A novel silk fibroin protein-based fusion system for enhancing the expression of nanobodies in Escherichia coli

Biomimetic peptide conjugates as emerging strategies for controlled release from protein-based materials

Biopolymers, such as collagens, elastin, silk fibroin, spider silk, fibrin, keratin, and resilin have gained significant interest for their potential biomedical applications due to their biocompatibility, biodegradability, and mechanical properties. This review focuses on the design and integration of biomimetic peptides into these biopolymer platforms to control the release of bioactive molecules, thereby enhancing their functionality for drug delivery, tissue engineering, and regenerative medicine. Elastin-like polypeptides (ELPs) and silk fibroin repeats, for example, demonstrate how engineered peptides can mimic natural protein domains to modulate material properties and drug release profiles. Recombinant spider silk proteins, fibrin-binding peptides, collagen-mimetic peptides, and keratin-derived structures similarly illustrate the ability to engineer precise interactions and to design controlled release systems. Additionally, the use of resilin-like peptides showcases the potential for creating highly elastic and resilient biomaterials. This review highlights current achievements and future perspectives in the field, emphasizing the potential of biomimetic peptides to transform biopolymer-based biomedical applications.

Technological advancement spurs Komagataella phaffii as a next-generation platform for sustainable biomanufacturing

Biomanufacturing stands as a cornerstone of sustainable industrial development, necessitating a shift toward non-food carbon feedstocks to alleviate agricultural resource competition and advance a circular bioeconomy. Methanol, a renewable one‑carbon substrate, has emerged as a pivotal candidate due to its abundance, cost-effectiveness, and high reduction potential, further bolstered by breakthroughs in CO₂ hydrogenation-based synthesis. Capitalizing on this momentum, the methylotrophic yeast Komagataella phaffii has undergone transformative technological upgrades, evolving from a conventional protein expression workhorse into an intelligent bioproduction chassis. This paradigm shift is fundamentally driven by converging innovations across CRISPR-empowered advancement in genome editing and AI-powered metabolic pathway design in K. phaffii. The integration of CRISPR systems with droplet microfluidics high-throughput screening has redefined strain engineering efficiency, achieving much higher editing precision than traditional homologous recombination while compressing the "design-build-test-learn" cycle. Concurrently, machine learning-enhanced genome-scale metabolic models facilitate dynamic flux balancing, enabling simultaneous improvements in product titers, carbon yields, and volumetric productivity. Finally, technological advancement promotes the application of K. phaffii, including directing more efficiently metabolic flux toward nutrient products, and strengthening efficient synthesis of excreted proteins. As DNA synthesis automation and robotic experimentation platforms mature, next-generation breakthroughs in genome modification, cofactor engineering, and AI-guided autonomous evolution will further cement K. phaffii as a next-generation platform for decarbonizing global manufacturing paradigms. This technological trajectory positions methanol-based biomanufacturing as a cornerstone of the low-carbon circular economy.

Genetically engineered silk fibroin with antibacterial and antioxidant properties

Bombyx mori silk fibroin and the antimicrobial peptide cecropin B are promising biomolecules for biomedical applications due to their unique and complementary properties. In this study, we successfully expressed recombinant silk fibroin (R. fib) alone and in fusion with cecropin B (R. fib-cec) in Pichia pastoris, with yields of 6 mg/L for R. fib and 1.3 mg/L for the R. fib-cec fusion protein. Characterization of the proteins through SDS-PAGE, Western blotting, and MALDI-TOF confirmed the successful expression and purity of the recombinant proteins. Notably, the fusion protein exhibited potent broad-spectrum antibacterial activity against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus, highlighting its potential as an antimicrobial agent. Furthermore, the R. fib and the R. fib-cec demonstrated significant protective effects against H2O2 and UVB-induced oxidative damage in human adult dermal fibroblast cells. Pretreatment with R. fib and R. fib-cec significantly improved cell viability and morphology. R. fib and R. fib-cec increased viable cell numbers in H₂O₂-treated cells (61.8% and 83.5%, respectively) compared to the control (33%), and in UVB-irradiated cells (67.7% and 87.3%, respectively) compared to the control (38%). Both proteins also significantly reduced LDH release, a marker of cell damage. These results demonstrate that R. fib, especially R. fib-cec, protects against oxidative stress-induced cellular damage, promoting cell proliferation and reducing cytotoxicity. These findings highlight the multifunctionality of the silk-cecropin B fusion protein, making it a promising candidate for diverse biomedical applications, including antimicrobial therapies, skin protection, and wound healing.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04293-7.

Native Silk Fibers: Protein Sequence and Structure Influences on Thermal and Mechanical Properties

Silk fibers produced by arthropods have inspired an array of materials with applications in healthcare, medical devices, textiles, and sustainability. Silks exhibit biodiversity with distinct variations in primary protein constituent sequences (fibroins, spidroins) and structures across taxonomic classifications, specifically the Lepidopteran and Araneae orders. Leveraging the biodiversity in arthropod silks offers advantages due to the diverse mechanical properties and thermal stabilities achievable, primarily attributed to variations in fiber crystallinity and repeating amino acid motifs. In this review, we aim to delineate known properties of silk fibers and correlate them with predicted protein sequences and secondary structures, informed by newly annotated genomes. We will discuss established patterns in repeat motifs governing specific properties and underscore the biological diversity within silk fibroin and spidroin sequences. Elucidating the relationship between protein sequences and properties of natural silk fibers will identify strategies for designing new materials through rational silk-based fiber design.

Biosynthetic small molecule antigens mimics medicated lateral flow immunoassay for mycotoxin Fumonisin B1 using nanobody fusion proteins

Lateral flow immunoassays (LFAs) are widely used in point-of-care testing (POCT) for detecting small molecules. However, their application is often hindered by the complex synthesis of traditional chemically synthesized antigens. Nanobody-based coating antigen mimics have shown excellent analytical performance in various immunoassay platforms, but their application in LFAs still faces challenges. Here, we demonstrate the use of nanobody fusion proteins as antigen mimics in the construction of LFAs for detecting small molecules. Anti-idiotypic nanobody (B26) specific to Fumonisin B1 (FB1) was selected as a case study, and the maltose binding protein (MBP)-fused B26 showed optimal performance. Adsorption studies revealed that MBP-B26 showed an approximately 8-fold enhancement in maximum equilibrium adsorption capacity compared to unmodified B26 on nitrocellulose filter (NC) membranes in LFAs, and nearly 1.5-fold increase compared to chemically synthesized antigens. Molecular dynamics simulations also indicated a 28.7 % increase in non-bonding interaction energies. The MBP-B26-based LFAs detection method for FB1 demonstrated high sensitivity (1.76 μg/kg) and more environmentally friendly compared to chemically synthesized antigens. This study establishes a theoretical framework and provides models for the use of nanobody fusion proteins-based LFAs, facilitating broader application in detecting small molecules in POCT.

Fusion Partner Facilitates Expression of Cell-Penetrating Peptide L2 in Pichia pastoris

BACKGROUND

L2 is formed by combining the pheromone of Streptococcus agalactiae (S. agalactiae) and a cell-penetrating peptide (CPP) with cell-penetrating selectivity. L2 has more significant penetration and better specificity for killing S. agalactiae. However, the production of AMPs by chemical synthesis is always a challenge because of the production cost.

METHODS

This study was devoted to the heterologous expression of the cell-penetrating peptide L2 in Pichia pastoris using SUMO and a short acidic fusion tag as fusion partners, and the high-density expression of SUMO-L2 was achieved in a 5 L fermenter.

RESULTS

The results showed that SUMO-L2 expression in the 5 L fermenter reached 629 mg/L. The antibacterial activity of recombinant L2 was examined; the minimum inhibitory concentration (MICs) and minimum bactericidal concentration (MBCs) of purified L2 were 4-8 μg/mL and 8-16 μg/mL against S. agalactiae after 84 h of lysis with 50% formic acid.

CONCLUSIONS

The findings suggest that SUMO is a suitable fusion tag to express cell-penetrating peptide L2.

Large-Scale Production of Anti-RNase A VHH Expressed in pyrG Auxotrophic Aspergillus oryzae

Nanobodies, also referred to as VHH antibodies, are the smallest fragments of naturally produced camelid antibodies and are ideal affinity reagents due to their remarkable properties. They are considered an alternative to monoclonal antibodies (mAbs) with potential utility in imaging, diagnostic, and other biotechnological applications given the difficulties associated with mAb expression. Aspergillus oryzae (A. oryzae) is a potential system for the large-scale expression and production of functional VHH antibodies that can be used to meet the demand for affinity reagents. In this study, anti-RNase A VHH was expressed under the control of the glucoamylase promoter in pyrG auxotrophic A. oryzae grown in a fermenter. The feature of pyrG auxotrophy, selected for the construction of a stable and efficient platform, was established using homologous recombination. Pull-down assay, size exclusion chromatography, and surface plasmon resonance were used to confirm the binding specificity of anti-RNase A VHH to RNase A. The affinity of anti-RNase A VHH was nearly 18.3-fold higher (1.9 nM) when expressed in pyrG auxotrophic A. oryzae rather than in Escherichia coli. This demonstrates that pyrG auxotrophic A. oryzae is a practical, industrially scalable, and promising biotechnological platform for the large-scale production of functional VHH antibodies with high binding activity.

Progress in silk and silk fiber-inspired polymeric nanomaterials for drug delivery

The fields of drug and gene delivery have been revolutionized by the discovery and characterization of polymer-based materials. Polymeric nanomaterials have emerged as a strategy for targeted delivery because of features such as their impressive biocompatibility and improved availability. Use of naturally derived polymers in these nanomaterials is advantageous due to their biodegradability and bioresorption. Natural biopolymer-based particles composed of silk fibroins and other silk fiber-inspired proteins have been the focus of research in drug delivery systems due to their simple synthesis, tunable characteristics, and ability to respond to stimuli. Several silk and silk-inspired polymers contain a high proportion of reactive side groups, allowing for functionalization and addition of targeting moieties. In this review, we discuss the main classes of silk and silk-inspired polymers that are being used in the creation of nanomaterials. We also focus on the fabrication techniques used in generating a tunable design space of silk-based polymeric nanomaterials and detail how that translates into use for drug delivery to several distinct microenvironments.

Recombinant protein polymer-antibody conjugates for applications in nanotechnology and biomedicine

Currently, there are over 100 antibody-based therapeutics on the market for the treatment of various diseases. The increasing importance of antibody treatment is further highlighted by the recent FDA emergency use authorization of certain antibody therapies for COVID-19 treatment. Protein-based materials have gained momentum for antibody delivery due to their biocompatibility, tunable chemistry, monodispersity, and straightforward synthesis and purification. In this review, we discuss progress in engineering the molecular features of protein-based biomaterials, in particular recombinant protein polymers, for introducing novel functionalities and enhancing the delivery properties of antibodies and related binding protein domains.