生物化学

Nucleases are key tools in molecular biology, enabling controlled nucleic acid digestion for applications such as ribosome profiling. Micrococcal nuclease (MNase) from Staphylococcus aureus is widely used as a tool in molecular biology and biochemistry, but its reduced activity under high-salt conditions necessitates higher enzyme input to achieve efficient digestion, increasing costs in studies of halophilic organisms. Here, we present an optimized protocol for the heterologous expression and purification of the recombinant staphylococcal MNase. The procedure enables reproducible production of a highly active, stable enzyme and incorporates an enzymatic activity assay to standardize batches to minimize variability. The resulting MNase exhibits robust activity in high-salt environments and remains stable during storage, providing a cost-effective and reliable alternative to commercial nucleases for ribosome profiling and related applications.

Antibody therapeutics have demonstrated transformative impacts on improving the quality of life of millions of patients, whereas advances in antibody discovery technologies have imposed a significant production challenge for the generation of a large diversity of therapeutic antibody candidates. A demand for the rapid production of dozens of purified antibodies in 10-mg quantities is entailed for functional screening and molecular assessment studies. Here, we present a robust semi-automated production protocol that bridges the gap between miniaturized high-throughput screenings and conventional custom-scale workflows. This methodology and workflow utilize a simple high-titer transient Chinese hamster ovary (CHO) cell host–CHO4Tx^® expression system, a procedure of magnetic protein-A bead in-culture antibody capturing, and a semi-automated purification process with the GenScript AmMag^TM SA Plus system. This production protocol has been proven to be robust and valuable for the routine production of dozens of antibody constructs per week in sufficient quality and quantity for cell-based and biophysical studies.

Nanobodies are recombinant single-domain antibodies (VHHs) derived from the heavy chain–only subset of camelid immunoglobulins that can be reverse-engineered into bivalent antibodies by fusion to immunoglobulin Fc constant regions. Mammalian cells are the system of choice to produce VHH-Fcs to ensure authentic folding and post-translation glycosylation of the expressed VHH-Fcs. In a recent project to find neutralising VHH-Fc binders to the spike proteins of SARS-CoV-2 viruses, we identified a need for rapid expression and purification of multiple VHH-Fc fusions from nanobodies selected by phage display. Here, we present a protocol for the construction of expression vectors by parallel ligase-independent cloning, transient small-scale expression in mammalian cells (4 mL culture volume), screening antigen-binding activity, and midi-scale purification (30 mL culture volume) for downstream activity assays. The workflow is completely transferable between different vector formats, of which three are described herein: Fc fusion dimers, monomeric CD4 fusions, and His-tagged monomers.

3-nitro-tyrosine (nitroTyr) is one of numerous oxidative protein modifications implicated in diseases such as cardiovascular disease, cancer, and amyotrophic lateral sclerosis (ALS). Because of this, the ability to site-specifically encode nitroTyr into recombinant proteins is a powerful approach for studying these disease pathways. However, producing proteins with defined nitration sites is technically challenging due to the limitations of traditional chemical nitration via peroxynitrite, which lacks residue and site-specificity. Genetic code expansion (GCE) offers a solution by enabling precise incorporation of nitroTyr at designated TAG codons using engineered aminoacyl-tRNA synthetase/tRNA pairs from Methanocaldococcus jannaschii and Methanomethylophilus alvus. This protocol provides a reliable, optimized workflow for incorporating nitroTyr into proteins in E. coli using GCE. It guides users through key considerations in selecting cell lines, media conditions, and GCE systems to minimize off-target effects such as release factor 1 competition, near-cognate suppression, and chemical reduction of nitroTyr. The method is demonstrated using wild-type and TAG-containing superfolder GFP but is broadly applicable to other proteins of interest.

ADGRL4 is an adhesion G protein–coupled receptor (aGPCR) implicated in multiple tumours. In our experience, conventional insect cell-based baculovirus expression systems have not yielded sufficient correctly folded ADGRL4 protein for purification and cryo-electron microscopy (cryo-EM) analysis. Here, we describe aGPCR-HEK, a six-week protocol that establishes stable tetracycline-inducible mammalian HEK293S GnTI- TetR cell lines expressing N-terminally HA- and GFP-tagged aGPCRs. The method comprises lentiviral production in Lenti-X 293T cells, transduction of target adherent HEK293S GnTI- TetR cells, flow cytometry enrichment of uninduced GFP-positive cells displaying leaky expression, adaptation to suspension culture, and large-scale tetracycline induction and harvesting of cells for downstream purification and cryo-EM. The system yields reproducible, milligram-scale quantities of folded aGPCR suitable for structural and biochemical studies.

Nowadays, recombinant proteins are the focus of various research fields, and their use ranges from therapeutic investigations to cellular model systems for the development of therapeutic approaches. Cell systems used for the expression of recombinant proteins should be comparable in terms of yield and expression efficiency. In many research fields, it is desirable to obtain high protein concentrations. A method that combines an easy workflow with rapid results and affordable costs remains missing, and a standardized approach to determining protein concentration in transgenic cell lines is essential for more reliable data analysis. Our protocol demonstrates the cluster fluorescence-linked immunosorbent assay (FLISA), a technique that allows the exact quantification of comparable protein expression amounts. Moreover, it enables the detection of clustered or bound subunits of a protein without necessitating ultracentrifugation. In the present protocol, we demonstrate the utilization of two transgene cell lines, each expressing distinct recombinant proteins, to provide comparability of protein yields and detectable subunit clustering.

The Sox (SRY-related HMG-box) protein family plays a crucial role in cellular differentiation, development, and gene regulation, with the HMG (high-mobility group) domain responsible for DNA binding and transcriptional regulation. Proteins in the SOX gene family contain an HMG domain that shares 50% homology with the HMG domain of the sex-determining factor SRY gene. The SOX gene family comprises 30 proteins, which are classified into 10 groups (A–H). As a member of this family, hSox2 has been shown to be involved in various biological processes, but its specific function remains unclear. Previous studies have used eukaryotic expression systems, GST-tag purification, and bacterial inclusion body refolding techniques to produce Sox family proteins. However, these methods are often limited by issues such as low yield, incorrect folding, or inefficient purification, restricting their application in functional and structural studies. In this study, a prokaryotic expression system for the hSox2-HMG domain was constructed using the pET22b vector and Escherichia coli BL21(DE3) as the host strain. Protein expression was induced by IPTG, and initial purification was performed using Ni-NTA affinity chromatography, followed by ultrafiltration concentration and size exclusion chromatography to improve purity. By optimizing lysis and elution conditions, we successfully obtained hSox2-HMG protein with high expression levels and purity. This method provides a cost-effective and scalable strategy for hSox2-HMG production, ensuring high purity and correct folding of the protein. The optimized experimental protocol lays a foundation for structural and functional studies of hSox2-HMG.

Zinc-finger (ZF) arrays are compact, sequence-specific polynucleotide-binding domains, which have been used to target the delivery of diverse effector domains, enabling applications such as gene identification, localization, regulation, and editing. To facilitate in vitro applications of ZF arrays, we have developed a general method for their expression and purification. Here, we describe a protocol involving two chromatographic steps that yields homogeneous and functional ZF arrays in milligram quantities.

The voltage-gated proton channel (H_v1) is a membrane protein that dissipates acute cell proton accumulations. To understand the molecular mechanisms explaining H_v1 function, methods for purifying the protein are needed. Previously, methods were developed for expressing and purifying human H_v1 (hH_v1) in yeast and later in bacteria. However, these methodologies produced low protein yields and had high production costs, considerably limiting their usefulness. The protocol described in this work was developed to overcome those limitations. hH_v1 is overexpressed in bacteria, solubilized with the detergent Anzergent 3–12, and purified by immobilized metal affinity chromatography (IMAC) and size-exclusion chromatography (SEC). Our protocol produced higher protein yields at lower costs than previously published methodologies.

Different research methods aim to clarify the intracellular trafficking of target proteins or unknown pathways. Currently, existing methods are mostly complex and expensive, requiring expert knowledge. Detailed microscopy for protein co-localization detection or omic technologies, which provide holistic network data, are elaborate, mostly complex, and expensive to apply. Our protocol illustrates a method to track a target protein by detecting expression changes of user-selected marker proteins that directly or indirectly interact with the target. Modulation of protein expression indicates interactions between the target and marker protein. Even without co-localization analysis, the results of the protein expression change are the first insights into the target's fate. Moreover, the use of the cell-sonar is straightforward and affordable, and the results are rapidly available. Furthermore, this method could also be used to determine if and how pathways are affected by compounds added to the cells. In conclusion, our method is adaptable to a wide range of proteins, easy to apply, inexpensive, and expandable with substances that affect proteins.