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  • Bioinformatics tools are becoming more powerful

    2024-07-09

    Bioinformatics tools are becoming more powerful and reliable due to the growing number and availability of experimentally determined protein structures (Arnold et al., 2006, Suplatov et al., 2015, Wiltgen and Tilz, 2009). The SWISS-MODEL and MODELLER programs are most frequently used for homology or comparative protein structure modelling (Arnold et al., 2006, Kashlan et al., 2011). Molecular dynamics (MD) simulation (e.g., NAMD and VMD) can also provide atomic-level and time-dependent information for structure and functionality of protein, which are difficult to obtain experimentally (Lin et al., 2012, Sotomayor and Schulten, 2007). Most importantly, MD simulation can also model aspects of protein structures in solution (Amorim, Netz, & Guimarães, 2010). Furthermore, secondary structure and solvent accessibility of proteins have frequently been predicted by the PHD and PROF programs of PredictProtein server (Devos et al., 2004, Rost, 1996, Rost, 2001). Given the above analyses, it will be of great theoretical importance and potential application to isolate, purify and identify AAP from A. oryzae 3.042, to characterise it and to elucidate its salt-tolerance molecular mechanisms.
    Materials and methods
    Results and discussion
    Acknowledgements The authors gratefully acknowledge the following programs for their financial support: the National Natural Science Foundation of China (31301538), the China Postdoctoral Science Foundation (2016M600380), the National Key Research and Development Program (2016YFD0400700-05), the Six Talent Peaks Project in Jiangsu Province (2015-NY-16), the Social Development Project of Jiangsu Science and Technology Department (SBE2016740834) and the Start-up Foundation for Advanced Talents of Jiangsu University (15JDG059).
    Introduction Endoplasmic reticulum aminopeptidase 1 (ERAP1) is a multifunctional enzyme belonging to the M1 family of aminopeptidases with roles in the regulation of blood pressure, angiogenesis, ectodomain shedding of several cytokine receptors, and processing of antigenic peptides presented to MHC class I glucagon receptor antagonist [[1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]]. We initially cloned its DNA as adipocyte-derived leucine aminopeptidase (A-LAP) by searching in a database [13]. Subsequently, the enzyme was found to be retained in the endoplasmic reticulum (ER) lumen despite the lack of an ER-retention signal in its amino acid sequence [[14], [15], [16]]. Because of its distinct role in antigen presentation in the ER, this enzyme is currently designated as ERAP1. In its initial characterization, ERAP1 was reported to be a secretory protein that is released into the culture medium when overexpressed in COS-7 cells [17]. Recently, ERAP1 was shown to be secreted from the murine macrophage cell line RAW264.7 upon stimulation with lipopolysaccharide (LPS) and interferon-γ (IFN-γ) [18,19]. Secreted ERAP1 acted as an activator of the phagocytosis and an Arg-supplier for nitric oxide (NO) synthesis in macrophages [18,20]. These data imply that ERAP1 is a “moonlighting protein” acting as a final processing enzyme of the precursors of MHC class I-presented antigenic peptides in the ER, as well as a macrophage activation factor in the extracellular milieu following secretion by inflammatory stimuli. It is believed that although ERAP1 is usually retained in the ER, it is intrinsically a secretory protein that is released into the extracellular milieu in response to specific stimuli. Using a mutant ERAP1 lacking the exon 10 coding sequence (ERAP1Δex10), we found that the sequence was essential for the ER-retention of the enzyme [21,22]. Recently, ERp44, an ER resident protein disulfide isomerase, was shown to be an ERAP1-binding protein responsible for ER-retention of the enzyme [23]. Exosomes are extracellular vesicles with diameters of 30–100 nm that are secreted from various types of cells, including reticulocytes, lymphocytes, dendritic cells, and intestinal epithelial cells [[24], [25], [26]]. They are released into the extracellular space upon fusion of multivesicular bodies with plasma membranes. Because exosomes contain various biomolecules, such as RNAs and proteins, and can transfer their contents to recipient cells at a distance, it is now recognized that they are involved in intercellular communication by interacting with target cells and delivering their contents [27,28].