Designed protein multimerization and polymerization for functionalization of proteins

DNA Tetrahedron Mass-Tagged Probe Set for the Programmed Detection of Protein Trimers by Point-to-Point Recognition and Induced Self-Assembly in Living Cells

Multimeric proteins normally perform different biological functions from their monomer components. Thus, precise recognition and quantitative detection of multimeric proteins can benefit a better understanding of complex biological processes and their roles in disease diagnosis and treatment. The challenge herein is to distinguish the multimeric proteins containing identical monomer components and recognize all the monomers in a multimeric protein on spatial scales. This situation is likely to become more significant for homomultimeric proteins. In this study, a DNA polyhedron mass-tagged probe set strategy was developed for the programmed detection of multimeric proteins in living cells. The probe set comprised recognition and displacement probes, a DNA polyhedron probe, and a mass-tagged probe. After point-to-point recognition of each monomer in the target protein complex by recognition and displacement probes, the DNA polyhedron probe could integrate the information on all the protein monomers by carrying out induced self-assembly via a cascaded toehold-mediated strand-displacement (TMSD) reaction. Afterward, the mass-tagged probe collected the integrated information, and the mass tag in the probe was released by ultraviolet (UV) irradiation and detected by mass spectrometry (MS). Using the tmTNF-α homotrimer as an example, its expression levels in different breast cancer cell lines were ultimately determined using this probe set containing a DNA tetrahedron probe. This study is among the first to quantitatively detect multimeric proteins in living cells. Using a similar strategy, more DNA polyhedron mass-tagged probe sets can be developed for the detection of higher-order multimeric proteins.

Peptidisc-Assisted Hydrophobic Clustering Toward the Production of Multimeric and Multispecific Nanobody Proteins

Multimerization is a powerful engineering strategy for enhancing protein structural stability, diversity and functional performance. Typical methods for clustering proteins include tandem linking, fusion to self-assembly domains and cross-linking. Here we present a novel approach that leverages the Peptidisc membrane mimetic to stabilize hydrophobic-driven protein clusters. We apply the method to nanobodies (Nbs), effective substitutes to traditional antibodies due to their production efficiency, cost-effectiveness and lower immunogenicity, and we demonstrate the formation of multimeric assemblies termed "polybodies" (Pbs). Starting with Nbs directed against the green fluorescent protein (GFP), we produce Pbs that display an increased affinity for GFP due to the avidity effect. The benefit of this increased avidity in affinity-based assays is demonstrated with Pbs directed against the human serum albumin. Using the same autoassembly principle, we produce bispecific and auto-fluorescent Pbs, validating our method as a versatile engineering strategy to generate multispecific and multifunctional protein entities. Peptidisc-assisted hydrophobic clustering thus expand the protein engineering toolbox to broaden the scope of protein multimerization in life sciences.

Engineering Thermoresponsive Enzyme-Polymer Conjugates via Glycan-Selective In Situ Polymerization for Recyclable Homogeneous Biocatalysis

Enzymes are crucial for various technological applications, but their inherent instability and short lifespan pose challenges. This study presents facile immobilized enzyme technology with the development of thermoresponsive enzyme-polymer conjugates (EPCs), using glucose oxidase (GOx) as a model enzyme, to address these limitations. By conjugating heteropolymers to the glycan moieties of GOx through a precise in situ polymerization process, we could modulate the lower critical solution temperature of the EPCs, enhancing enzyme performance without compromising its active site. The EPCs demonstrate a switchable behavior that facilitates efficient homogeneous catalysis and easy heterogeneous separation, reducing costs and environmental impact in industrial applications. Our strategy presents a versatile platform for creating efficient biocatalysts with tunable properties, marking a step forward in sustainable and cost-effective bioprocessing.

Enhancement of stability and activity of RSD amylase from Paenibacillus lactis OPSA3 for biotechnological applications by covalent immobilization on green silver nanoparticles

The key challenge to the biotechnological applications of amylases is achieving high activity and stability under extreme pH, temperature and often high levels of enzyme denaturants. This study immobilized a novel raw starch-digesting (RSD) amylase from Paenibacillus lactis OPSA3 on glutaraldehyde-activated silver nanoparticles. Effects of time, glutaraldehyde concentration, pH, temperature, and enzyme concentration on immobilization were studied, and the immobilized enzymes were characterized. pH 9.0 was optimum for the enzyme immobilization. The maximum immobilization efficiency of 82.23 ± 7.99 % was achieved at 25 °C for 120 min. After immobilization, the optimum pH and temperature changed from 9.0 to 11.0 and 60 to 70, respectively. Immobilization reduced the amylase's activation energy (KJ/mol) from the initial 58.862 to 45.449 following immobilization. The Km of the amylase decreased after immobilization, while the Vmax increased. The immobilized amylase showed significantly greater storage and thermal stability than the free amylase. At 80, enzyme half-life (min) and D value (min) increased from 12.33 to 179.11 and 40.94 to 594.98, respectively. The immobilized amylase (80-88 %) had more stability to the effects of the studied surfactants than the free enzyme. It also showed improved stability in the presence of commercial detergents compared to the free enzyme. The amylase's enhanced kinetic parameters and stability following successful immobilization on silver nanoparticles indicate its potential for application in the range of biotechnological processes where alkaline- and temperature-stable amylases are employed.

Stability of Protein Pharmaceuticals: Recent Advances

There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'

Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines

Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.

Snoopligase-catalyzed molecular glue enables efficient generation of hyperoligomerized TRAIL variant with enhanced antitumor effect

Clinical application of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is predominantly limited by its inefficient apoptosis induction in tumor cells, which might be improved by using molecular superglue-mediated hyperoligomerization to increase its valency. Here, the minimal superglue peptide pairs, including Snoopligase-catalyzed SnoopTagJr/SnoopDogTag and SpyStapler-catalyzed SpyTag/SpyBDTag, were individually fused at the N- or C-terminus of the TRAIL promoter to produce superglue-fusion TRAIL variants. Similar to native trivalent TRAIL, these superglue-fusion TRAIL variants were highly expressed in Escherichia coli (E. coli) and spontaneously trimerized. In the presence of Snoopligase or SpyStapler, the trivalent superglue-fusion TRAIL variants were predominantly crosslinked into hexavalent TRAIL variants. Nevertheless, Snoopligase was more efficient than SpyStapler in the production of hexavalent TRAIL variants. In particular, Snoopligase-catalyzed trivalent TRAIL variants with N-terminal fusion of SnoopTagJr/SnoopDogTag produced hexavalent SnHexaTR with the highest yield (∼70%). The in vitro cytotoxicity of SnHexaTR was 10-40 times greater than that of TRAIL in several tumor cells. In addition, compared to trivalent TRAIL, hexavalent SnHexaTR showed a longer serum half-life and greater tumor uptake, which resulted in eradication of 50% of tumor xenografts of TRAIL-sensitive COLO 205. In mice bearing TRAIL-resistant HT-29 tumor xenografts, hexavalent SnHexaTR combined with bortezomib encapsulated in liposomes also showed robust tumor growth suppression, indicating that hyperoligomerization mediated by minimal molecular superglue significantly increased the cytotoxicity and antitumor effect of TRAIL. As a novel anticancer agent candidate, the hexavalent SnHexaTR has great potential for clinical application in cancer therapy.

Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers

Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.