Peptides ; chemistry ; Polyethylene Glycols ; chemistry ; Proteins ; chemistry

Isopeptide bond-mediated molecular superglue is the irreversible covalent bond spontaneously formed by the side chains of lysine (Lys) and asparagine/aspartic acid (Asn/Asp) residues. The peptide-peptide interaction is specific, stable, and can be achieved quickly without any particular physicochemical factor. In the light of recent progress by domestic and foreign researchers, here we summarize the origin, assembly system and mechanism of isopeptide bond reaction, as well as the molecular cyclization and protein topological structure mediated by it. The prospect for its application in synthetic vaccine, hydrogel and bacterial nanobiological reactor is further discussed.
Cyclization ; Lysine ; Peptides ; chemistry ; Proteins

Many factors influence the elastin-like polypeptides (ELPs) self-assembled into micron-sized particles. However, few efforts were made to investigate these factors. Using the ELPs [KV8F]n as the target, we studied systematically the factors with the dynamic light scattering. Our results show that the particle size increased and the uniform of particles decreased with the increase of the molecular weight. The analysis of size variation in self-assembled ELPs in response to changes in salt concentration indicated that the size increased with increasing the salt concentration, and the opposite response was observed when the concentration was above 0.4 mol/L. Under these conditions, the particles are micron-sized and larger than 1.1 μm. However, when the fusions containing the same ELPs and xylanase or 1,3-propanediol oxidoreductase, the size of the self-assembled ELPs particles decreased dramatically, which was only about 1/10 of that of the free ELPs. We proposed that the solvent accessible charged area of the enzymes could interact with the ELPs, the sterical hindrance of the enzymes prevent the aggregation of the ELPs. This might be the most important parameter in altering the particle size sharply.
Elastin ; chemistry ; Molecular Weight ; Particle Size ; Peptides ; chemistry ; Salts ; chemistry

Proteins, which exist mainly in linear form in vivo, are easily affected by the change of ambient temperature and pH. The application of proteins (enzymes) in the fields of industrial catalyzing, food manufacturing and medicine are restricted due to their properties. The cyclic structure of natural cyclic peptides confers high thermal stability on itself; such mechanism can be referred to in further enhancement of the thermal stability and transformation of the structure of enzymes. This article reviewed the latest progress in the domestic and international studies on protein cyclization and summarized the traditional methods (such as protein trans-splicing, expressed protein ligation and sortase-catalyzed transpeptidation) in protein cyclization. A novel method based on SpyTag/SpyCather-mediated enzyme cyclization was discussed in more detail.
Cyclization ; Peptides, Cyclic ; chemistry ; Protein Processing, Post-Translational ; Proteins ; chemistry

Based on the self-assembly process occurring in the human body all the time, self-assembled nanomaterials were designed by the researchers. The self-assembled nanomaterials have controllability, biocompatibility and functional advantages in vivo. The self-assembled nanomaterials constructed in situ under a physiological environment display various biological characteristics which can be used for imaging, therapy, and broad clinical applications. In situ self-assembled nanomaterials can boost drug function, reduce toxic and side effects, prolong imaging time and enlarge signal-to-noise ratio. By using pathological conditions to trigger specific responses in vivo, well-ordered nanoaggregates can be spontaneously formed by multiple weak bonding interactions. The assembly shows higher accumulation and longer retention in situ. Endogenous triggers for in situ assembly, such as enzymes, pH, reactive oxygen species and ligand receptor interaction, can be used to transform the materials into a variety of controllable nanostructures including nanoparticles, nanofibers and gels through bioactivated in vivo assembly (BIVA) strategies. BIVA strategies can be applied for treatment, imaging or participate in the physiological activities of cells at the lesion site. This review summarized and prospected the design of self-assembled peptide materials based on BIVA technology and their biomedical applications. The nanostructures of the self-assembly enable some beneficial biological effects, such as assembly induced retention (AIR) effect, enhanced targeting effect, multivalent bond effect, and membrane disturbance. Thus, the BIVA nanotechnology is promising for efficient drug delivery, enhancement of targeting and treatment, as well as optimization of the biological distribution of drugs.
Drug Delivery Systems ; Humans ; Nanofibers/chemistry* ; Nanoparticles ; Nanostructures/chemistry* ; Peptides

Antimicrobial peptides (AMPs) are small molecule peptides that are widely found in living organisms with broad-spectrum antibacterial activity and immunomodulatory effect. Due to slower emergence of resistance, excellent clinical potential and wide range of application, AMP is a strong alternative to conventional antibiotics. AMP recognition is a significant direction in the field of AMP research. The high cost, low efficiency and long period shortcomings of the wet experiment methods prevent it from meeting the need for the large-scale AMP recognition. Therefore, computer-aided identification methods are important supplements to AMP recognition approaches, and one of the key issues is how to improve the accuracy. Protein sequences could be approximated as a language composed of amino acids. Consequently, rich features may be extracted using natural language processing (NLP) techniques. In this paper, we combine the pre-trained model BERT and the fine-tuned structure Text-CNN in the field of NLP to model protein languages, develop an open-source available antimicrobial peptide recognition tool and conduct a comparison with other five published tools. The experimental results show that the optimization of the two-phase training approach brings an overall improvement in accuracy, sensitivity, specificity, and Matthew correlation coefficient, offering a novel approach for further research on AMP recognition.
Anti-Bacterial Agents/chemistry* ; Amino Acid Sequence ; Antimicrobial Cationic Peptides/chemistry* ; Antimicrobial Peptides ; Natural Language Processing

Functional designing of natural amino acids (NAA) has received considerable attention in recent years due to its excellent biocompatibility. A novel self-assembling NAA, peptide RAG-16, was designed by hybridizing the characteristic silk fibroin motif (Gly-Ala) with an ionic complementary peptide sequence (Arg-Ala-Asp-Ala) in our study. The self-assembly structure, viscoelastic property, and cyto compatibility of the peptide were investigated by atomic force microscopy, rheometer, Fourier transform infrared spectrum, and inverted fluorescence microscope. RAG-16 was able to form a three-dimensional compact network structure in water. High mechanical performance of the peptide hydrogel was found due to the increase of the silk I structure from inserted fibroin motif segment. Fluorescence staining showed that vast majority of MC3T3-E1 cells in the RAG-16 hydrogel could adhere to, survive, and distribute on different planes. To sum up, in this experiment, the functional designing of the NAA has exhibited its potential application in biomedical field.
Amino Acids ; chemistry ; Biocompatible Materials ; chemistry ; Fibroins ; chemistry ; Hydrogels ; chemistry ; Models, Molecular ; Nanostructures ; chemistry ; ultrastructure ; Peptides ; chemistry ; Silk ; chemistry

Fungal pathogens represent major problems for human health and agriculture. As eukaryotic organisms, fungi share some important features with mammalian cells. Therefore, current anti-fungal antibiotics often can not distinguish between fungi and mammalian cells, resulting in serious side effects in mammalian cells. Accordingly, there is strong impetus to develop antifungal alternatives that are both safe and effective. The E1 family of colicin are channel-forming bacteriocins produced by Escherichia coli, which are bactericidal only to E. coli and related species. To target the channel-forming domain of colicin to fungal cell membrane, we engineered a sexual mating pheromone of Candida albicans, α-factor pheromone to colicin Ia. A peptide was constructed consisting of an α mating pheromone of C. albicans fused to the channel-forming domain of colicin Ia to create a new fusion protein, pheromonicin-CA (PMC-CA). Indirect immunolabeling showed that the PMC-CA bound to fungal cells and inhibited growth in the laboratory and field. In the field, the protective activity of pheromonicin against rice blast disease was significantly greater, on a molar basis, than that of triazoles, tricyclazole or isoprothiolane. These results suggest that fusion peptides may be of value as fungicidal agents under agricultural conditions.
Candida albicans ; chemistry ; Colicins ; chemistry ; Fungicides, Industrial ; chemistry ; Mating Factor ; Peptides ; chemistry ; Protein Engineering

Antimicrobial peptides (AMPs) are a class of peptides widely existing in nature with broad-spectrum antimicrobial activity. It is considered as a new alternative to traditional antibiotics because of its unique mechanism of antimicrobial activity. The development and application of natural AMPs are limited due to their drawbacks such as low antimicrobial activity and unstable metabolism. Therefore, the design and optimization of derived peptides based on natural antimicrobial peptides have become recent research hotspots. In this paper, we focus on ribosomal AMPs and summarize the design and optimization strategies of some related derived peptides, which include reasonable primary structure modification, cyclization strategy and computer-aided strategy. We expect to provide ideas for the design and optimization of antimicrobial peptides and the development of anti-infective drugs through analysis and summary in this paper.
Antimicrobial Cationic Peptides/chemistry* ; Antimicrobial Peptides ; Drug Design ; Anti-Infective Agents/pharmacology* ; Anti-Bacterial Agents

Amyloid fibrils belong to a category of abnormal aggregations of natural proteins, which are closely related to many human diseases. Recently, some critical peptide sequences have been extensively studied for clarifying the molecular mechanism of natural proteins to form amyloid fibrils. In the present study, we designed a short peptide GGAAVV (GAV-6) composed of hydrophobic amino acids glycine (G), alanine (A) and valine (V) and studied its ability to form amyloid fibrils. As characterized by atomic force microscopy (AFM) and dynamic light scattering (DLS), the peptide could self-assemble into smooth nanofibers without branches. Congo red staining/binding and thioflavin-T (ThT) binding experiments show that the nanofibers formed by GAV-6 shared identical properties with typical amyloid fibrils. These results show that the designed peptide GAV-6 could self-assemble into typical amyloid fibrils, which might make it a useful model molecule to clarify the mechanism for the formation of amyloid fibrils in the future.
Amino Acid Sequence ; Amyloid ; chemistry ; Humans ; Microscopy, Atomic Force ; Models, Molecular ; Nanofibers ; chemistry ; Peptides ; chemistry