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Semi-rational design mainly refers to the purposeful modification of proteins based on the three-dimensional structure of proteins, comparison of homologous protein sequences, or acquisition of existing knowledge through bioinformatics methods. The key is to obtain potential beneficial mutation sites through computer simulation and then use saturation mutation technology to construct a mutation library of appropriate size. Semi-rational design is a purposeful modification method based on a certain understanding of the sequence, structure, and catalytic mechanism of enzymes. This method is between irrational design and rational design. It uses known information and means to perform evolutionary modification on the specific functions of the target enzyme. The characteristic of semi-rational design is that it does not rely solely on random mutation and screening, but combines the concept of directed evolution. It creates a library of random mutants with diverse sequences through mutagenesis, error-prone RCR, DNA recombination, and site-saturation mutagenesis. At the same time, it uses the understanding of enzymes and design principles to purposefully screen out mutants with desired characteristics.

The methodology of semi-rational design emphasizes the in-depth understanding of enzymes and the control of the evolutionary process. It allows researchers to use known information to guide the evolutionary process, thereby improving efficiency and success rate. This method plays an important role in protein function modification because it can combine the advantages of irrational design and rational design, and can explore unknown space and use known knowledge for targeted modification.

Semi-rational design has a wide range of applications, including but not limited to enzyme optimization, modification of drug targets, evolution of biocatalysts, etc. Through this method, researchers can more effectively improve the functional properties of proteins to meet specific biotechnology or medical needs. Although this method has high requirements for information and technology and is relatively difficult to implement, with the development of computing technology and bioinformatics, the application prospects of semi-rational design in protein engineering are becoming more and more broad.