Multiple sequence alignment (MSA) is a fundamental way to gain information that cannot be obtained from the analysis of any individual sequence included in the alignment. It provides ways to investigate the relationship between sequence and function from a perspective of evolution. Thus, the MSA of proteins can be employed as a reference for protein engineering. In this paper, we reviewed the recent advances to highlight how protein engineering was benefited from the MSA of proteins. These methods include (1) engineering the thermostability or solubility of proteins by making it closer to the consensus sequence of the alignment through introducing site mutations; (2) structure-based engineering proteins with comparative modeling; (3) creating paleoenzymes featured with high thermostability and promiscuity by constructing the ancestral sequences derived from multiple sequence alignment; and (4) incorporating site-mutations targeting the evolutionarily coupled sites identified from multiple sequence alignment.

中文翻译：

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大比对的小设计：以多序列比对为起点的工程蛋白质

多序列比对 (MSA) 是一种获取信息的基本方法，这些信息无法从比对中包含的任何单个序列的分析中获得。它提供了从进化的角度研究序列和功能之间关系的方法。因此，蛋白质的 MSA 可以作为蛋白质工程的参考。在本文中，我们回顾了最近的进展，以强调蛋白质工程如何从蛋白质的 MSA 中受益。这些方法包括（1）通过引入位点突变使其更接近比对的共有序列，从而改造蛋白质的热稳定性或溶解性；(2) 具有比较建模的基于结构的工程蛋白；(3)通过构建多序列比对得到的祖先序列，创造出具有高热稳定性和混杂性的古酶；(4) 结合针对从多序列比对鉴定的进化耦合位点的位点突变。