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Proteomics Mar 2023Peptide-mediated interactions (PMIs) play a crucial role in cell signaling network, which are responsible for about half of cellular protein-protein associations in the... (Review)
Review
Peptide-mediated interactions (PMIs) play a crucial role in cell signaling network, which are responsible for about half of cellular protein-protein associations in the human interactome and have recently been recognized as a new kind of promising druggable target for drug development and disease therapy. In this article, we give a systematic review regarding the proteome-wide discovery of PMIs and targeting druggable PMIs (dPMIs) with chemical drugs, self-inhibitory peptides (SIPs) and protein agents, particularly focusing on their implications and applications for therapeutic purpose in omics. We also introduce computational peptidology strategies used to model, analyze, and design PMI-targeted molecular entities and further extend the concepts of protein context, direct/indirect readout, and enthalpy/entropy effect involved in PMIs. Current issues and future perspective on this topic are discussed. There is still a long way to go before establishment of efficient therapeutic strategies to target PMIs on the omics scale.
Topics: Humans; Peptides; Proteins; Entropy
PubMed: 36461811
DOI: 10.1002/pmic.202200175 -
Saudi Medical Journal Oct 2020Food containing gluten and casein could play a role in autism spectrum disorders (ASD) symptoms. The present review aimed to update the evidence about the role of the...
Food containing gluten and casein could play a role in autism spectrum disorders (ASD) symptoms. The present review aimed to update the evidence about the role of the gluten- and casein-free diet (GCFD) on the management of ASD. Web of Science, Science Direct, Google Scholar, and PubMed databases were used to search for randomized controlled trials (RCT) conducted between January 2000 and February 2020. In total, 9 RCT were included (521 participants) with age range between 2 to 18 years. Four of these studies did not show a significant improvement regarding the symptoms of ASD. The rest of these studies (n=5) showed improvement in communication, stereotyped movements, aggressiveness, language, hyperactivity, tantrums, and signs of attention deficit hyperactivity disorder compared to control group. Hence, the data remains insu cient to support the use of GCFD to improve the symptoms of ASD in children.
Topics: Adolescent; Autism Spectrum Disorder; Caseins; Child; Child, Preschool; Clinical Decision-Making; Diet, Gluten-Free; Diet, Protein-Restricted; Dietary Proteins; Female; Humans; Male
PubMed: 33026043
DOI: 10.15537/smj.2020.10.25308 -
Pharmacological Reviews Apr 2021The complement system was discovered at the end of the 19th century as a heat-labile plasma component that "complemented" the antibodies in killing microbes, hence the...
The complement system was discovered at the end of the 19th century as a heat-labile plasma component that "complemented" the antibodies in killing microbes, hence the name "complement." Complement is also part of the innate immune system, protecting the host by recognition of pathogen-associated molecular patterns. However, complement is multifunctional far beyond infectious defense. It contributes to organ development, such as sculpting neuron synapses, promoting tissue regeneration and repair, and rapidly engaging and synergizing with a number of processes, including hemostasis leading to thromboinflammation. Complement is a double-edged sword. Although it usually protects the host, it may cause tissue damage when dysregulated or overactivated, such as in the systemic inflammatory reaction seen in trauma and sepsis and severe coronavirus disease 2019 (COVID-19). Damage-associated molecular patterns generated during ischemia-reperfusion injuries (myocardial infarction, stroke, and transplant dysfunction) and in chronic neurologic and rheumatic disease activate complement, thereby increasing damaging inflammation. Despite the long list of diseases with potential for ameliorating complement modulation, only a few rare diseases are approved for clinical treatment targeting complement. Those currently being efficiently treated include paroxysmal nocturnal hemoglobinuria, atypical hemolytic-uremic syndrome, myasthenia gravis, and neuromyelitis optica spectrum disorders. Rare diseases, unfortunately, preclude robust clinical trials. The increasing evidence for complement as a pathogenetic driver in many more common diseases suggests an opportunity for future complement therapy, which, however, requires robust clinical trials; one ongoing example is COVID-19 disease. The current review aims to discuss complement in disease pathogenesis and discuss future pharmacological strategies to treat these diseases with complement-targeted therapies. SIGNIFICANCE STATEMENT: The complement system is the host's defense friend by protecting it from invading pathogens, promoting tissue repair, and maintaining homeostasis. Complement is a double-edged sword, since when dysregulated or overactivated it becomes the host's enemy, leading to tissue damage, organ failure, and, in worst case, death. A number of acute and chronic diseases are candidates for pharmacological treatment to avoid complement-dependent damage, ranging from the well established treatment for rare diseases to possible future treatment of large patient groups like the pandemic coronavirus disease 2019.
Topics: COVID-19; Collectins; Complement Activating Enzymes; Complement C3; Complement Inactivating Agents; Complement System Proteins; Genetic Therapy; Humans; Inflammation Mediators; Lectins; Mannose-Binding Protein-Associated Serine Proteases; Pandemics; Rare Diseases; SARS-CoV-2; Synapses; Ficolins
PubMed: 33687995
DOI: 10.1124/pharmrev.120.000072 -
Food Research International (Ottawa,... Oct 2022The phenomenon of protein aggregation in food science is very common, but the formation mechanism is unclear. The formation of protein aggregates (PAs) is influenced by... (Review)
Review
The phenomenon of protein aggregation in food science is very common, but the formation mechanism is unclear. The formation of protein aggregates (PAs) is influenced by various factors, and aggregates with different sizes and shapes play an important role in food systems. Although there have been many reports on food PAs, many challenges still need to be addressed, and a systematic literature review is lacking. Thus, hypotheses about the PAs formation mechanism were summarized, and the fibrosis aggregates formation mechanism was described. The main findings of this paper indicate that the forces driving protein aggregation are covalent and non-covalent cross-linking interactions. The determination of PAs is mainly based on protein particle size combined with multispectral methods. PAs are not only associated with protein functional properties (such as emulsion and gel) but also related to harmful substances (such as advanced glycation end products, AGEs) formation. Finally, the applications of PAs in food science were summarized. Outlook and challenges were described from the perspectives of food processing conditions and parameters, food components and their interactions, food nutrition and health relationships, etc. This review will attract more food scientists to participate in related research on protein aggregation in the future.
Topics: Biophysical Phenomena; Emulsions; Food Handling; Protein Aggregates; Proteins
PubMed: 36076462
DOI: 10.1016/j.foodres.2022.111725 -
Emerging protein degradation strategies: expanding the scope to extracellular and membrane proteins.Theranostics 2021Classic small molecule inhibitors that directly target pathogenic proteins typically rely on the accessible binding sites to achieve prolonged occupancy and influence... (Review)
Review
Classic small molecule inhibitors that directly target pathogenic proteins typically rely on the accessible binding sites to achieve prolonged occupancy and influence protein functions. The emerging targeted protein degradation (TPD) strategies exemplified by PROteolysis TArgeting Chimeras (PROTACs) are revolutionizing conventional drug discovery modality to target proteins of interest (POIs) that were categorized as "undruggable" before, however, these strategies are limited within intracellular POIs. The novel new degrader technologies such as LYsosome-TArgeting Chimaeras (LYTACs) and Antibody-based PROTACs (AbTACs) have been successfully developed to expand the scope of TPD to extracellular and membrane proteins, fulfilling huge unmet medical needs. Here, we systematically review the currently viable protein degradation strategies, emphasize that LYTACs and AbTACs turn a new avenue for the development of TPD, and highlight the potential challenges and directions in this vibrant field.
Topics: Animals; Cellular Microenvironment; Drug Delivery Systems; Drug Discovery; Humans; Lysosomes; Membrane Proteins; Proteasome Endopeptidase Complex; Proteins; Proteolysis
PubMed: 34373745
DOI: 10.7150/thno.62686 -
Food & Function Apr 2021Food industries are challenged to reformulate foods and beverages with higher protein contents to lower fat and sugar content. However, increasing protein concentration...
Food industries are challenged to reformulate foods and beverages with higher protein contents to lower fat and sugar content. However, increasing protein concentration can reduce sensory acceptability due to astringency perception. Since the properties of food-saliva mixtures govern mouthfeel perception, understanding how saliva and protein interact is key to guide development of future protein-rich reformulations with optimal sensory attributes. Hence, this systematic review investigated protein-saliva interaction using both model and real human saliva, including a quality assessment. A literature search of five databases (Medline, Pubmed, Embase, Scopus and Web of Science) was undertaken covering the last 20 years, yielding 36 604 articles. Using pre-defined criteria, this was reduced to a set of 33 articles with bulk protein solutions (n = 17), protein-stabilized emulsions (n = 13) and protein-rich food systems (n = 4). Interaction of dairy proteins, lysozyme and gelatine with model or human saliva dominated the literature. The pH was shown to have a strong effect on electrostatic interaction of proteins with negatively-charged salivary mucins, with greater interactions occurring below the isoelectric point of proteins. The effect of protein concentration was unclear due to the limited range of concentrations being studied. Most studies employed a 1 : 1 w/w protein : saliva ratio, which is not representative of true oral conditions. The interaction between protein and saliva appears to affect mouthfeel through aggregation and increased friction. The searches identified a gap in research on plant proteins. Accurate simulation of in vivo oral conditions should clarify understanding of protein-saliva interaction and its influence on sensory perception.
Topics: Dietary Proteins; Humans; Saliva
PubMed: 33900320
DOI: 10.1039/d0fo03180a -
Immunity, Inflammation and Disease Jun 2016There are no reference guidelines for health care providers regarding appropriate use and interpretation of urine eosinophil protein X (u-EPX) in clinical practice.... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
There are no reference guidelines for health care providers regarding appropriate use and interpretation of urine eosinophil protein X (u-EPX) in clinical practice. Currently, there are no clear-cut clinical or laboratory parameters to diagnose asthma in young children.
OBJECTIVE
In this study, we (1) systematically reviewed and qualitatively appraised the epidemiological evidence to determine diagnostic u-EPX cut points for pediatric asthma, and (2) performed a meta-analysis to provide u-EPX estimates for diagnosing pediatric asthma.
METHODS
Research articles in literature were identified from PubMed/Medline and Web of Science databases from 1966 to August 2015. Children <18 years of age were included. Both serum and urine EPX were included. Twenty-seven studies met the inclusion criteria for the systematic review and nine studies for the meta-analysis. Details regarding EPX analyses, treatment efficacy, and outcomes were assessed. For meta-analyses, effect estimates were abstracted using standardized means.
RESULTS
Over 70% of studies found a significant relationship between u-EPX and childhood asthma. There was 1.94 times higher standardized means of u-EPX among acute asthmatics compared to healthy controls (confidence interval [CI]: 1.67-2.22). Similarly, the difference in standardized means between asymptomatic asthmatics and healthy controls was 1.58 times higher (CI: 1.27-1.88).
CONCLUSIONS AND CLINICAL RELEVANCE
Despite differences in sample sizes, EPX processing and measurement, and ages of children, a consistent trend of higher EPX levels with childhood asthma was revealed.
Topics: Asthma; Blood Proteins; Child; Eosinophil-Derived Neurotoxin; Humans; Ribonucleases
PubMed: 27957324
DOI: 10.1002/iid3.104 -
Traffic (Copenhagen, Denmark) Dec 2021Endoplasmic reticulum (ER)-to-Golgi trafficking is an essential and highly conserved cellular process. The coat protein complex-II (COPII) arm of the trafficking... (Review)
Review
Endoplasmic reticulum (ER)-to-Golgi trafficking is an essential and highly conserved cellular process. The coat protein complex-II (COPII) arm of the trafficking machinery incorporates a wide array of cargo proteins into vesicles through direct or indirect interactions with Sec24, the principal subunit of the COPII coat. Approximately one-third of all mammalian proteins rely on the COPII-mediated secretory pathway for membrane insertion or secretion. There are four mammalian Sec24 paralogs and three yeast Sec24 paralogs with emerging evidence of paralog-specific cargo interaction motifs. Furthermore, individual paralogs also differ in their affinity for a subset of sorting motifs present on cargo proteins. As with many aspects of protein trafficking, we lack a systematic and thorough understanding of the interaction of Sec24 with cargoes. This systematic review focuses on the current knowledge of cargo binding to both yeast and mammalian Sec24 paralogs and their ER export motifs. The analyses show that Sec24 paralog specificity of cargo (and cargo receptors) range from exclusive paralog dependence or preference to partial redundancy. We also discuss how the Sec24 secretion system is hijacked by viral (eg, VSV-G, Hepatitis B envelope protein) and bacterial (eg, the enteropathogenic Escherichia coli type III secretion system effector NleA/EspI) pathogens.
Topics: Animals; COP-Coated Vesicles; Endoplasmic Reticulum; Golgi Apparatus; Mammals; Membrane Proteins; Protein Transport; Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Secretory Pathway
PubMed: 34533884
DOI: 10.1111/tra.12817 -
Nutrients Jan 2022The effect of diet on the composition of gut microbiota and the consequent impact on disease risk have been of expanding interest. The present review focuses on current... (Review)
Review
The effect of diet on the composition of gut microbiota and the consequent impact on disease risk have been of expanding interest. The present review focuses on current insights of changes associated with dietary protein-induced gut microbial populations and examines their potential roles in the metabolism, health, and disease of animals. Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol was used, and 29 highly relevant articles were obtained, which included 6 mouse studies, 7 pig studies, 15 rat studies, and 1 in vitro study. Analysis of these studies indicated that several factors, such as protein source, protein content, dietary composition (such as carbohydrate content), glycation of protein, processing factors, and protein oxidation, affect the digestibility and bioavailability of dietary proteins. These factors can influence protein fermentation, absorption, and functional properties in the gut and, consequently, impact the composition of gut microbiota and affect human health. While gut microbiota can release metabolites that can affect host physiology either positively or negatively, the selection of quality of protein and suitable food processing conditions are important to have a positive effect of dietary protein on gut microbiota and human health.
Topics: Animals; Diet; Dietary Proteins; Fermentation; Food Handling; Gastrointestinal Microbiome; Mice; Rats; Swine
PubMed: 35276812
DOI: 10.3390/nu14030453 -
Clinical Nephrology Jun 2017The relationship between the sieving coefficient (SC) or extraction ratio (ER) and the molecular weight (MW) of peptide and protein solutes during hemofiltration has not... (Review)
Review
The relationship between the sieving coefficient (SC) or extraction ratio (ER) and the molecular weight (MW) of peptide and protein solutes during hemofiltration has not been investigated; it is possible that the SC and ER correlate with MW, permitting an estimate of peptide and protein clearance by hemofiltration in the absence of empiric data. A search for studies of the SC and/or ER for peptide and protein solutes during hemofiltration identified data for β-microglobulin, brain natriuretic peptide, carperitide, IL-1β, IL-1RA, IL-6, IL-8, lysozyme, myoglobin, neutrophil gelatinase-associated lipocalin, procalcitonin, retinol-binding protein, TNF-α, soluble TNFR-1, soluble TNFR-II, and vasopressin using polyacrylonitrile, polysulfone, polyamide, and cellulose hemofilters. The SC correlated with MW using polyacrylonitrile, polyamide, and cellulose hemofilters. With fewer data, the ER did not correlate with MW using polyacrylonitrile hemofilters, and not enough data were available to assess the ER with any other hemofilters. These results may help predict peptide and protein convective clearance during hemofiltration with polyacrylonitrile, polyamide, and cellulose hemofilters when empiric data are not available. .
Topics: Acrylic Resins; Blood Proteins; Hemofiltration; Humans
PubMed: 28211786
DOI: 10.5414/CN108841