As we traverse the landscape of the "post-genomic" era, a monumental challenge lies before us: deciphering the multifaceted functions, structures, and interaction networks of the proteome. This endeavor undeniably demands high-throughput methodologies to generate a myriad of proteins on a grand scale. However, traditional in vivo expression systems, like Escherichia coli, pose not only time constraints but also financial burdens. Despite some strides made through engineered strains and protein fusion tactics to enhance soluble protein yields, these methods are not universally applicable and often necessitate case-by-case optimization.
Liberalizing High-Throughput Protein Expression and Screening
Cell-free protein expression systems lay the groundwork for high-throughput (HT) and automated platforms for protein production. For instance, DNA molecules can be amplified, transcribed, and translated within microwell plate pores, facilitating immediate protein determination for swift screening and functional analysis. Large-scale expression and screening hold particular promise in proteomics and protein engineering, enabling the identification of desired proteins from libraries boasting high sequence diversity. Since cell-free systems can express a population of proteins in a single reaction, they serve as ideal deconvolution systems for comprehensive screening and isolation of cloned proteins from libraries.
Additionally, the fusion of deep learning and CFPS, demonstrated by Amir Pandi et al., has birthed a cell-free protein synthesis (CFPS) pipeline for the rapid and cost-effective production of antimicrobial peptides (AMPs) directly from DNA templates. This provides a high-throughput and time-saving method for peptide production and screening.
Overcoming the Challenges of Hard-to-Express Proteins
Cell-free protein expression systems hold significant promise in synthesizing hard-to-express proteins, evident in several realms:
- Synthesis of Structurally Complex Proteins: For proteins boasting unique or intricate structures, such as membrane proteins, cell-free systems provide a comparatively simplistic environment, minimizing the influence of intricate intracellular factors and thereby enhancing the efficiency of synthesizing these proteins.
- Post-Translational Modification of Proteins: Many proteins necessitate a series of post-translational modifications post-synthesis, such as glycosylation and phosphorylation. Cell-free systems can simulate these modification processes in vitro by incorporating the corresponding modifying enzymes and substrates, thereby synthesizing fully functional modified proteins.
- Synthesis of Toxic Proteins: Certain proteins may exert toxic effects on cells, rendering stable expression within cells challenging. Cell-free systems circumvent this limitation, allowing for the in vitro synthesis of these toxic proteins, facilitating pertinent research.
Pioneering Cell-Free Display Technologies
Display technologies intertwine genetic information (genotype) with the proteins they encode (phenotype), selecting proteins from libraries. Cell-free methods bypass cell transformation, making it feasible to construct larger libraries and select new molecules. Furthermore, the direct utilization of DNA templates enables continuous expansion of genetic diversity during selection, providing an effective tool for in vitro molecular evolution, wherein protein variants are continuously generated and enriched based on their activities. Cell-free display methods find widespread utility in the in vitro screening and evolution of proteins, encompassing antibodies, peptides, receptors, and enzymes. Recent advancements have leveraged the unique advantages of cell-free protein expression technology to develop novel protein technologies such as ribosome display and cell-free protein arrays, for the selection, evolution, and functional screening of proteins in vitro.
Deciphering Molecular Interactions
Cell-free protein expression furnishes a straightforward tool for investigating molecular interactions such as protein-protein, protein-DNA, protein-RNA, protein-ligand, DNA-RNA, and even RNA-RNA interactions. To ascertain protein interactions, an entity (protein, nucleic acid, or ligand) is labeled and then co-incubated with proteins synthesized in a cell-free system. The resultant complexes are subsequently separated, for instance, through immunoprecipitation or by directly detecting changes in electrophoretic mobility.
Harnessing Cell-Free Protein Array Technology
Protein arrays serve as a proteomic tool for miniaturized, highly parallel detection and analysis of proteins and antibodies. Traditional cell-based protein array generation methods are often time-consuming, requiring the expression and purification of individual proteins for arraying, and have limitations in maintaining protein affinity. Cell-free protein array technologies, such as protein in situ array (PISA) and nucleic acid programmable protein array (NAPPA), utilize the principles of cell-free protein synthesis, enabling the direct in situ synthesis of proteins on specific carriers. This approach not only facilitates the rapid creation of protein microarrays but also simultaneously maintains the spatial correspondence between DNA and the corresponding protein, proving valuable for applications such as immune response marker identification, cancer autoantibody analysis, and isolation of target proteins from cDNA libraries.
In Conclusion
In summation, cell-free protein expression technology, with its simplicity, efficiency, and flexibility, has significantly propelled large-scale protein analysis and functional screening in biotechnology and proteomics. With ongoing technological innovation and application expansion, cell-free protein synthesis systems will play an increasingly pivotal role in future research. It is foreseeable that cell-free protein synthesis will emerge as a major focal point in the field of biotechnology, contributing more robustly to the health and advancement of human society.
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