Helical structure motifs made searchable for functional peptide design

The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/.

Functionalized self-assembled peptide RAD/Dentonin hydrogel scaffold promotes dental pulp regeneration

RADA16-Ⅰ is an ion-complementary self-assembled peptide with a regular folded secondary conformation and can be assembled into an ordered nanostructure. Dentonin is an extracellular matrix phosphate glycoprotein functional peptide motif-containing RGD and SGDG motifs. In this experiment, we propose to combine RAD and Dentonin to form a functionalized self-assembled peptide RAD/Dentonin hydrogel scaffold. Furthermore, we expect that the RAD with the addition of functional motif Dentonin can promote pulp regeneration. The study analyzed the physicochemical properties of RAD/Dentonin through Circular dichroism, Morphology scanning, and Rheology. Besides, we examined the scaffold’s biocompatibility by Immunofluorescent staining, CCK-8 method, Live/Dead fluorescent staining, and 3D reconstruction. Finally, we applied ALP activity assay, RT-qPCR, and Alizarin red S staining to detect the effect of RAD/Dentonin on the odontogenic differentiation of human dental pulp stem cells (hDPSCs). The results showed that RAD/Dentonin spontaneously assembles into a hydrogel with a β-sheet-based nanofiber network structure. In vitro, RAD/Dentonin has superior biocompatibility and enhances adhesive proliferation, migration, odontogenic differentiation, and mineralization deposition of hDPSCs. In conclusion, the novel self-assembled peptide RAD/Dentonin is a new scaffold material suitable for cell culture and has promising applications as a scaffold for endodontic tissue engineering.

Emerging self-assembling peptide nanomaterial for anti-cancer therapy

Recently it is mainly focused on anti-tumor comprehensive treatments like finding target tumor cells or activating immune cells to inhibit tumor recurrence and metastasis. At present, chemotherapy and molecular-targeted drugs can inhibit tumor cell growth to a certain extent. However, multi-drug resistance and immune escape often make it difficult for new drugs to achieve expected effects. Peptide hydrogel nanoparticles is a new type of biological material with functional peptide chains as the core and self-assembling peptide (SAP) as the framework. It has a variety of significant biological functions, including effective local inflammation suppression and non-drug-resistant cell killing. Besides, it can induce immune activation more persistently in an adjuvant independent manner when compared with simple peptides. Thus, SAP nanomaterial has great potential in regulating cell physiological functions, drug delivery and sensitization, vaccine design and immunotherapy. Not only that, it is also a potential way to focus on some specific proteins and cells through peptides, which has already been examined in previous research. A full understanding of the function and application of SAP nanoparticles can provide a simple and practical strategy for the development of anti-tumor drugs and vaccine design, which contributes to the historical transition of peptide nanohydrogels from bench to bedside and brings as much survival benefits as possible to cancer patients.

Temporal and spatial expression of adrenomedullin and its receptors in the porcine uterus and peri-implantation conceptuses

Adrenomedullin (ADM) is an evolutionarily conserved multi-functional peptide hormone that regulates implantation, embryo spacing and placentation in humans and rodents. However, the potential roles of ADM in implantation and placentation in pigs, as a litter-bearing species, are not known. This study determined abundances of ADM in uterine luminal fluid, and the patterns of expression of ADM and its receptor components (CALCRL, RAMP2, RAMP3, and ACKR3) in uteri from cyclic and pregnant gilts, as well as conceptuses (embryonic/fetus and its extra-embryonic membranes) during the peri-implantation period of pregnancy. Total recoverable ADM was greater in the uterine fluid of pregnant compared with cyclic gilts between Days 10 and 16 post-estrus, and was from uterine luminal epithelial (LE) and conceptus trophectoderm (Tr) cells. Uterine expression of CALCRL, RAMP2, and ACKR3 were affected by day (P < 0.05), pregnant status (P < 0.01) and/or day x status (P < 0.05). Within porcine conceptuses, expression of CALCRL, RAMP2 and ACKR3 increased between Days 10 and 16 of pregnancy. Using an established porcine trophectoderm (pTr1) cell line, it was determined that 10−7 M ADM stimulated proliferation of pTr1 cells (P < 0.05) at 48 h, and increased phosphorylated mechanistic target of rapamycin (p-MTOR) and 4E binding protein 1 (p-4EBP1) by 6.1- and 4.9-fold (P < 0.0001), respectively. These novel results indicate a significant role for ADM in uterine receptivity for implantation and conceptus growth and development in pigs. They also provide a framework for future studies of ADM signaling to affect proliferation and migration of Tr cells, spacing of blastocysts, implantation and placentation in pigs.

Evolution of KIPPIS as a versatile platform for evaluating intracellularly functional peptide aptamers

Chimeric proteins have been widely used to evaluate intracellular protein–protein interactions (PPIs) in living cells with various readouts. By combining an interleukin-3-dependent murine cells and chimeric proteins containing a receptor tyrosine kinase c-kit, we previously established a c-kit-based PPI screening (KIPPIS) system to evaluate and select protein binders. In the KIPPIS components, proteins of interest are connected with a chemically inducible helper module and the intracellular domain of the growth-signaling receptor c-kit, which detects PPIs based on cell proliferation as a readout. In this system, proteins of interest can be incorporated into chimeric proteins without any scaffold proteins, which would be advantageous for evaluating interaction between small peptides/domains. To prove this superiority, we apply KIPPIS to 6 peptide aptamer–polypeptide pairs, which are derived from endogenous, synthetic, and viral proteins. Consequently, all of the 6 peptide aptamer–polypeptide interactions are successfully detected by cell proliferation. The detection sensitivity can be modulated in a helper ligand-dependent manner. The assay results of KIPPIS correlate with the activation levels of Src, which is located downstream of c-kit-mediated signal transduction. Control experiments reveal that KIPPIS clearly discriminates interacting aptamers from non-interacting ones. Thus, KIPPIS proves to be a versatile platform for evaluating the binding properties of peptide aptamers.

Identification of cathelicidin gene from Hoplobatrachus rugulosus and the antioxidant capacity of PC29 peptide

Cathelicidins, a group of vertebrate multifunctional molecules, play a role in innate immunity. Cathelicidins are antimicrobial peptides (AMPs) that are involved in protection against microbial invasion. Presently, cathelicidin peptides have been identified from only 14 amphibian species. In the study, a novel cathelicidin was identified from the lungs of frogs, Hoplobatrachus rugulosus. A 474 base pairs (bp) complementary DNA (cDNA) sequence encoded a 157 amino acid residue prepropeptide of H. rugulosus cathelicidin (cathelicidin-HR), which consisting of a 20-residue signal peptide sequence, a 108-residue cathelin region, and a 29-residue cathelicidin peptide (PC29). Amino acid sequence alignment and cladogram analysis illustrated that cathelicidin-HR have a high degree of similarity to further amphibian cathelicidins. The PC29 peptide displays antimicrobial activity only against Bacillus subtilis and Enterococcus faecalis. However, the PC29 peptide performed dose-dependent antioxidant activity. This is the first cathelicidin antioxidant peptide identified from the lung which provided a template for the development of potent bi-functional peptide therapeutic agents.