分子伴侣作用下的蛋白质稳定与进化

doi:10.12211/2096-8280.2022-013

摘要/Abstract

摘要：

新生多肽链通常需要折叠成独特的三维结构来发挥其生物学功能。天然存在的蛋白质仅具有边缘稳定性，少量突变或轻微环境扰动就可能影响蛋白质的正确折叠。蛋白质组的稳定性，即蛋白质稳态，由蛋白质组中较不稳定的蛋白质决定，因而也具有边缘稳定性。蛋白质以及蛋白质组的边缘稳定性决定了细胞内存在着复杂的质量控制机制，用来帮助蛋白质正确折叠、修复或降解错误折叠的蛋白质。本文详细介绍了以热休克蛋白家族为代表的分子伴侣协助蛋白质折叠的内部机制，并回顾了通过过量表达分子伴侣、转录因子等手段提高蛋白质稳态的研究。蛋白质在保持稳定性的同时也在不断进化，本文介绍了蛋白质稳定性与可进化性关系的研究。实验证明，稳定性增强的蛋白质提高了对随机突变的包容度，有助于积累更多突变。相较于野生型蛋白质，这些蛋白质突变体在不同环境的选择下，会产生更多功能适应性突变体，即发生进化。因而蛋白质的稳定性是影响其进化的重要因素。分子伴侣作为蛋白质折叠的参与者，直接协助了蛋白质的定向进化。本文围绕蛋白质折叠的稳定性、蛋白质稳态和蛋白质进化的问题，讨论了以分子伴侣为主的分子机器帮助维持蛋白质稳定、促进蛋白质进化的相关研究。鉴于生物系统的复杂程度，我们对生物进化的理解仍然有限。希望关于影响蛋白质稳定性和可进化性的研究能够为理解蛋白质结构功能的构效关系提供独特见解，同时也为探究蛋白质相关疾病致病机理提供理论基础。

关键词: 蛋白质折叠, 边缘稳定性, 定向进化, 分子伴侣

Abstract:

Native proteins are only marginally stable. Therefore, a few mutations or slight perturbation in the environment could easily destroy their functional structures, causing them to misfold or even aggregate. The proteome is also believed to be marginally stable as the malfunction of a handful of proteins could rapidly overload the ubiquitin-protease network, threatening the integrity of the entire proteome. The disruption of proteostasis would render tremendous side effects including tumors and diseases. Extensive molecular machineries, such as heat shock proteins, are employed by cells to assist certain protein folding, salvage misfolded proteins, and break down protein aggregates. Owing to this fact, many natively occurred molecular chaperones have the potency to be engineered as stabilizers for the expression of aggregation-prone proteins both in vitro and in vivo, or into specialized disaggregates towards disease-related proteins. Remarkably, these modifications could be achieved with minor changes in the primary sequence of typical molecular chaperones, which are often proved to be single-site mutations. Instead of focusing on particular molecular chaperones, an up-regulation of the entire proteostasis network components is proved to be a viable strategy in maintaining protein homeostasis. Mutations could also render proteins to evolve new or improved functions in given environments, even though most mutations are detrimental. Both theoretical and experimental studies have found that extra thermodynamic stability could promote evolvability by allowing a protein's native structure and function to tolerate random mutations more robustly. Increased mutational tolerance allows proteins to evolve faster to adapt to new environments. Molecular chaperones are also found to serve as a buffering system, alleviating stability constraints, and rescuing deleterious mutations that could mediate new or improved functions. Hopefully, with the advancement in biotechnology and computational analysis, more studies that reveal influences of molecular chaperones on protein stability and evolvability can provide better insights into deciphering the relationship between protein structures and functions, as well as fundamental theories exploring the pathogenesis of protein-related diseases.

Key words: protein folding, marginal stability, directed evolution, molecular chaperones

唐宇琦, 叶松涛, 刘嘉, 张鑫. 分子伴侣作用下的蛋白质稳定与进化[J]. 合成生物学, 2022, 3(3): 445-464.

Yuqi TANG, Songtao YE, Jia LIU, Xin ZHANG. Molecular chaperones promote protein stability and evolution[J]. Synthetic Biology Journal, 2022, 3(3): 445-464.

图/表 5

图1 大肠杆菌中由分子伴侣和蛋白酶调节的蛋白质稳态网络

Fig. 1 Proteostasis network modulated by molecular chaperones and proteases in E. coli

图2 ADP结合（左）和ATP结合（右，PDB代码：4B9Q）［55］的Hsp70构象［在ADP结合状态下，肽链结合结构域（PDB代码：1DKZ）［50］和 ATP酶结构域（PDB代码：3HSC）［51］通过灵活的氨基酸链连接］

Fig. 2 ADP-bound (left) and ATP-bound (right, PDB code: 4B9Q)[55] conformations of Hsp70[In the ADP-bound state, the peptide-binding domain (PDB code: 1DKZ)[50] and ATPase domain (PDB code: 3HSC)[51] are connected by a flexible linker]

图3 Hsp60七元环（左，PDB代码：1IOK）［65］和Hsp60/Hsp10复合物（中，PDB代码：1AON）［67］的结构，以及Hsp60/Hsp10作用机理（右）

Fig. 3 Structures of the 7-membered ring in GroEL (left, PDB code: 1IOK)[65] and the Hsp60/Hsp10(middle, PDB code: 1AON)[67], as well as the working mechanism of Hsp60/Hsp10 (right)

图4 ADP结合（左，PDB代码：2O1V）［79］和ATP结合（右，PDB代码：2CG9）［76］的Hsp90构象

Fig. 4 ADP-bound (left, PDB code: 2O1V)[79] and ATP-bound (right, PDB code: 2CG9)[76] conformations of Hsp90

图5 稳定性的增加增强了模型晶格蛋白和P450 BM3血红素结构域的可进化性［111］

Fig. 5 Increased stability enhances evolvability of model lattice protein and P450 BM3 heme domain[111]

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