If you have been reading about peptide and want a single page that covers the useful parts, this is it: definitions, context, how it is studied, and the questions that come up repeatedly.
Updated 2025-10-23. Numbers and descriptions here follow the published literature rather than marketing material.
B cells can internalize antigen that binds to their B cell receptor and present it to helper T cells. Unlike T cells, B cells can recognize soluble antigen for which their B cell receptor is specific. They can then process the antigen and present peptides using MHC class II molecules. When a T helper cell with a TCR specific for that peptide binds, the B cell marker CD40 binds to CD40L on the T cell surface. When activated by a T cell, a B cell can undergo antibody isotype switching, affinity maturation, as well as formation of memory cells.
APEKTx1 is a highly selective blocker of the voltage-gated potassium channel Kv1.1 with no effect on other tested potassium channels (Kv1.2, Kv1.3, Kv1.4, Kv1.5, Kv1.6, Shaker IR, Kv2.1, Kv3.1, Kv4.2 and Kv4.3). APEKTx1 selectively blocks Kv1.1 channels with an IC50 value of 0.9 nM, which makes it between a 700 to 3000 times more potent inhibitor than the two known sea anemone peptides targeted against Kv channels (kalicludines and SHTX II). APEKTx1 is thought to interact with Kv1.1 through the aliphatic residue alanine (A352), an acidic residue glutamate (E353), and an aromatic residue tyrosine (Y379), as a mutation in these sites causes a loss in affinity of the toxin for Kv1.1. These residues are located in the H5-loop between the S5 and S6 domains and are part of the channel’s pore. In addition, APEKTx1 acts as a potent trypsin inhibitor (Kd= 124 nM), probably a competitive one. However, trypsin inhibition is more potent (as it has a higher affinity) in BPTI, which can be explained by the presence of Phe13 and Pro19 in APEKTx1, causing an unfavorable interaction.
The Bergmann degradation begins with benzoylation at the alpha-group of a peptide and subsequent conversion to an acyl azide. As in the Curtius rearrangement, the acyl azide, in the presence of benzyl alcohol and heat, rearranges to a highly reactive isocyanate intermediate, releasing nitrogen gas in the process. The isocyanate in turn reacts with benzyl alcohol to form a benzylurethane (also referred to as carboxybenzyl), a compound possessing a carbamate amine protecting group. Subsequent removal of the carbamate protecting group is carried out by catalytic hydrogenation in the presence of hydrochloric acid followed by addition to boiling water, yielding an unstable intermediate that rapidly rearranges to release carbon dioxide, driving the reaction forward. This leads to further rearrangement and subsequent hydrolysis, ultimately resulting in the formation of an aldehyde bearing the next amino acid residue in the sequencing series and the expulsion of the residual peptide in amide form.
All the proteolytic activity of the asparagine peptide lyases is only self-cleavages, then no further peptidase activity occurs. The main residue of the active site is the asparagine and there are other residues involved in the catalytic mechanism, which are different between the different families of asparagine peptide lyases. The cleavage mechanism consists in the cyclization of the asparagine, assisted by other active site residues. In certain conditions, the asparagine cyclic structure nucleophilically attacks its C-terminal peptide bond to the main chain forming a new bond to create a stable succinimide, cleaving itself from the main chain and consequently releasing the two halves of the product. No inhibitors are known.
The Bergmann degradation is a series of chemical reactions designed to remove a single amino acid from the carboxylic acid (C-terminal) end of a peptide. First demonstrated by Max Bergmann in 1934, it is a rarely used method for sequencing peptides. The later developed Edman degradation is an improvement upon the Bergmann degradation, instead cleaving the N-terminal amino acid of peptides to produce a hydantoin containing the desired amino acid. The Bergmann degradation follows the earlier work of Bergmann and his close colleague Leonidas Zervas, combining the organic azide degradation of the Curtius rearrangement with the Bergmann-Zervas carbobenzoxy method, which they designed to occur under relatively mild conditions so as to allow peptide sequencing. A single round of the Bergmann degradation yields an aldehyde containing the sought after amino acid residue and the remaining fragment of the original peptide in amide form.
Sources: en.wikipedia.org
In 1988, Bio-Synthesis helped in the synthesis and characterization of a new class of peptides with novel antimicrobial properties discovered at the NIH. In 1989, OCS became incorporated as Bio-synthesis, Inc. and moved its laboratories to Lewisville, Texas. In 1993, Bio-Synthesis was one of the first peptide synthesis companies to acquire a Finnigan MALDI-TOF mass spectrometer for the accurate quality control of synthetic peptides produced in-house. In 1994, Bio-synthesis pioneered the use of molecular methods for HLA analysis which is applied in organ matching for transplantation purposes. Later in the same year Bio-Synthesis held the first major HLA DNA typing workshop with the attendance of HLA laboratory directors from around the country in conjunction with University of North Texas in Denton Texas.
Beta-peptides (β-peptides) are peptides derived from β-amino acids, in which the amino group is attached to the β-carbon (i.e. the carbon two atoms away from the carboxylate group). The parent β-amino acid is β-alanine (H2NCH2CH2CO2H), a common natural substance, but most examples feature substituents in place of one or more C-H bonds. β-peptides usually do not occur in nature. β-Peptide-based antibiotics are being explored as ways of evading antibiotic resistance. Early studies in this field were published in 1996 by the group of Dieter Seebach and that of Samuel Gellman.
Founded in 1984, Bio-Synthesis, Inc. was known as OCS Laboratories and was one of the first companies providing commercially available synthetic oligonucleotides to the biomedical research community worldwide. It was the first producer of commercially available synthetic DNA and became a producer of synthetic peptides in 1985, and became the only company to provide both synthetic DNA and peptide under one roof. Also in 1985 the process, now known as PCR, was discovered by Mullis et al. A key activity for Bio-Synthesis was to synthesize large number of PCR primer thus assisting and solidifying the early adoption of this now common and crucial process in biology.
Founded in 1984, Bio-Synthesis, Inc. was known as OCS Laboratories and was one of the first companies providing commercially available synthetic oligonucleotides to the biomedical research community worldwide. It was the first producer of commercially available synthetic DNA and became a producer of synthetic peptides in 1985, and became the only company to provide both synthetic DNA and peptide under one roof. Also in 1985 the process, now known as PCR, was discovered by Mullis et al. A key activity for Bio-Synthesis was to synthesize large number of PCR primer thus assisting and solidifying the early adoption of this now common and crucial process in biology.
APCs naturally have a role in fighting tumors, via stimulation of B and cytotoxic T cells to respectively produce antibodies against tumor-related antigen and kill malignant cells. Dendritic cells, presenting tumor-specific antigen to T cells, are key to this process. Cancer therapies have included treating the patient with increased numbers of dendritic cells or cancer-specific T cells. However, newer therapies have turned to genetically engineered artificial antigen-presenting cells designed to prime the immune system to attack malignant cells. Some artificial APCs are derived from human cells; others are acellular, containing MHC proteins, co-stimulatory molecules and the necessary peptides. The APC activator IMP321 is being tested in clinical trials to accelerate the immune reaction to eliminate metastatic breast cancer or melanoma. Antigen: protease degradation on YouTube – PMAP animation Antigen-Presenting+Cells at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
Sources: en.wikipedia.org
Scaffolds are used to display the heterologous protein on the bacterial cell surface. There are various scaffolds which have been used such as outer membrane proteins, fimbriae/flagella proteins and CPX (circularly permuted OmpX). The CPX scaffold allows peptide fusion at both termini of the scaffold. OMPs are common scaffolds for bacterial display. Proteins can also be displayed on the bacterial cell surface through the use of autotransporters. Autotransporters form part of the type V secretion system. They usually have three domains: leader sequence at the N-terminal; central passenger domain; autotransporter domain at the C-terminal. The heterologous protein is inserted at the passenger domain. Another method of heterologous protein fusion is fusion with fimbriae/flagella, which are filamentous protrusions on the cell surface. There are many fimbriae on mainly Gram-negative bacteria, so displaying proteins on fimbriae is advantageous over some other surface proteins which are less numerous. A disadvantage of using fimbriae is that there is a relatively small insert size limit of 10-30 amino acids.
The Edman degradation is an alternative method for peptide sequencing that cleaves amino acid residues from the N-terminus of a peptide. In 1950 Edman designed a reaction with phenylthiocyanate (the idea for which was borrowed from a 1927 study by Bergmann, Kann and Miekeley ) to give phenylthiocarbamyl peptides followed by hydrolysis under relatively mild conditions to cleave N-terminal amino acid as phenylthiohydantoin. Phenylthiohydantoin is stable enough to undergo various sequencing procedures such as those which involve chromatography and mass spectrometry. This was an improvement on an earlier method proposed by Abderhalden and Brockmann in 1930 that demonstrated N-terminal amino acid conversion to a hydantoin under stronger hydrolytic conditions, where some cleavage of the residual peptide proved problematic. The primary advantage the Edman degradation has over the Bergmann degradation is the ease with which the residual peptide can re-enter the process due to retention of its structure throughout sequential cleaving. Repetition of the Bergmann degradation is presumably not as straightforward, as the remaining peptide is in amide form.
Founded in 1984, Bio-Synthesis, Inc. was known as OCS Laboratories and was one of the first companies providing commercially available synthetic oligonucleotides to the biomedical research community worldwide. It was the first producer of commercially available synthetic DNA and became a producer of synthetic peptides in 1985, and became the only company to provide both synthetic DNA and peptide under one roof. Also in 1985 the process, now known as PCR, was discovered by Mullis et al. A key activity for Bio-Synthesis was to synthesize large number of PCR primer thus assisting and solidifying the early adoption of this now common and crucial process in biology.
APEKTx1 is a highly selective blocker of the voltage-gated potassium channel Kv1.1 with no effect on other tested potassium channels (Kv1.2, Kv1.3, Kv1.4, Kv1.5, Kv1.6, Shaker IR, Kv2.1, Kv3.1, Kv4.2 and Kv4.3). APEKTx1 selectively blocks Kv1.1 channels with an IC50 value of 0.9 nM, which makes it between a 700 to 3000 times more potent inhibitor than the two known sea anemone peptides targeted against Kv channels (kalicludines and SHTX II). APEKTx1 is thought to interact with Kv1.1 through the aliphatic residue alanine (A352), an acidic residue glutamate (E353), and an aromatic residue tyrosine (Y379), as a mutation in these sites causes a loss in affinity of the toxin for Kv1.1. These residues are located in the H5-loop between the S5 and S6 domains and are part of the channel’s pore. In addition, APEKTx1 acts as a potent trypsin inhibitor (Kd= 124 nM), probably a competitive one. However, trypsin inhibition is more potent (as it has a higher affinity) in BPTI, which can be explained by the presence of Phe13 and Pro19 in APEKTx1, causing an unfavorable interaction.
Sources: en.wikipedia.org