Addressing epistasis in the design of protein function

• 成果类型: Article
• 署名作者: Lipsh-Sokolik, Rosalie; Fleishman, Sarel J.
• 署名单位: Weizmann Institute of Science
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8591
• DOI: 10.1073/pnas.2314999121
• 发表日期: 2024-08-20
• 关键词: empirical fitness landscapes; computational design; directed evolution; building-blocks; sequence space; web server; STABILITY; Robustness; prediction; mutations

摘要

Mutations in protein active sites can dramatically improve function. The active site, however, is densely packed and extremely sensitive to mutations. Therefore, some mutations may only be tolerated in combination with others in a phenomenon known as epistasis. Epistasis reduces the likelihood of obtaining improved functional variants and dramatically slows natural and lab evolutionary processes. Research has shed light on the molecular origins of epistasis and its role in shaping evolutionary trajectories and outcomes. In addition, sequence- and AI- based strategies that infer epistatic relationships from mutational patterns in natural or experimental evolution data have been used to design functional protein variants. In recent years, combinations of such approaches and atomistic design calculations have successfully predicted highly functional combinatorial mutations in active sites. These were used to design thousands of functional activesite variants, demonstrating that, while our understanding of epistasis remains incomplete, some of the determinants that are critical for accurate design are now sufficiently understood. We conclude that the space of active- site variants that has been explored by evolution may be expanded dramatically to enhance natural activities or discover new ones. Furthermore, design opens the way to systematically exploring sequence and structure space understanding and control over protein activity.