Applications of cell free protein synthesis in protein design

• Published in: Protein science 2024-09, Vol.33 (9), p.e5148-n/a
• Main Authors: Thornton, Ella Lucille, Paterson, Sarah Maria, Stam, Michael J., Wood, Christopher W., Laohakunakorn, Nadanai, Regan, Lynne
• Format: Article
• Language: English
• Subjects: Cell-Free System - metabolism; cell‐free protein synthesis; Design; In vivo methods and tests; Machine learning; medium throughput; Protein Biosynthesis; protein design; Protein Engineering - methods; Protein synthesis; Proteins; Proteins - chemistry; Proteins - metabolism; Screening; Structure-function relationships; surface immobilization; Yeasts
• ISSN: 0961-8368; 1469-896X; 1469-896X
• DOI: 10.1002/pro.5148

In protein design, the ultimate test of success is that the designs function as desired. Here, we discuss the utility of cell free protein synthesis (CFPS) as a rapid, convenient and versatile method to screen for activity. We champion the use of CFPS in screening potential designs. Compared to in vivo protein screening, a wider range of different activities can be evaluated using CFPS, and the scale on which it can easily be used—screening tens to hundreds of designed proteins—is ideally suited to current needs. Protein design using physics‐based strategies tended to have a relatively low success rate, compared with current machine‐learning based methods. Screening steps (such as yeast display) were often used to identify proteins that displayed the desired activity from many designs that were highly ranked computationally. We also describe how CFPS is well‐suited to identify the reasons designs fail, which may include problems with transcription, translation, and solubility, in addition to not achieving the desired structure and function.