蛋白质稳定性计算设计与定向进化前沿工具

阮青云; 黄莘; 孟子钧; 全舒

doi:10.12211/2096-8280.2022-038

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蛋白质稳定性计算设计与定向进化前沿工具

特约评述 | 更新时间：2025-03-20

- 蛋白质稳定性计算设计与定向进化前沿工具
- Computational design and directed evolution strategies for optimizing protein stability
- 合成生物学 2023年4卷第1期页码：5-29
- 作者机构：
  
  1.华东理工大学生物工程学院，生物反应器工程国家重点实验室，上海生物制造技术协同创新中心，上海 200237
  2.上海市细胞代谢光遗传学技术前沿科学研究基地，上海 200237
- 作者简介：
  
  [ "阮青云（1996—），男，博士研究生。研究方向为蛋白质稳定性检测探针的开发与应用。 E-mail： alessandroruan@mail.ecust.edu.cn" ]
  [ " 全舒（1982—），女，教授，博士生导师。课题组聚焦于蛋白质折叠领域的工具开发与机制解析，发展了一系列蛋白质体内稳定性检测探针，建立了以分子伴侣活力改造为基础的蛋白质折叠调控策略，为基础研究及蛋白质在生物催化、生物医药等领域的应用提供了支撑 E-mail： shuquan@ecust.edu.cn" ]
- 基金信息：
  
  国家自然科学基金面上项目(31870054;32171269)
- DOI：10.12211/2096-8280.2022-038
  中图分类号： Q816
- 收稿：2022-07-02，
  
  修回：2022-07-30，
  
  纸质出版：2023-02-28
- 稿件说明：
移动端阅览
阮青云，黄莘，孟子钧，全舒. 蛋白质稳定性计算设计与定向进化前沿工具［J］. 合成生物学， 2023， 4（1）： 5-29

RUAN Qingyun， HUANG Xin， MENG Zijun， QUAN Shu. Computational design and directed evolution strategies for optimizing protein stability［J］. Synthetic Biology Journal， 2023， 4（1）： 5-29
阮青云，黄莘，孟子钧，全舒. 蛋白质稳定性计算设计与定向进化前沿工具［J］. 合成生物学， 2023， 4（1）： 5-29 DOI： 10.12211/2096-8280.2022-038.

RUAN Qingyun， HUANG Xin， MENG Zijun， QUAN Shu. Computational design and directed evolution strategies for optimizing protein stability［J］. Synthetic Biology Journal， 2023， 4（1）： 5-29 DOI： 10.12211/2096-8280.2022-038.

摘要

天然蛋白质具有临界稳定性的特征，这种较低的稳定性使蛋白质结构具有足够的灵活性，从而支持其发挥生物学功能。然而，临界稳定性使得蛋白质遭受胁迫压力后极易发生错误折叠并失去功能，导致天然蛋白质往往无法满足科学研究与工业应用的需求。此外，体内蛋白质在错误折叠后产生的聚集沉淀被认为是多种疾病发生发展的原因，包括阿尔兹海默病、帕金森综合征等。因此，优化蛋白质的稳定性是科学研究与工程应用领域亟待解决的关键问题。本文从蛋白质的折叠与稳定性机制出发，聚焦于序列优化与折叠环境优化两种改善蛋白质稳定性的手段，综述了基于理性设计、计算机辅助设计改善蛋白质稳定性的研究方法，介绍了用于高通量筛选蛋白质稳定化突变体或折叠相关因子的定向进化技术。通过多项蛋白质序列改良、折叠环境优化的案例介绍，展示了蛋白质稳定化技术在蛋白质工程与生物医药领域的广阔应用，包括酶的稳定化设计、疫苗蛋白质的构象控制、分子伴侣与蛋白质聚集抑制剂的筛选、蛋白质稳态药物的开发等。最后，展望了蛋白质稳定化技术未来的研究方向与前景，定制化的蛋白质稳定性检测技术将会迎来蓬勃发展。

Abstract

Most natural proteins tend to be marginally stable

which allows them to gain flexibility for biological functions. However

marginal stability is often associated with protein misfolding and aggregation under stress conditions

presenting a challenge for protein research and applications such as proteins as biocatalysts and therapeutic agents. In addition

protein instability has been increasingly recognized as one of the major factors causing human diseases. For example

the formation of toxic protein aggregates is the hallmark of many neurodegenerative diseases

including Alzheimer's and Parkinson's diseases. Therefore

optimizing protein folding and maintaining protein homeostasis in cells are long-standing goals for the scientific community. Confronting these challenges

various methods have been developed to stabilize proteins. In this review

we classify and summarize various techniques for engineering protein stability

with a focus on strategies for optimizing protein sequences or cellular folding environments. We first outline the principles of protein folding

and describe factors that affect protein stability. Then

we describe two main approaches for protein stability engineering

namely

computational design and directed evolution. Computational design can be further classified into structure-based

phylogeny-based

folding energy calculation-based and artificial intelligence-assisted methods. We present the principles of several methods under each category

and also introduce easily accessible web-based tools. For directed evolution approaches

we focus on library-based

high-throughput screening or selection techniques

including cellular or cell-free display and stability biosensors

which link protein stability to easily detectable phenotypes. We not only introduce the applications of these techniques in protein sequence optimization

but also highlight their roles in identifying novel folding factors

including molecular chaperones

chemical chaperones

and inhibitors of protein aggregation. Moreover

we demonstrate the applications of protein stability engineering in biomedicine and pharmacotherapeutics

including identifying small molecules to stabilize disease-related

aggregation-prone proteins

obtaining conformation-fixed and stable antigens for vaccine development

and targeting protein stability as a means to control protein homeostasis. Finally

we look forward to the trends and prospects of protein stabilization technologies

and believe that protein stability engineering will lead to a better understanding of protein folding processes to facilitate the development of precision medicine.

关键词

Keywords

references

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