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The Inducible Defense System: Antibody Molecules and Antigen-Antibody Reactions
Published in Julius P. Kreier, Infection, Resistance, and Immunity, 2022
Each H or L chain has a variable (V) region at the amino-terminal end and a constant or (C) region at the carboxyl-terminal end (Figure 7.3). As the name implies, the amino acid sequences in the variable regions differ more than the amino acid sequences in the constant regions. The two regions of the immunoglobulin molecule, variable and constant, are produced by different DNA (gene) segments (see below).
An Analysis of Protein Interaction and Its Methods, Metabolite Pathway and Drug Discovery
Published in Ayodeji Olalekan Salau, Shruti Jain, Meenakshi Sood, Computational Intelligence and Data Sciences, 2022
Proteins are the collection of 20 amino acids with the composed polypeptide amino acid sequences. They contain –NH2 (amine) or –COOH (carboxyl) with side chain R group. The protein’s primary structure is represented in Figure 13.2 [14].
Polymer Materials for Oral and Craniofacial Tissue Engineering
Published in Vincenzo Guarino, Marco Antonio Alvarez-Pérez, Current Advances in Oral and Craniofacial Tissue Engineering, 2020
Iriczalli Cruz Maya, Vincenzo Guarino
Zein is a vegetable protein found in the endosperm of corn that has been explored for tissue engineering and drug delivery application due to its excellent biocompatibility (Dong et al. 2004; Zhang et al. 2016). The amino acid sequence is characterized by hydrophobic and neutral amino acids, and sole polar amino acids. Due to its composition, zein is a hydrophobic protein, which may contribute to controlling the material degradation for tissue engineering, and allowing longer and sustained release of drugs as carrier (Ali et al. 2014; Zhang et al. 2016).
Thymosin β4, a potential marker of malignancy and prognosis in hepatocellular carcinoma
Published in Scandinavian Journal of Gastroenterology, 2023
Wen-chao Wang, Xiao-feng Zhang, Er-jiang Tang, A-jian Li, Lei Chen, Jia-qi Wang, Jun-yong Ma, Xiao-feng Zhang, Bin Sun
In the proposed bead-based proteomic technology, the potential marker at m/z 2370.1 Da was highest presented in HCC group (Figure 2(B)). The sequences of 2370.1 Da peptide was identified by LTQ Orbit rap XL MS/MS analysis, the MS fingerprints were subjected to an IPI search and NCBI database search. We subsequently identified proteins by ion-spray mass spectroscopy. The mass spectrum with a fragmentation pattern was identified through b and y ions, as shown in Figure 2(C). The peptide contained 21 amino acid sequences (QEKNPLPSKETIEQEKQAGES). The results revealed that there were 9 proteins fragment having the same 21 amino acid sequences: Thymosin beta-4-like protein 3, Thymosin beta-4 (Tβ4), Thymosin beta-4-like protein 6, TMSB4X protein (Fragment1), TMSB4X protein (Fragment2), TMSB4X protein (Fragment3), TMSB4X protein (Fragment4), TMSB4X protein (Fragment5), and Thymosin beta-4-like protein 1. Among them, only Tβ4 can be presented and detected in the blood circulation. Therefore, Tβ4 was chose to carry out subsequent experiments.
What’s next in cancer immunotherapy? - The promise and challenges of neoantigen vaccination
Published in OncoImmunology, 2022
Alec J. Redwood, Ian M. Dick, Jenette Creaney, Bruce W. S. Robinson
For some cancers, for example, clear-cell renal-cell carcinoma (ccRCC), the number of SNV mutations is low and SNV burden is not linked to successful ICI.25 Vaccines targeting SNV neoantigen are unlikely to be useful in this patient cohort. However, ccRCC’s, as well as DNA mismatch repair deficient, microsatellite instability-high (MSI-H) tumors, are rich in indel-induced frameshift mutations.26 Frameshift mutations generate an entirely novel amino acid sequence. Neoantigens derived from frameshift mutations appear to be highly immunogenic because indel burden is associated with elevated and activated TILs26–31 and because MSI-H tumors have high response rates to ICI immunotherapy.32,33 Frameshift derived neoantigens are therefore likely to be highly effective vaccine targets.
Metalloproteinases and NAD(P)H-dependent oxidoreductase within of Bay nettle (Chrysaora chesapeakei) venom
Published in Toxin Reviews, 2022
Mayra Pamela Becerra-Amezcua, Mónica Alejandra Rincón-Guevara, Irma Hernández-Calderas, Xochitl Guzmán-García, Isabel Guerrero-Legarreta, Humberto González-Márquez
Raw file data from mass spectrometry analysis were processed for database spectral matching using Mascot with the following variable modifications: methionine oxidation, phosphorylation on serine, threonine, and tyrosine, deamidation on asparagine and aspartic acid. Carbamidomethyl cysteine was chosen as a fixed modification. A digestion enzyme of trypsin was set allowing up to two missed cleavages. The data was searched with a fragment ion tolerance of 0.6 Da. The MS and MS/MS spectra were analyzed with the database of SwissProt 2016_05 with 551,193 sequences and 196,822,649 residues; the protein identification was selected with individual scores greater than threshold according to the Peptide Summary Report of Mascot Search Results at a 95% confidence level (p < 0.05). The MS/MS spectra were selected for manual de novo sequencing. CID produced primarily b-series and y-series ions in the mass spectrometric analysis, which allows us to analyze conventionally amino acid residues between two adjacent fragment peaks. All de novo sequences were obtained with their corresponding monoisotopic mass value. The peptidés amino acid sequence was construed manually and later confirmed using bioinformatics tools. All protein sequences were searched against databases created from Uniprot entries retrieved from separate keyword searches from venom and public database of the National Center for Biotechnology Information (NCBI) using the Blastp program on the non-redundant protein databases.