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Molecular Modeling of the Interaction Between Stem Cell Peptide and Immune Receptor in Plants.
Naseem, M, Srivastava, M, Osmanoglu, O, Iqbal, J, Howari, FM, AlRemeithi, FA, Dandekar, T
Methods in molecular biology (Clifton, N.J.). 2020;:67-77
Abstract
Molecular docking enables comprehensive exploration of interactions between chemical moieties and proteins. Modeling and docking approaches are useful to determine the three-dimensional (3D) structure of experimentally uncrystallized proteins and subsequently their interactions with various inhibitors and activators or peptides. Here, we describe a protocol for carrying out molecular modeling and docking of stem cell peptide CLV3p on plant innate immune receptor FLS2.
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Current state of art after twenty years of the discovery of bioactive peptide lunasin.
Fernández-Tomé, S, Hernández-Ledesma, B
Food research international (Ottawa, Ont.). 2019;:71-78
Abstract
Non-communicable diseases have become the medical challenge of the 21st century because of their high incidence and mortality rates. Accumulating evidence has suggested that the modulation of diet and other lifestyle habits is the best strategy for the prevention of these diseases. An increasing number of dietary compounds have been found to exert health promoting benefits beyond their nutritional effects. Among them, lunasin is considered one of the most studied bioactive peptides. Since its discovery in soybean twenty years ago, many researchers around the world have focused their studies on demonstrating the chemopreventive and chemotherapeutic activity of lunasin. Moreover, in the last years, promising protective effects of this peptide against hypercholesterolemia, obesity, metabolic syndrome and associated cardiovascular disorders, and inflammatory and immune-regulated diseases have been described. This review summarizes recent remarkable advances on the use of peptide lunasin as a potential functional ingredient to provide health benefits. Moreover, novel aspects related to the influence of lunasin's digestion and bioavailability, the mechanisms of action proposed to explain the underlying biological properties, and the incorporation of this peptide into nutritional supplements are critically discussed.
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ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user's research.
Ramos-Martín, F, Annaval, T, Buchoux, S, Sarazin, C, D'Amelio, N
Life science alliance. 2019;(6)
Abstract
Antimicrobial peptides (AMPs) are part of the innate immune response to pathogens in all of the kingdoms of life. They have received significant attention because of their extraordinary variety of activities, in particular, as candidate drugs against the threat of super-bacteria. A systematic study of the relation between the sequence and the mechanism of action is urgently needed, given the thousands of sequences already in multiple web resources. ADAPTABLE web platform (http://gec.u-picardie.fr/adaptable) introduces the concept of "property alignment" to create families of property and sequence-related peptides (SR families). This feature provides the researcher with a tool to select those AMPs meaningful to their research from among more than 40,000 nonredundant sequences. Selectable properties include the target organism and experimental activity concentration, allowing selection of peptides with multiple simultaneous actions. This is made possible by ADAPTABLE because it not only merges sequences of AMP databases but also merges their data, thereby standardizing values and handling non-proteinogenic amino acids. In this unified platform, SR families allow the creation of peptide scaffolds based on common traits in peptides with similar activity, independently of their source.
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4.
Anticancer Activities of Natural and Synthetic Peptides.
Hilchie, AL, Hoskin, DW, Power Coombs, MR
Advances in experimental medicine and biology. 2019;:131-147
Abstract
Anticancer peptides (ACPs) are cationic amphipathic peptides that bind to and kill cancer cells either by a direct- or indirect-acting mechanism. ACPs provide a novel treatment strategy, and selected ACPs are currently in phase I clinical trials to examine their safety and overall benefit in cancer patients. Increasing the selectivity of ACPs is important so that these peptides kill cancer cells without harming normal cells. Peptide sequence modifications may help to improve ACP selectivity. ACPs also have immune-modulatory effects, including the release of danger signals from dying cancer cells, induction of chemokine genes, increasing T-cell immune responses, and inhibiting T regulatory cells. These effects ultimately increase the potential for an effective anticancer immune response that may contribute to long-term benefits and increased patient survival. Packaging ACPs in nanoparticles or fusogenic liposomes may be beneficial for increasing ACP half-life and enhancing the delivery of ACPs to tumor target cells. Additionally, engineering ACP-producing oncolytic viruses may be an effective future treatment strategy. Overall research in this area has been slow to progress, but with ongoing ACP-based clinical trials, the potential for ACPs in cancer treatments is closer to being realized. The integration of basic research with computer modeling of ACPs is predicted to substantially advance this field of research.
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5.
Gluten Immunogenic Peptides as Standard for the Evaluation of Potential Harmful Prolamin Content in Food and Human Specimen.
Cebolla, Á, Moreno, ML, Coto, L, Sousa, C
Nutrients. 2018;(12)
Abstract
Gluten is a complex mixture of storage proteins in cereals like wheat, barley, and rye. Prolamins are the main components of gluten. Their high content in proline and glutamine makes them water-insoluble and difficult to digest in the gastrointestinal tract. Partial digestion generates peptide sequences which trigger immune responses in celiac and gluten-sensitive patients. Gluten detection in food is challenging because of the diversity, in various food matrices, of protein proportions or modifications and the huge number of immunogenic sequences with differential potential immunoactivity. Attempts to develop standard reference materials have been unsuccessful. Recent studies have reported the detection of a limited number of dominant Gluten Immunogenic Peptides (GIP) that share similarities to epitopes presented in the α-gliadin 33-mer, which showed to be highly proteolytic resistant and is considered to be the most immunodominant peptide within gluten in celiac disease (CD). GIP were detectable and quantifiable in very different kind of difficult to analyze food, revealing the potential immunogenicity by detecting T-cell activity of celiac patients. But GIP were also found in stool and urine of celiac patients on a supposedly gluten-free diet (GFD), showing the capacity to resist and be absorbed and excreted from the body, providing the first simple and objective means to assess adherence to the GFD. Methods to specifically and sensitively detect the most active GIP in food and biological fluids are rational candidates may use similar analytical standard references for determination of the immunopathological risk of gluten exposure in gluten-related diseases.
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6.
Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis.
Bartholomae, M, Buivydas, A, Viel, JH, Montalbán-López, M, Kuipers, OP
Molecular microbiology. 2017;(2):186-206
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Abstract
Post-translationally modified peptides commonly display antimicrobial activity, but can also aid the development of bacterial colonies, giving a competitive advantage in the ecological niche. The production of post-translationally modified peptides by bacteria is a complex and energetically costly process that is strictly orchestrated in the cell. The onset of peptide production is linked to the different enzymes that take part during maturation, the transporters and the immunity determinants (if required). Thus, the population can make optimal use of available resources and obtain the benefits of production at an advantageous moment during growth, avoiding toxicity to itself. The timing and level of expression of the different operons is controlled by diverse (complex) regulatory pathways in response to environmental changes, stress or master regulators during specific growth transition phases. In this review, we highlight the basic principles and mechanisms of regulation of expression of post-translationally modified peptides and the relationship with the overall culture developmental processes and/or cellular differentiation. We also discuss the biotechnological consequences derived from the understanding of regulatory networks involved in the biosynthesis of these natural products.
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Mimics of Host Defense Proteins; Strategies for Translation to Therapeutic Applications.
Scott, RW, Tew, GN
Current topics in medicinal chemistry. 2017;(5):576-589
Abstract
New infection treatments are urgently needed to combat the rising threat of multi-drug resistant bacteria. Despite early clinical set-backs attention has re-focused on host defense proteins (HDPs), as potential sources for new and effective antimicrobial treatments. HDPs appear to act at multiple targets and their repertoire includes disruptive membrane and intracellular activities against numerous types of pathogens as well as immune modulatory functions in the host. Importantly, these novel activities are associated with a low potential for emergence of resistance and little crossresistance with other antimicrobial agents. Based on these properties, HDPs appear to be ideal candidates for new antibiotics; however, their development has been plagued by the many therapeutic limitations associated with natural peptidic agents. This review focuses on HDP mimetic approaches aimed to improve metabolic stability, pharmacokinetics, safety and manufacturing processes. Early efforts with β-peptide or peptoid analogs focused on recreating stable facially amphiphilic structures but demonstrated that antimicrobial activity was modulated by more, complex structural properties. Several approaches have used lipidation to increase the hydrophobicity and membrane activity. One lead compound, LTX-109, has entered clinical study as a topical agent to treat impetigo and nasal decolonization. In a more significant departure from the amino acid like peptidomimetics, considerable effort has been directed at developing amphiphilic compounds that recapitulate the structural and biological properties of HDPs on small abiotic scaffolds. The lead compound from this approach, brilacidin, has completed two phase 2 studies as an intravenous agent for skin infections.
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HLA class I binding prediction via convolutional neural networks.
Vang, YS, Xie, X
Bioinformatics (Oxford, England). 2017;(17):2658-2665
Abstract
MOTIVATION Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and non-self cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases. RESULTS We apply machine learning techniques from the natural language processing (NLP) domain to address the task of MHC-peptide binding prediction. More specifically, we introduce a new distributed representation of amino acids, name HLA-Vec, that can be used for a variety of downstream proteomic machine learning tasks. We then propose a deep convolutional neural network architecture, name HLA-CNN, for the task of HLA class I-peptide binding prediction. Experimental results show combining the new distributed representation with our HLA-CNN architecture achieves state-of-the-art results in the majority of the latest two Immune Epitope Database (IEDB) weekly automated benchmark datasets. We further apply our model to predict binding on the human genome and identify 15 genes with potential for self binding. AVAILABILITY AND IMPLEMENTATION Codes to generate the HLA-Vec and HLA-CNN are publicly available at: https://github.com/uci-cbcl/HLA-bind . CONTACT xhx@ics.uci.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Increased seroreactivity to proinsulin and homologous mycobacterial peptides in latent autoimmune diabetes in adults.
Niegowska, M, Delitala, A, Pes, GM, Delitala, G, Sechi, LA
PloS one. 2017;(5):e0176584
Abstract
Latent Autoimmune Diabetes in Adults (LADA) is a slowly progressing form of immune-mediated diabetes that combines phenotypical features of type 2 diabetes (T2D) with the presence of islet cell antigens detected in type 1 diabetes (T1D). Heterogeneous clinical picture have led to the classification of patients based on the levels of antibodies against glutamic acid decarboxylase 65 (GADA) that correlate with clinical phenotypes closer to T1D or T2D when GADA titers are high or low, respectively. To date, LADA etiology remains elusive despite numerous studies investigating on genetic predisposition and environmental risk factors. To our knowledge, this is the first study aimed at evaluation of a putative role played by Mycobacterium avium subsp. paratuberculosis (MAP) as an infective agent in LADA pathogenesis. MAP is known to cause chronic enteritis in ruminants and has been associated with autoimmune disorders in humans. We analyzed seroreactivity of 223 Sardinian LADA subjects and 182 healthy volunteers against MAP-derived peptides and their human homologs of proinsulin and zinc transporter 8 protein. A significantly elevated positivity for MAP/proinsulin was detected among patients, with the highest prevalence in the 32-41-year-old T1D-like LADA subgroup, supporting our hypothesis of a possible MAP contribution in the development of autoimmunity.