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Interleukin-8
Published in Jason Kelley, Cytokines of the Lung, 2022
Robert M. Strieter, Theodore J. Standiford, Mark W. Rolfe, Steven L. Kunkel
The molecular cloning of IL-8 (Matsushima et al., 1988) has identified that the cDNA is essentially identical with the previously described cDNA sequence for 3–10C from staphylococcal enterotoxin-stimulated peripheral blood mononuclear cells (Schmid and Weissmann, 1987). The 1.6-kb sequenced cDNA for IL-8 consists of a 101-base 5′ untranslated region, a 297-base coding region, and a 1.2-kb 3′ untranslated region, with one region of the TATTTATT motif common to several inflammatory cytokines (Caput et al., 1986). The coding region encodes a 99-amino acid polypeptide with a NH2-terminal end having a high degree of hydrophobicity, consistent with a typical signal peptide sequence (von Heijne, 1983). Several mature forms of IL-8 have been identified that are a result of repeated NH2-terminal amino acid cleavage (Yoshimura et al., 1989). One of these NH2-terminal amino acid cleavage products is the result of a cleavage of the 20-amino acid residue signal peptide, whereas the remaining various cleavage forms of IL-8 are due to proteolytic cleavage in culture at an R-S bond, including the major 72-amino acid form (Yoshimura et al., 1989). On the basis of the cDNA and amino acid sequence, IL-8 has significant similarity with a number of known polypeptides that are thought to be involved in mediating inflammation.
Vaccine Adjuvants in Immunotoxicology
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
In peptide sequence antigen structures, modification does not occur very successfully without affecting the immunogenic properties. This problem has been overcome by developing a peptide antigen in a nanoparticle structure. Peptide antigens are hydrophilic; therefore, they are obtained by self-conjugating these molecules using hydrophobic partial polymer, lipid, and some special peptides (Tornesello et al. 2020)
The Major Histocompatibility Complex
Published in Constantin A. Bona, Francisco A. Bonilla, Textbook of Immunology, 2019
Constantin A. Bona, Francisco A. Bonilla
The presentation of particular peptides via the endogenous pathway is regulated by some specificity, since a peptide sequence is consistently produced, irrespectively of flanking regions in the parent protein. For example, a nonapeptide derived from a cytomegalovirus protein when inserted into various positions in an unrelated protein was still consistently presented, albeit in different quantities. Similarly, a peptide of influenza virus nucleoprotein inserted into an immunoglobulin molecule was recognized by CTLs. This phenomenon is generally thought to reflect binding interactions involving MHC molecules, and is the basis of determinant selection (see below). Whether or not any of the protease or chaperone/transport molecules also contribute “specificity” to antigen presentation is not known.
Proteomic repository data submission, dissemination, and reuse: key messages
Published in Expert Review of Proteomics, 2022
MassIVE-KB (https://massive.ucsd.edu/ProteoSAFe/static/massive-kb-libraries.jsp) [24] and PRIDE Peptidome (https://www.ebi.ac.uk/pride/peptidome) [5] are two new resources from ProteomeXchange partners MassIVE and PRIDE to provide peptide and protein identification evidence from original submitted datasets or reanalyses. MassIVE-KB uses clustering to analyze 227 human datasets, and 27’404 LC/MS runs to finally obtain 2.1 million high-quality precursors (peptide + modifications + charge state) representing 19,610 human proteins. PRIDE Peptidome uses a combination of clustering and the protein inference tool (PIA) to access the quality of each PSM. The best peptide per project is selected based on three rules: (i) the peptidoform passes the peptide FDR threshold for the assay; (ii) the cluster where the peptidoform belongs only contains that peptidoform; and (ii) the peptide sequence is longer than seven amino acids. The sparkMS (https://github.com/bigbio/sparkms) used Spark (https://spark.apache.org/) and PySpark to group millions of PSMs in less than 6 hours, which enabled the data analysis of such a large-scale amount of data. PRIDE Peptidome is not only focused on human datasets by containing other species such as Mouse, Arabidopsis, Gallus, etc.
Possible roles of brain derived neurotrophic factor and corticotropin releasing hormone neurons in the nucleus of hippocampal commissure functioning within the avian neuroendocrine regulation of stress
Published in Stress, 2021
Hakeem J. Kadhim, Seong W. Kang, Wayne J. Kuenzel
Polyclonal antibodies to a sequence of the chicken CRHR1 were produced in guinea pigs by a commercial company (21st Century Biochemicals Inc., Marlboro, MA, USA). Briefly, guinea pigs (n = 4) were injected with synthetic peptides comprising 13 or 14 amino acids from the 1st extracellular domain of chicken CRHR1 (residues 180-193; TMNPEVHESNVVWC). The amino acid sequence of the protein was probed against the nonredundant GenBank protein database using NCBI-BLAST software (NCBI reference sequence: NP_989652.1) and was specific to the chicken CRHR1. Two versions of the same peptide sequence were used. To enhance the immune system, KLH (keyhole limpet hemocyanin) was conjugated to a cysteine residue that was added to either the N-terminus or the C-terminus. The peptides were mixed and injected with complete Freund’s adjuvant at day zero, with boosts on days 14, 28, 42 and 63 using incomplete Freund’s adjuvant. Production bleeds were taken on days 49, 70 and 77. The final bleed from one of the guinea pigs was affinity purified. The peptide sequence was confirmed using tandem mass spectrophotometry (MS).
Discovery, characterization, and remediation of a C-terminal Fc-extension in proteins expressed in CHO cells
Published in mAbs, 2018
Christopher S. Spahr, Mark E. Daris, Kevin C. Graham, Brian D. Soriano, Jennitte L. Stevens, Stone D.-H. Shi
For de novo sequencing of the modified peptide, the most complete and best-quality targeted HCD spectra for m/z 919.43 using NCE = 20 were averaged, then deconvoluted as described above. To establish linear peptide sequence, different fragment ions in the spectra were manually selected in the Thermo software (“label relative to selected mass”) to look for single amino acid mass shifts between neighboring fragment ions. If a single amino acid mass shift was observed, the process was repeated on the new fragment ion with the goal of looking for additional single amino acid extensions. Linking together enough amino acid mass shifts may be suitable for establishing peptide sequence. As the instrumental mass accuracy is 5ppm or greater, any mass discrepancies (precursor or fragment ion) significantly greater than that indicates an error somewhere in the de novo sequencing results. Leu/Ile cannot be discriminated with our current instrument and must be determined by other means including MS3 (ETD-HCD).34-36