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Macronutrients
Published in Chuong Pham-Huy, Bruno Pham Huy, Food and Lifestyle in Health and Disease, 2022
Chuong Pham-Huy, Bruno Pham Huy
In cells, a peptide is formed when two adjacent amino acids are linked together through the carboxyl (COOH) group of one amino acid with the amino (NH2) group of another to form an amide bond (-CONH-), also called peptide bond. The chain, thus formed, by linking together of many amino acid units is called a peptide chain (36, 38, 41). The two amino acids at the ends of the chain are called N-terminal and C-terminal where the groups NH2 and COOH are not linked – free or intact. Depending on the number of amino acid molecules composing a chain, the peptides may be termed as a dipeptide (containing 2 amino acid units), a tripeptide (containing 3 amino acid units) and so on. If a peptide is made up of no more than ten amino acids, it is called an oligopeptide; beyond that, it is a polypeptide. Peptide chain may possess from 50 to millions of amino acid units. When they are made up of over 100 amino acids, polypepties are sometimes called macro-peptides. Strictly speaking, proteins are polypeptides with more than 100 amino acids (38). However, this classification is arbitrary, and the number of amino acids can vary according to each author.
What Are Polymeric Carriers?
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
Gülderen Karakuş, Dolunay Şakar Daşdan
Depending on the peptide sequence, as in the conjugation region proteins, the N-terminus of the sequence may be the C-terminus or a point within it. The conjugation point may be carboxyl (-COOH), amino (-NH2), or sulfhydryl (-SH) ends. Synthetic peptides, haptens, etc., when used as a vaccine, have a significant effect. Nowadays, it is widely used to create specific antibodies. However, therapeutic agents and synthetic peptides or haptens, due to their low solubility, instability, low molecular weight, low antigenic properties, undesirable properties such as biocompatibility, and non-specificity or cytokine toxicity have greatly reduced their ability to act. However, the formation of conjugates of proteins, antigens, or actives with water-soluble polymers significantly changes the properties and immunogenicity of the therapeutic agents.
Modulating Cytolytic Responses to Infectious Pathogens
Published in Thomas F. Kresina, Immune Modulating Agents, 2020
Rebecca Pogue Caley, Jeffrey A. Frelinger
Structural crystal analysis of MHC class I was used to examine the nature of the interaction between the peptide and the binding cleft [52,53]. The peptide was shown to bind within a cleft formed by the heavy chain that consists of two alpha helices over a floor of eight beta pleated sheets [52,53] (Figure 2). Within this groove, the amino acid residues form multiple interaction sites, originally termed binding pockets [52]. The amino terminus of the peptide fits into the A pocket and maintains conserved hydrogen bond interactions with the heavy chain. The C terminus fits into the F pocket with similar conserved interactions. The anchor residues fit down into other pockets which line the cleft (Figure 2). The complete submersion of the anchor residue’s amino acid side chain in a pocket suggests how these “favored” amino acids significantly contribute to peptide/HC affinity. However, mutational analysis of both peptides and heavy chain has clearly shown that the primary anchor residues are not the sole determinant of peptide affinity [54,55].
VERITAS: Harnessing the power of nomenclature in biologic discovery
Published in mAbs, 2023
Riti Biswas, Ed Belouski, Kevin Graham, Michelle Hortter, Marissa Mock, Christine E. Tinberg, Alan J. Russell
The following example illustrates the VERITAS scheme and its ability to describe structure. Consider the molecule format called [Fab*scFv]-heteroFc in the 1 + 1 section of Figure 1. When the heteroFc is designated as the central focus, i.e., “multimerization center”, of the molecule, the Fab and scFv are both attached to the N-terminus of the center. Amino acid sequences are read N-terminus to C-terminus and are therefore written left to right. Thus, it is logical to place “Fab” and “scFv” to the left of “heteroFc”. Now, how can we relay the relationship between the Fab and the scFv? These modules are attached to two separate chains of the heteroFc, so let us use an asterisk (“*”) between them. “Fab*scFv”, which is the description of the N-terminal appendages to the “heteroFc” center, is enclosed in square brackets (“[]”) for readability and to quickly indicate that this molecule format is asymmetric.
Generation of robust bispecific antibodies through fusion of single-domain antibodies on IgG scaffolds: a comprehensive comparison of formats
Published in mAbs, 2023
Andreas V. Madsen, Peter Kristensen, Alexander K. Buell, Steffen Goletz
The presence of an Fc region could sterically limit the sdAb rotation and access of the antigen, and thus explain why a reduction in sdAb binding affinity is not as pronounced for C-terminal fusions to HC as for C-terminal fusions to LC. It may be possible that linkers other than the 10-aa (GGGGS)x2 linker used in this study could alleviate some of the steric restraints for both N-terminal and C-terminal fusion by allowing more space and flexibility for re-orienting the sdAb. Additional studies under physiological conditions may further confirm the stability of GS linkers and the molecule as a whole under these conditions. The main effects on antigen binding affinity from fusion of sdAbs onto IgG1 scaffolds are summarized in Figure 4c. In addition to antigen binding, we further investigated if the Fc effector functions were intact for the engineered bsAbs. Using FcγRIIIa as a model receptor, we did not find that any of the tested sdAb fusion formats has an effect on Fc binding to the FcγRIIIa receptor, which is a prerequisite for ADCC-mediated cell killing. Further studies will be needed to address comparative FcRn-mediated recirculation and half-life of the antibody formats.
A molecular perspective on identifying TRPV1 thermosensitive regions and disentangling polymodal activation
Published in Temperature, 2023
Dustin D. Luu, Aerial M. Owens, Mubark D. Mebrat, Wade D. Van Horn
Beyond the two membrane domains, the majority of the TRPV1 N-terminus comprises six ankyrin repeat domains (ARDs) linked to the S1-S4 domain by a diminutive N-terminal linker region. The C-terminus is composed of a functionally crucial amphipathic TRP helix and a small C-terminal domain. The arrangement of these domains is shown in Figure 2. While it is difficult to overstate the importance of the cryo-EM TRPV1 structures in molecular studies, we note that currently, all TRPV1 structures arise from the rat ortholog. About half are from the full-length channel and the rest are from an engineered rat construct that is missing ~30% of the protein. The engineered construct lacks residues 1–109 from the N-terminus, 765–838 from the C-terminus, and 604–626 from the pore turret loop in the PD. Given the species differences between the rat and human TRPV1 orthologs [1,6], additional structures would benefit the field.