The Major Histocompatibility Complex
Constantin A. Bona, Francisco A. Bonilla in Textbook of Immunology, 2019
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.
Interleukin-8
Jason Kelley in Cytokines of the Lung, 2022
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.
Genetics of chronic pain: crucial concepts in genetics and research tools to understand the molecular biology of pain and analgesia
Peter R Wilson, Paul J Watson, Jennifer A Haythornthwaite, Troels S Jensen in Clinical Pain Management, 2008
More recently, mass spectroscopy promises to advance the field of proteomics. Two different methods of mass spectroscopy are being applied: peptide mass fingerprinting and tandem mass spectroscopy. Peptide mass fingerprinting identifies a protein by cleaving it into short peptides and uses a peptide sequence database to align the short peptides and then deduce the protein’s identity by matching it against proteins in the database. By comparison, tandem mass spectrometry derives sequence information from individual peptides that are isolated and then collided with a nonreactive gas. Data on the array of fragment ions produced is recorded and analyzed. Unlike genome- and transcriptome-based methods, proteomic analyses struggle to attain the same level of throughput. The major limitation is that proteins cannot be amplified in a manner similar to nucleic acid amplification and the cost of mass spectroscopy is prohibitive.
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.
Recent advances in proteolytic stability for peptide, protein, and antibody drug discovery
Published in Expert Opinion on Drug Discovery, 2021
Xianyin Lai, Jason Tang, Mohamed E.H. ElSayed
In addition to the 20 proteinogenic amino acids, more than 800 natural amino acids are known in the literature, while thousands of synthetic amino acids have been reported [98]. The incorporation of non-proteinogenic amino acids that are not found in natural polypeptide chains into a peptide sequence likely will increase the metabolic stability of an analog because the new groups cannot be recognized by the same enzymes. The approach has been applied to many peptide drugs which are on the market [99]. Non-proteinogenic amino acids can be classified into many categories with various terms based on chirality (L vs. D), specific atoms introduced (such as F, S), specific groups introduced (such as CH3), the backbone length (α- vs. β-amino acids), and their combinations. In this section, the most commonly used non-proteinogenic amino acids are discussed as examples.
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
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