Tag Archives: Protein-protein interactions

Synthetic Peptides as Protein Mimics in Biological Research

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Synthetic Peptides as Protein Mimics

Synthetic peptides have proven an excellent type of molecule for the mimicry of protein sites. The modified peptides increase the proteolytic stability of the molecules, enhancing their utility for biological applications.

Toolbox for Peptide Synthesis: Non-Proteinogenic Amino Acids and Site-Selective Ligation

The long peptides can be synthesized by the ligation method. Amino acid derivatives with modified backbone length and side-chain orientation, such as d-amino acids, N-alkyl glycine monomers, or proteolytically stable amino acid derivatives can be introduced to the peptides.

Protein Secondary Structure Mimics: α-Helix Mimics, β-Sheet Mimics
Peptide chains can be organized into secondary structures, such as α-helices and β-sheets. Peptides that mimic α-helices and β-sheets of proteins are attractive targets for drug development and tools to explore protein binding mechanism.

The α-helical conformation of a peptide can be induced by adding covalent links between amino acid side chains at selected positions. These links can be formed by lactam and disulfide bridges, triazole-based linkages, and hydrocarbon staples.

In β-sheets, β-strands are connected via loops or turns. Methods to mimic turn structures include macrocyclization, dipeptide of d-proline and l-proline, or α-aminoisobutyric acid in combination with either a d-α-amino acid or an achiral α-amino acid. An example of stimuli-responsive peptides is the temperature-dependent formation of hydrogels by β-sheet peptides. The β-hairpin mimic undergoes gelation upon heating at 60°C, and is completely reversible while cooling.

Protein Mimics in Biomedical Research

Peptides mimicking the CHR region of gp41 were developed to inhibit the formation of the six-helical bundle. Peptides that mimic these receptors are useful tools to explore the details of virus infection mechanism, as well as to develop new drugs against HIV-1. Peptides that mimic the extracellular domains of seven transmembrane G protein-coupled receptors (GPCRs), which is composed of the N-terminus (NT) and the three extracellular loops (ECLs) were explored. Peptide Ac-RERF-NH2 has a high propensity to adopt an α-turn structure and could be a promising drug candidate against cancer.

The design of peptides as protein mimics has evolved as a promising strategy for the exploration of protein-protein interactions, as they are biocompatible, biodegradable, and functionally selective.

New drug discovery: Protein-protein interactions

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Protein-protein interactions (PPI) are highly specific electrostatic attractions between protein structures. The interactions regulate cell function and influence physiology and development. Mass spectrometry is often used to detect protein-protein interactions. However, all proteomic screens are differential and require two samples such as IP and mock IP, POI and wildtype, or POI and knockout.

The peptide/ biotin-peptide or peptide/fluorescence-labeled peptide are excellent tools for studying protein-protein interactions. Check this link for details: Protein-Protein Interactions: Methods for Detection and Analysis.
https://www.lifetein.com/Peptide_Modifications_biotinylation.html

The compounds that can modulate PPI are hard to discover because the proteins have multiple binding sites and the screening assays are not reliable. In many cases, two or more proteins may interact with one another and form a complex. The optical fluorescence-based methods such as the Cy5, Cy7, FAM, FITC, TAMRA-labeled peptides, or FRET assay are particularly useful in these circumstances. Click for more details: https://www.lifetein.com/Peptide-Synthesis-FITC-modification.html.

The interactions between a fluorescently labeled or intrinsically fluorescent sample and a binding patterner are measured during the application. The changes in intrinsic fluorescence from tryptophan and tyrosine residues in the protein can be measured, which indicates transitions in the protein’s folding state.

The scientists have been working on fusion-based bifunctional proteins in cancer immunotherapy. The bifunctional protein sent an apoptotic signal to the tumor cells and enhanced their killing. The click chemistry is the perfect tool for the drug-protein or protein-protein conjugation. The more we understand the natural receptor-ligand complex and how it might signal, the better we can guide the design of therapeutic agonists. Click here for the peptide conjugation details: https://www.lifetein.com/price_modification_labeling.html