole protein isolates and the protease inhibitor fraction formed translucent gels at pH 3.0 and ionic strength 15 mM, while patatin formed translucent gels at both pH 3.0 and pH 7.5 at low salt concentration. All other conditions resulted in opaque gels.

Background and objectives: More than 2 billion people suffer with malnutrition arising from dietary protein and micronutrients deficiencies. To enhance the dietary nutrient quality, the current study used two largely grown varieties of finger millet, pearl millet, pigeonpea, and chickpea to evaluate the effect of millet–legume blends for their enhanced protein digestibility, amino acid profiles, and essential micronutrients. Findings: Our study revealed the presence of significant levels of proteins (6.3%– 22.3%), essential amino acids, and micronutrients (Fe: 2.6–8.5 mg; Zn: 2–5.5 mg; Ca: 22‐450 mg in 100 g) in these varieties. When specific millets combined with legumes in 3:1 proportion, significantly enhanced nutritional value of food by providing a balanced amino acid with good protein digestibility, and high levels of iron (7.58 mg) and zinc (4.96 mg) with 100 g of pearl millet and calcium (400.57 mg) with 100 g of finger millet. Conclusions: Pigeonpea and chickpea have a good level of proteins with essential amino acids except methionine and cysteine, whereas millet had balanced amino acid including methionine and cysteine (50% higher) and much higher levels of micronutrients (Fe, Zn and Ca). Therefore, specific millets and legumes combination complemented higher levels of micronutrients in addition to complete proteins to support comprehensive human nutrition. Significance and novelty: This study opens prospects for selecting complementary nutrient‐dense varieties for household consumption. Industries can explore these product developments significantly to reduce malnutrition if consumed adequately, which is not possible with polished rice, refined wheat flour or maize even if it is combined with legumes.

Background Malnutrition is a common finding after major abdominal surgeries especially after prolonged period of fasting in children. Enteral feeding is the commonest support way postoperatively for stimulating gut hormones, modulating immunity, and maintaining the barrier function of the intestinal mucosa. Our aim was to compare the results and outcome regarding tolerance, nutritional status, and hospital stay following a postoperative diet of peptide-based enteral formula against a whole protein enteral formula after major intestinal surgeries in pediatric patients who had resection and re-anastomosis after intussusception. Results This is a prospective cohort study on two groups of patients with a total of 30 patients during the period between January 2019 and June 2020. All patients in both groups underwent major intestinal surgeries (resection and re-anastomosis after intussusception). The first group received postoperative whole protein formula exclusively on the 3rd postoperative day while the other group received peptide-based formula exclusively on the same day. Postoperative mean serum albumin and pre-albumin levels were significantly higher in peptide-based formula group compared to those who had protein-based formula as their initial feeds (P value Conclusion Peptide-based enteral formulas are better tolerated and more useful as regards nutritional status than whole-protein formulas in post-operative course of pediatric patients regarding clinical outcome and better economically with shorter hospital stay.

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.

Motivation Protein–protein interactions (PPIs) play important roles in many biological processes. Conventional biological experiments for identifying PPI sites are costly and time-consuming. Thus, many computational approaches have been proposed to predict PPI sites. Existing computational methods usually use local contextual features to predict PPI sites. Actually, global features of protein sequences are critical for PPI site prediction. Results A new end-to-end deep learning framework, named DeepPPISP, through combining local contextual and global sequence features, is proposed for PPI site prediction. For local contextual features, we use a sliding window to capture features of neighbors of a target amino acid as in previous studies. For global sequence features, a text convolutional neural network is applied to extract features from the whole protein sequence. Then the local contextual and global sequence features are combined to predict PPI sites. By integrating local contextual and global sequence features, DeepPPISP achieves the state-of-the-art performance, which is better than the other competing methods. In order to investigate if global sequence features are helpful in our deep learning model, we remove or change some components in DeepPPISP. Detailed analyses show that global sequence features play important roles in DeepPPISP. Availability and implementation The DeepPPISP web server is available at http://bioinformatics.csu.edu.cn/PPISP/. The source code can be obtained from https://github.com/CSUBioGroup/DeepPPISP. Supplementary information Supplementary data are available at Bioinformatics online.

The research results of the mass yield and composition of the anatomical areas of rabbits carcass, the mechanisms of autolysis of rabbit meat and histomorphological changes during the course of autolysis were presented in the work. The degree of protein digestibility of rabbit muscle tissue was determined. The object of research was the California rabbit carcass. It was established that the process of meat maturing would be completed in 8 hours. Matured meat is characterized by higher nutritional value and quality. The developing in the rabbit carcass processes affect the functional and technological properties of meat during the rigor mortis resolution and at the beginning of the maturing stage. Functional and technological properties are: 53.7% - water-binding capacity and 50.6% - water-holding capacity. 24 hours later after slaughter, the functional and technological properties as a whole increased to 64.1 and 61.7, respectively, which corresponds to 85% of fresh-killed meat. Such indicators of functional and technological properties are due to the high content of high-quality complete proteins. The high digestibility of the protein components of rabbits muscle tissue was observed. The autolysis stages were illustrated by the microstructural and qualitative characteristics of rabbit meat. The deep character of autolytic processes in the longest back muscle 12 hours after rabbit slaughter, which resulted in the formation of physico-chemical, biochemical, organoleptic properties of meat, ensuring products high quality was identified. Less intensive processes took place in the muscle tissue of piriformis muscle, as well as the pre-blade muscle, which was explained by the structure peculiarities of these parts of the muscular system. The research results indicate the prospects of rabbit meat using in functional products manufacturing. The technologies developed allow to take into account preferences and income level of consumers.

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.

Crystallization of proteins is a very delicate process, which is influenced by many known and unknown factors. Of tested factors, many factors are exclusively related to individual amino-acid characters such as molecular weight or protein characters such as protein length. It is considered necessary to test factors that combine both individual amino-acid characters and protein characters with respect to success rate of crystallization. In this study, two combined characters characterizing individual amino-acid character and protein character, amino acid distribution probability and future composition, were used to correlate the success rate of crystallization of proteins from Lactobacillus via modeling. The results obtained from logistic regression and neural network were compared against the results obtained from each of 533 individual amino-acid characters. This study demonstrated that the combined characters are involved in crystallization process and should be taken into account for predicting the success rate of crystallization process.

High-intensity ultrasound (HIUS) has been widely utilized as an emerging technique to modify the functionality of proteins. However, those findings exclusively pertained to the whole protein after the treatment of HIUS. Such protein consists of not only water-soluble proteins but other insoluble constituents, which cannot reflect the role of HIUS on the protein functionality. The objective of this study is to understand the influences of ultrasonic treatment (20 kHz) at varying power (200, 300 or 500 W) and time (5, 10 or 20 min) exclusively on structural and functional properties of water-soluble fraction (WPPI) harvested from HIUS treated pea protein isolate (PPI). Relevant parameters of ultrasound including ultrasonic intensity and ultrasonic density were determined. No significant changes on the primary structure of WPPI were observed from electrophoresis and size exclusion chromatography analysis. Fourier-transform infrared spectroscopy analysis as well as intrinsic and extrinsic fluorescence spectroscopy showed that HIUS was able to change the secondary and tertiary structure of WPPI. HIUS treatment drastically improved protein content and absolute solubility of pea protein. The underlying mechanism lies in the roles of HIUS to change the secondary and tertiary structure and to increase the magnitude of surface charge of WPPI, as well as to facilitate the coexistence of both smaller particle size pea protein and soluble aggregates. HIUS exerted an adverse effect on emulsification properties but improved foaming stability. The results of this study provide a theoretical basis to unravel the essential role of HIUS on modifying the structure of plant protein and the corresponding functionality.

Chicken-based ingredients are commonly used in pet food products, but vary greatly in nutrient composition and processing conditions that may affect their protein quality and digestibility. Testing the quality of protein sources undergoing different processing conditions provides important information to pet food producers. The objective of this study was to determine the chemical composition, nutrient digestibility, protein, and AA digestibility scores, and nitrogen-corrected true metabolizable energy (TMEn) of chicken-based ingredients that had undergone different processing conditions (i.e., chicken meal, raw chicken, retorted chicken, and steamed chicken) using the precision-fed cecectomized rooster assay. True nutrient digestibility was variable among the protein sources (60% to 76% of DM, 66% to 81% of OM, 83% to 90% of AHF, 50% to 95% of AA and 73% to 85% of TMEn/GE). In general, the chicken meal had a lower (P < 0.05) nutrient digestibility than other ingredients tested, including DM, OM, and most indispensable and dispensable AA, with most having a true digestibility between 75% and 85%. The steamed chicken had the highest indispensable AA digestibilities, with all having a true digestibility greater than 88% and most being over 90%. TMEn value and digestible indispensable AA scores (DIAAS)-like values were higher (P < 0.0001) in the less processed chicken-based ingredients in comparison to chicken meal. Although animal proteins are often considered to be complete proteins, DIAAS-like values

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.

Increased protein intake is suggested as a strategy to slow or reverse the loss of muscle mass and strength observed in sarcopenia, but results from studies that directly tested this possibility have been inconsistent.We assessed the evidence on the effects of whole protein supplementation or higher-protein diets, without the use of amino acids or supplements known to stimulate hypertrophy, alone or in combination with resistance exercise (RE) interventions, on lean body mass (LBM) and strength in older adults.A systematic search was conducted using PubMed, Medline, Web of Science, and Cochrane CENTRAL databases from January 1990 to July 2021. Randomized controlled trials that assessed the effects of protein supplementation and/or higher-protein dietary interventions in older adults (mean age ≥50 y) on total LBM, appendicular lean mass (ALM), and handgrip (HG) and knee extension (KE) strength were included.Twenty-eight studies were identified. In pooled analysis, compared with lower protein controls, protein supplementation did not have a significant positive effect on total LBM [weighted mean difference in change (WMD): 0.34; 95% CI: -0.21, 0.89; I2 = 90.01%], ALM (WMD: 0.4; 95% CI: -0.01, 0.81; I2 = 90.38%), HG strength (WMD: 0.69; 95% CI: -0.69, 2.06; I2 = 94.52%), or KE strength (WMD: 1.88; 95% CI: -0.6, 4.35; I2 = 95.35%). However, in interventions that used also RE, statistically significant positive effects of protein were observed for ALM (WMD: 0.54; 95% CI: 0.03, 1.05; I2 = 89.76%) and HG (WMD: 1.71; 95% CI: 0.12, 3.30; I2 = 88.71%). Meta-regression revealed no significant association between age, per-meal protein dose, duration, and baseline protein intake with change in any outcome. Subgroup analysis revealed the statistically significant effects on ALM occurred only in sarcopenic/frail populations (WMD: 0.88; 95% CI: 0.51, 1.25; I2 = 79.0%). Most studies (n = 22) had some risk of bias.In older adults performing RE, increased protein intake leads to greater ALM and HG strength compared with lower protein controls. Without RE, protein has no additional benefit on changes in total LBM, ALM, or HG strength.

Achieving adequate nutrition for exercising humans is especially important for improving both muscle mass and metabolic health. One of the most common misunderstandings in the fitness industry is that the human body has requirements for dietary whole protein and that exercising individuals must consume only whole protein to meet their physiological needs. This view, however, is incorrect. Instead, humans at rest or during exercise have requirements for dietary amino acids (AAs), and dietary protein is a source of AAs in the body. The requirements for AAs must be met each day to avoid a negative nitrogen balance in individuals with moderate or intense physical activity. By properly meeting increased requirements for AAs through increased intake of high-quality protein (the source of AAs) plus supplemental AAs, athletes can improve their overall athletic performance. AAs or metabolites that are of special importance for exercising individuals include arginine, branched-chain AAs, creatine, glycine, taurine, and glutamine. The AAs play vital roles as both substrates for protein synthesis and molecules for regulating blood flow and nutrient metabolism. The functional roles of AAs include the maintenance of cell and tissue integrity; stimulation of mechanistic target of rapamycin and AMP-activated protein kinase cell signaling pathways; energy sources for the small intestine, cells of the immune system, and skeletal muscle; antioxidant and anti-inflammatory reactions; production of neurotransmitters; modulation of acid–base balance in the body. All of those roles are crucial for the overall goal of improving exercise performance. Therefore, adequate intakes of proteinogenic AAs and their functional metabolites, especially those noted in this review, are essential for optimal human health (including optimum muscle mass and function) and should be a primary goal of exercising individuals.

The primary aim of this review is to evaluate the efficacy of essential amino acid (EAA) supplementation as a strategy to increase dietary protein intake and improve muscle mass, strength and function in older adults. A sufficient daily protein intake is widely recognised to be fundamental for the successful management of sarcopenia in older undernourished adults. In practice, optimising protein intakes in older adults is complex, requiring consideration of the dose and amino acid composition (i.e. a complete EAA profile and abundant leucine content) of ingested protein on a per meal basis, alongside the age-related decline in appetite and the satiating properties of protein. Recent studies in older adults demonstrate that EAA-based supplements are non-satiating and can be administered alongside food to enhance the anabolic properties of a meal containing a suboptimal dose of protein; an effect magnified when combined with resistance exercise training. These findings support the notion that EAA supplementation could serve as an effective strategy to improve musculoskeletal health in older adults suffering from non-communicable diseases such as sarcopenia. Compliance is critical for the long-term success of complex interventions. Hence, aspects of palatability and desire to eat are important considerations regarding EAA supplementation. In conclusion, EAA-based supplements enriched with l-leucine offer an alternative strategy to whole protein sources to assist older adults in meeting protein recommendations. In practice, EAA supplements could be administered alongside meals of suboptimal protein content, or alternatively between meals on occasions when older adults achieve their per meal protein intake recommendations.

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.

In a living cell, protein function is regulated in several ways, including post-translational modifications (PTMs), protein-protein interaction, or by the global environment (e.g. crowding or phase separation). While site-specific PTMs act very locally on the protein, specific protein interactions typically affect larger (sub-)domains, and global changes affect the whole protein non-specifically. Herein, we directly observe protein regulation under three different degrees of localization, and present the effects on the Hsp90 chaperone system at the levels of conformational steady states, kinetics and protein function. Interestingly using single-molecule FRET, we find that similar functional and conformational steady states are caused by completely different underlying kinetics. We disentangle specific and non-specific effects that control Hsp90’s ATPase function, which has remained a puzzle up to now. Lastly, we introduce a new mechanistic concept: functional stimulation through conformational confinement. Our results demonstrate how cellular protein regulation works by fine-tuning the conformational state space of proteins., eLife digest Proteins play a wide variety of roles in the cell and interact with many other molecules. The behavior of proteins depends on their structure; yet, proteins are often flexible and will change shape, much like a tree in the wind. Nevertheless, for some of the activities that it performs, a protein must adopt one specific shape. Therefore, the likelihood that the protein will take on this specific shape directly determines how efficiently that protein can perform a specific job. The shape of a protein can be regulated by changes at several levels; these could include modifying one of the amino acid building blocks that make up that protein, binding to another protein, or by placing the protein in a part of the cell that is crowded with other large molecules. Schmid and Hugel wanted to understand how these three different types of regulation affect the structure of a protein and how they relate to its activities. The protein Hsp90 was used as a test case. It typically exists with two copies of the protein bound together, either in a parallel or a V-shape. Hsp90 plays several important roles in metabolism and can break down molecules of ATP, the so-called energy currency of the cell. All three types of regulation favored the Hsp90 pairs taking the parallel structure and increased its breakdown of ATP. The results suggest that the Hsp90 pair has a flexible structure, and that reducing this flexibility can improve Hsp90’s efficiency in carrying out its role. It was particularly unexpected that the large-scale, unspecific effect of placing the protein in a crowded environment could have such similar results to a small-scale, precise change of a single amino acid within the protein. While all three forms of regulation help to stabilize the parallel structure for Hsp90, they do this through different mechanisms, which influence the speed and the way that the protein transitions between the two structures. Schmid and Hugel believe that these results offer a new perspective on how diversely the shape and function of proteins is controlled at the molecular level, which could have wider implications for medical diagnostics and treatment.

Single amino acid variation (SAV) is an amino acid substitution of the protein sequence and might influence the whole protein structure, binding affinity, or functional domain and related to disease, even cancer. However, to clarify the relationship between SAV and cancer using traditional experiments is time and resource consuming. Though there are some SAVs predicted methods using the computational approach, most of them predict the protein stability changed caused by SAV. In this work, all of the SAV characteristics generated from protein sequences, structures, and micro-environment would be converted into feature vectors and fed into an integrated predicting system by using Support Vector Machine and genetic algorithm. The critical features were used to estimate the relationship between their properties and cancer caused by SAVs. In the results, we have developed a prediction system based on protein sequence and structure, which could distinguish the SAV is related to cancer or not, and the accuracy, the Matthews correlation coefficient, and the F1-score yield to 90.88%, 0.77 and 0.83, respectively. Moreover, an online prediction server called CanSavPre was built (http://bioinfo.cmu.edu.tw/CanSavPre/), which will be a useful, practical tool for cancer research and precision medicine.

Rotaviruses (RVs) account for severe diarrhea in children and young animals globally. In the current study, the fecal samples of diarrheic calves from a beef farm in Inner Mongolia were screened for RVA by ELISA and RT-PCR, followed by culture of three positive RVA samples in the MA-104 cell line. After 10 blind passages, cytopathic effects (CPE) appeared as detachment, granulation, and clustering of the inoculated cells. The virus isolates were identified by RT-PCR (VP6 gene RVA) and ESI-LC-MS/MS for whole protein sequencing. The protein sequences demonstrated the presence of two strains from species A rotavirus and one RVB strain; RVA/Cow-tc/CHN/35333/2019/G6P[5] was mixed with one RVB strain (RVB/Cow-tc/CHN/35334/2019/G5P[3]) in two samples, and RVA/Cow-tc/CHN/10927/2019/G8P[7] was found in one sample. They are of genotype constellations (G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3), (G8-P[7]-I5-R1-C1- M2-A1-N1-T1-E1-H1), and (G5-P[3]-I3-R5-C5-A5-N4-H5), respectively. Besides, phylogenetic analysis of the obtained sequences demonstrated viral evolution.

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.

In a living cell, protein function is regulated in several ways, including post-translational modifications (PTMs), protein-protein interaction, or by the global environment (e.g. crowding or phase separation). While site-specific PTMs act very locally on the protein, specific protein interactions typically affect larger (sub-)domains, and global changes affect the whole protein in non-specific ways.Herein, we directly observe protein regulation in three different degrees of localization, and present the effects on the Hsp90 chaperone system at the levels of conformational equilibria, kinetics and protein function. Interestingly using single-molecule FRET, we find that similar functional and conformational steady-states are caused by completely different underlying kinetics. Solving the complete kinetic rate model allows us to disentangle specific and non-specific effects controlling Hsp90’s ATPase function, which has remained a puzzle up to this day. Lastly, we introduce a new mechanistic concept: functional stimulation through conformational confinement. Our results highlight how cellular protein regulation works by fine-tuning the conformational state space of proteins.SignificanceProteins are perceived more and more as dynamic systems whose function depends critically on local and global flexibility. While 3D structures of proteins are frequently available today, our models often lack the time component, namely rate constants that determine protein function and regulation.Here we used single-molecule FRET to elucidate how the chaperone protein Hsp90 is regulated on various levels, locally and globally. We find that ATPase stimulation occurs not only through specific interactions, but also non-specifically by reducing non-productive conformational flexibility; i.e. by changing kinetics rather than thermodynamics. Our work introduces ‘stimulation through conformational confinement’ as a general mechanistic concept. We anticipate that this concept plays an important role in protein regulation, phase separation, and in dynamic protein systems in general.

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.

Infants with complex medical conditions often display faltering growth due to elevated nutritional requirements, poor intake and intolerance of feeding with malabsorption and maldigestion. As a result their nutritional management can be extremely challenging and enteral nutritional support is required. This study aimed to investigate the effectiveness, tolerance and acceptability of nutritional support with a specially formulated, paediatric peptide feed in infants with complex disease and signs of growth faltering with their current nutritional management.This prospective intervention study investigated gastrointestinal (GI) tolerance, nutritional intake and compliance with feeding, anthropometry and growth in 18 infants (mean age 6.11 months ± 4.69, mean weight 4.97 kg ± 1.71) during 28 days of enteral nutritional support with a paediatric (1 kcal/ml) readymade peptide feed.GI tolerance to nutritional support with a peptide enteral feed was good and either improved or remained stable over the study. Compliance was excellent (94.0% ± 12.6), total energy intake improved (+23 ± 42 kcal/kg, p = 0.037) and mean weight (0.61 kg ± 0.31, p = 0.0001), length (1.89 ± 1.77 cm, p = 0.0001), head circumference (1.33 ± 1.29 cm, p = 0.001), weight for length Z score (p 0.05), and weight for age Z score (p 0.05) significantly improved. Sixty one percent (n = 11) of the infants showed signs of increased growth velocity, moving upwards in terms of their centiles. All 18 infants continued with the paediatric, peptide enteral feed once the study was complete.This prospective study showed that nutrition support with a specially formulated, paediatric peptide readymade feed was well tolerated, helped to promote growth, and can be considered suitable for use in infants with complex disease and faltering growth who are unable to tolerate a whole protein feed.

Adhesive process in the abdominal cavity was simulated in Wistar rats. The animals were divided into two groups: the main one - simulation of adhesive process in the abdominal cavity and introduction of 3 ml of saline into the abdominal cavity; and the controls - simulation of adhesive process in the abdominal cavity and introduction of 3 ml of new antiadhesive preparation. We evaluated biochemical parameters at eight time points during the period from 2 hours to 28 days. The introduced drug for adhesion prevention did not affect the protein-synthetic function of the liver: the blood level of whole protein was the same in both groups and remained within the normal range throughout the follow-up period. The blood level of creatinine, which is the end product of protein metabolism reflecting the renal excretory function, was within normal values in both groups throughout the observation period. Significant differences between the groups were noted only on the 28th day of the experiment: in the main group creatinine level was higher as compared to the control group (p = 0.014), but remained within the normal range. The same pattern was observed when evaluating the blood urea level, which reflects the renal excretory function - the blood urea level remained normal in both groups throughout the experiment. Hence, the new antiadhesive drug does not produce toxic effect on liver and kidneys in a single intraperitoneal introduction in experiment. Biochemical indices are the same as in single intraperitoneal infusion of saline.

Due to the high price of animal feed additive, a number of studies have been carried out to find an alternative diet with comparable nutritional profile and cost competitiveness. The photosynthetic bacterium Rhodopseudomonas faecalis PA2 was recently proposed as a new carotenoid producer with relatively high biomass production but the mass production using a cheap substrate remains unclear. In this study, Rps. faecalis PA2 was cultivated in domestic wastewater. The optimum light intensity and agitation speed were 4000 lux and 150 rpm, respectively. Batch cultivation in a photo-bioreactor showed that specific growth rate was 1.61/day with the maximum biomass production of 33.9 g/L. Carotenoid yield, carotenoid production rate and carotenoid productivity were found to be 7.2 mg/g, 74.3 and 40.9 mg/L day, respectively. The nutritional profile of the freeze-dried biomass contained 64.8% protein and 10.6% lipid. The contents of essential amino acids accounted for approximately 72.6% of the whole protein content which is comparable with dietary amino acids required for penaeid shrimp. The amounts of unsaturated fatty acids were higher than saturated fatty acids consisting of polyunsaturated fatty acid including omega-3 (alpha-linolenic acid [18, n − 3]) and omega-6 fatty acids. Cultivation of this bacterium in domestic wastewater is considered a promising technology for microbial feed additive production with price competitiveness. Moreover, biochemical composition of Rps. faecalis grown in domestic wastewater is first reported in this study.

Background The development of effective nutritional strategies in support of muscle growth for patients with chronic obstructive pulmonary disease (COPD) remains challenging. Dietary essential amino acids (EAAs) are the main driver of postprandial net protein anabolism. In agreement, EAA supplements in healthy older adults are more effective than supplements with the composition of complete proteins. In patients with COPD it is still unknown whether complete protein supplements can be substituted with only EAAs, and whether they are as effective as in healthy older adults. Methods According to a double-blind randomized crossover design, we examined in 23 patients with moderate to very severe COPD (age: 65±2 years, FEV 1 : 40±2% of predicted) and 19 healthy age-matched subjects (age: 64±2 years), whether a free EAA mixture with a high proportion (40%) of leucine (EAA mixture) stimulated whole body net protein gain more than a similar mixture of balanced free EAAs and non-EAAs as present in whey protein (TAA mixture). Whole body net protein gain and splanchnic extraction of phenylalanine (PHE) were assessed by continuous IV infusion of L-[ring- 2 H 5 ]-PHE and L-[ring- 2 H 2 ]-tyrosine, and enteral intake of L-[ 15 N]-PHE (added to the mixtures). Results Besides an excellent positive linear relationship between PHE intake and net protein gain in both groups (r=0.84–0.91, P P P P Conclusions In COPD patients, similarly to healthy older adults, free EAA supplements stimulate whole body protein anabolism more than free amino acid supplements with the composition of complete proteins. Therefore, free EAA supplements may aid in the prevention and treatment of muscle wasting in this patient population.

Стаття присвячена вивченню впливу спрямованого годування на амінокислотний склад м’яса свиней. Біологічна цінність білка характеризується ступенем відповідності його амінокислотного складу потребам організму в амінокислотах для синтезу білка. Білкові речовини, до складу яких не входить хоча б одна з життєво необхідних амінокислот чи міститься їх у дуже незначній кількості, що не може забезпечити нормальну діяльність організму, належать до неповноцінних. Тому, визначаючи харчову цінність м’яса враховували насамперед, якою мірою кількісне співвідношення незамінних амінокислот, що міститься в ньому, наближається до оптимального, визначеного міжнародною комісією ФАО/ВООЗ, а також сумарне співвідношення незамінних та замінних амінокислот. Амінокислотний склад білкових речовин може змінюватися залежно від виду, статі, віку і навіть фізіологічного стану тварин перед забоєм. Співвідношення вмісту в м’язовій тканині незамінних амінокислот наближається до оптимального. Тому м’язову тканину продуктивних тварин потрібно розглядати як основне джерело білкових ресурсів харчування і як найціннішу складову м’яса. В зразках, отриманих від дослідних груп свиней породи ландрас, виявили підвищення синтезу незамінних амінокислот порівняно з контрольною групою. У 100 г білка м’язової тканини, отриманої від туш контрольної групи свиней міститься 4,051 г незамінних амінокислот; у м’ясі туш І дослідної групи – 4,202 г, у м’ясі туш ІІ дослідної групи – 4,505 г. Для оцінки біологічної цінності м’яса визначили амінокислотний скор білків найдовшого м’яза спини. Амінокислотний скор білків м’яса свиней в дослідних групах порівняно з контрольною збільшується для лізину, сірковмісних (метіонін, цистин), треоніну, ізолейцину, валіну та ароматичних (фенілаланін + тирозин) амінокислот. Розроблені раціони позитивно вплинули на амінокислотний склад свинини. Співвідношення незамінних амінокислот до замінних підвищується в дослідних групах, що свідчить про зниження вмісту сполучної тканини та поліпшення ніжності м’яса.

In this contribution, we provide new insights on the temporal fluctuations of surface enhanced Raman spectra (SERS) of large single molecules such as proteins. Because they can only fit partly into small active volume, SERS analysis is referred to spectral pointillism where only protein subdomains are shined and the whole protein landscape is built from the dynamics of successive individual spectra. By applying our approach on bovine serum albumin, we show that single protein subdomains are mostly comprised of three distinct amino acids. Surface amino acids such as lysine are preferentially detected in the open form of the protein. The investigation of the tryptophan Fermi doublet in the single protein regime is highly instructive on the protein conformation. We finally demonstrate that spectral pointillism enables to correlate individual amino acids with structural information.

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.

[Image: see text] Human endothelial cells (ECs) have been employed to monitor the protein changes induced by [3-(3-pyridinyl)-1-(4-pyridinyl)-2-propen-1-one] (3PO), a compound able to inhibit the glycolytic flux partially and transiently and to reduce pathological angiogenesis in a variety of disease models. Normal and TNFα induced inflamed ECs were incubated with and without 3PO at a concentration (20 μM) able to inhibit cell proliferation without cell death. At the end of the incubation period, samples were submitted to the following steps: (a) whole protein extraction, reduction, alkylation, and digestion by trypsin; (b) peptide separation by nano-LC–MS/MS analysis using a high-resolution mass spectrometer; (c) data analysis including protein identification, quantification, and statistical analysis. An altered protein expression profiling in combination with protein network analysis was employed by using a mass spectrometry-based label-free quantification approach to explore the underlying mechanisms of 3PO at cellular level.

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.

Soybean is a valuable protein crop. Promotion of its production in the northwestern direction became possible by the creation of varieties of the Northern ecotype. The physiological mechanisms of the adaptive potential of these varieties and, in particular, the features of protein accumulation in grain under contrasting weather conditions are insufficiently studied. Physiological factors that determine the level of whole protein accumulation in vegetative organs and in plant grain were studied on 7 varieties and 2 lines of breeding of the FRC of LGC. Effective assimilation activity of leaves; adaptive changes in the pigment complex, consisting in an increase in the number of carotenoids in adverse conditions; active nitrogen fixation of nodule bacteria lead to increased accumulation of nitrogen in the plant, followed by its remobilization into generative organs. The intensity of nitrogen accumulation and reutilization processes in soybean varieties of the Northern ecotype is especially high in unfavorable conditions of high humidity and lack of heat. In adverse weather conditions, correlations were established between the protein content in leaves and grains and elements of the pigment and symbiotic systems.