Definition of HLA-Dw Determinants Using Homozygous Typing Cells and the Mixed Lymphocyte Culture
M. Kam, Jeffrey L. Bidwell in Handbook of HLA TYPING TECHNIQUES, 2020
HLA-DR11/DW5, -Dw"FES", and -Dw//JVM,/. Officially, only three Dw specificities associated with DR11 have been found: Dw5, Dw"FES", and Dw"JVM",33 but a fourth HTC defined specificity (TISI) corresponding to the DRB1*1103 allele has recently been described.59 Of the various subtypes, Dw5 (DRB1 *1101) is the most common allele found in Caucasoids and normally is in association with DQ7(3). Dw"FES", originally described in an Ashkenazi Jew in association with DQ6(1),60 has also been found in Negroids and other population groups associated with either DQ6(1) or DQ7(3).46,47 Amino acid sequence analysis of the DRB1 genes of these cells has demonstrated that apart from the different DQ association, the main differences between these alleles are amino acid substitutions found in the HV3 of their DRB1 genes.33
Introduction to Cell Biology
Anthony R. Mundy, John M. Fitzpatrick, David E. Neal, Nicholas J. R. George in The Scientific Basis of Urology, 2010
Proteins are macromolecules comprising a chain of amino acids (Fig. 1A). There are 20 different amino acids that can be stringed together in any order by peptide bonds to make up an almost infinite number of proteins. Usually, proteins are of 100 to 1000 amino acids in length. The primary structure of a protein refers to its amino acid sequence. Once assembled, small sections of a protein will fold into a secondary structure stabilized by hydrogen bonding between neighboring or proximal amino acids. These secondary structures include a-helices, β-sheets, and turns, and a protein may contain many regions with different secondary structures that stabilize each other. The overall three-dimensional or tertiary structure of a protein in its entirety is determined by the intramolecular bonds between local and distant amino acids. These bonds are weaker than those maintaining secondary structure, and thus the tertiary structure can be manipulated or altered in certain conditions. This propensity for flexibility has allowed proteins to assume enumerable functional roles in the cell, as will be discussed later. Finally, a single protein, or monomer, can assemble with other monomers to form multimeric structures, and in many cases, multimeric assembly is required for protein function. This quaternary structure is defined by the number and relative order of protein monomers within a multimeric complex.
Monoclonal Antibodies Used for the Diagnosis of the Small Round Cell Tumors of Childhood
John T. Kemshead in Pediatric Tumors: Immunological and Molecular Markers, 2020
Using DNA sequencing techniques, it is possible to predict the amino acid sequence of a particular gene. Based on this sequence it is possible to produce synthetic peptides that can be used as immunogens. To determine the amino acid sequence of peptides to be synthesized, a hydrophobicity plot (Figure 1) is often produced to determine sequences that lie in either particular hydrophilic or hydrophobic regions of the molecule.12 Synthetic peptides are then usually linked to a carrier molecule such as Keyhole Limpet Hemocyanin to render them more immunogenic. Antisera and/or monoclonal antibodies produced in this way can be purified by affinity chromatography, as it is possible to obtain the synthetic peptide/immunogen in relatively large amounts. Examples of antisera prepared by this approach are reagents recognizing oncogene products such as the C-myc13 and N-myc proteins. While the expression of the C-myc gene occurs in a relatively wide variety of tumors/tissues, the N-myc gene product is far more restricted. (See Garson et al., Chapter 10.)
Recent advances in automated protein design and its future challenges
Published in Expert Opinion on Drug Discovery, 2018
Dani Setiawan, Jeffrey Brender, Yang Zhang
Thus, the holy grail of protein science is to understand the interplay between amino acid sequences with their corresponding spatial structures, which in return, determines their functions. The first protein sequencing was done in 1949 by Sanger [5], while the first protein structure elucidation by X-ray crystallography was made in the late 1950s by Kendrew and Perutz [6,7]; both leading to the rise of the question of protein folding as famously addressed by Levinthal in 1969 [8]. Since then, there have been an enormous number of protein sequence-structure studies done from a physics, chemistry, biology, and informatics point of view – a quest that still continues to the present day. After 50 years of studies, our understanding is still far from complete. Nevertheless, the knowledge accumulated from these studies has given rise to interesting questions: (1) Is it possible to infer protein structure and functions solely from the amino acid sequence? (2) Is it possible to build a protein with a novel (de novo) sequence, while still having control toward the outcome of the structural topology, stability and function?
Acetylcholine regulates the development of experimental autoimmune encephalomyelitis via the CD4+ cells proliferation and differentiation
Published in International Journal of Neuroscience, 2020
Linli Zhou, Xiuli Lin, Xiaomeng Ma, Yingying Liu, Lili Ma, Zhaoyu Chen, Hao Chen, Lei Si, Xiaohong Chen
Female C57BL/6 mice (5–7 weeks of age) were purchased from the Experimental Animal Center of Sun Yat-sen University (Guangzhou, China). All experiments were carried out according to the National Institutes of Health guide for the care and use of Laboratory animals (NIH Publications No. 8023, revised 1978) and were approved by the Bioethics Committee of Sun Yat-sen University. MOG35–55 (MEVGWYRSPFSRVVHLYRNGK) was synthesized by CL BioScientific (Xi’an, China). Amino acid sequences were confirmed by amino acid analysis and mass spectroscopy. The purity of the peptide was ≥95%. Mycobacterium tuberculosis H37RA was obtained from Difco (Detroit, MI). Pertussis toxin was purchased from Alexis (San Diego, CA). Complete Freund’s adjuvant (CFA) was purchased from Sigma-Aldrich (St. Louis, MO). The Amplex Red ACh/Acetylcholinesterase Assay Kit was purchased from Invitrogen (Carlsbad, CA). The cytokine assay by enzyme-linked immuno sorbent assay (ELISA) Kits for IL-6, IFN-γ, IL-4 and IL-17A were purchased from RayBiotech (Norcross, GA). The following antibodies and reagents were obtained from eBioscience (San Diego, CA): purified anti-mouse CD16/CD32 antibodies; eFluor450 conjugated anti-mouse CD4, PE-Cyanine7 conjugated anti-mouse CD25; AF-647 conjugated anti-mouse IL-17A; PE conjugated anti-mouse IFN-γ; PE-Cyanine7 conjugated anti-mouse IL-4; PE conjugated anti-mouse Foxp3. The rabbit anti-ChAT antibody, goat anti-rabbit IgG H&L (FITC) preadsorbed were purchased from Abcam (London, UK).
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.
Related Knowledge Centers
- Amine
- Carboxylic Acid
- Peptide
- Peptide Synthesis
- Protein
- Protein Sequencing
- Ribosome
- Amino Acid
- Protein Biosynthesis
- Nucleic Acid Sequence