Synthetic Biology Journal ›› 2023, Vol. 4 ›› Issue (1): 5-29.DOI: 10.12211/2096-8280.2022-038
• Invited Review • Previous Articles Next Articles
Qingyun RUAN1, Xin HUANG1, Zijun MENG1, Shu QUAN1,2
Received:
2022-07-02
Revised:
2022-07-30
Online:
2023-03-07
Published:
2023-02-28
Contact:
Shu QUAN
阮青云1, 黄莘1, 孟子钧1, 全舒1,2
通讯作者:
全舒
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。基金资助:
CLC Number:
Qingyun RUAN, Xin HUANG, Zijun MENG, Shu QUAN. 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.
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URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2022-038
符号 | 稳定性类型 | 度量 | 定义 |
---|---|---|---|
ΔGUN | 热力学 | 折叠自由能 | 蛋白质未折叠状态到天然构象的吉布斯自由能变化 |
ΔGNU | 热力学 | 去折叠自由能 | 蛋白质天然构象到未折叠状态的吉布斯自由能变化 |
ΔΔG | 热力学 | 折叠自由能变化 | 蛋白质突变前后折叠自由能的变化 |
Tm | 热力学 | 熔解温度 | 使一半的蛋白质解折叠时的温度 |
C1/2 | 热力学 | 半变性浓度 | 使一半的蛋白质解折叠时的变性剂浓度 |
KU | 热力学 | 解折叠平衡常数 | 未折叠状态与天然状态的浓度比值 |
kf | 动力学 | 折叠速率常数 | 蛋白质折叠过程的速率常数 |
ku | 动力学 | 去折叠速率常数 | 蛋白质去折叠过程的速率常数 |
kd, obs | 动力学 | 表观失活速率常数 | 从天然状态到完全失活(deactivation)的表观速率常数 |
T50 | ― | 半数失活温度 | 在一定时间内酶活降至一半时的温度 |
t1/2 | 动力学 | 半衰期 | 酶活降至初始的一半时所需的时间 |
Table 1 Definitions of stability parameters
符号 | 稳定性类型 | 度量 | 定义 |
---|---|---|---|
ΔGUN | 热力学 | 折叠自由能 | 蛋白质未折叠状态到天然构象的吉布斯自由能变化 |
ΔGNU | 热力学 | 去折叠自由能 | 蛋白质天然构象到未折叠状态的吉布斯自由能变化 |
ΔΔG | 热力学 | 折叠自由能变化 | 蛋白质突变前后折叠自由能的变化 |
Tm | 热力学 | 熔解温度 | 使一半的蛋白质解折叠时的温度 |
C1/2 | 热力学 | 半变性浓度 | 使一半的蛋白质解折叠时的变性剂浓度 |
KU | 热力学 | 解折叠平衡常数 | 未折叠状态与天然状态的浓度比值 |
kf | 动力学 | 折叠速率常数 | 蛋白质折叠过程的速率常数 |
ku | 动力学 | 去折叠速率常数 | 蛋白质去折叠过程的速率常数 |
kd, obs | 动力学 | 表观失活速率常数 | 从天然状态到完全失活(deactivation)的表观速率常数 |
T50 | ― | 半数失活温度 | 在一定时间内酶活降至一半时的温度 |
t1/2 | 动力学 | 半衰期 | 酶活降至初始的一半时所需的时间 |
类别 | 软件名称 | 输入 | 网站/本地安装 | 参考文献 |
---|---|---|---|---|
基于结构分析 | ||||
优化蛋白质表面电荷 | TKSA-MC | 结构 | http://tksamc.df.ibilce.unesp.br | [ |
PHEPS | 结构 | http://pheps.orgchm.bas.bg/home.html | [ | |
基于温度因子 | B-FITTER | 结构 | Windows系统本地安装 | [ |
设计二硫键 | Disulfide By Design | 结构 | http://cptweb.cpt.wayne.edu/DbD2 | [ |
DISULFIDE | 结构 | http://disulfind.disi.unitn.it | [ | |
破坏表面大面积疏水区域 | AGGRESCAN3D | 结构/序列 | http://biocomp.chem.uw.edu.pl/A3D2 | [ |
基于进化分析 | ||||
同源序列比对 | 3DM | 序列 | https://3dm.bio-prodict.com | [ |
Consensus Finder | 序列 | http://kazlab.umn.edu | [ | |
祖先酶重构 | Ancestors 1.0 | 序列 | http://ancestors.bioinfo.uqam.ca/ancestorWeb | [ |
FireProt ASR | 序列 | https://loschmidt.chemi.muni.cz/fireprotasr | [ | |
基于折叠自由能计算 | ||||
单纯ΔΔG计算 | FoldX | 结构 | 全平台本地安装 | [ |
Rosetta | 结构 | Linux系统本地安装 | [ | |
PoPMuSiC | 结构 | http://babylone.ulb.ac.be/popmusic | [ | |
组合其他策略的ΔΔG计算 | PROSS | 结构 | http://pross.weizmann.ac.il/step/pross-terms | [ |
FireProt | 结构/序列 | https://loschmidt.chemi.muni.cz/fireprot | [ | |
基于机器学习 | ||||
支持向量机 | I-mutant | 结构/序列 | http://gpcr.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi | [ |
SRP神经网络 | DeepDDG | 结构 | http://protein.org.cn/ddg.html | [ |
卷积神经网络 | MutCompute | 结构 | https://mutcompute.com | [ |
Table 2 Summary of software for protein stability rational design
类别 | 软件名称 | 输入 | 网站/本地安装 | 参考文献 |
---|---|---|---|---|
基于结构分析 | ||||
优化蛋白质表面电荷 | TKSA-MC | 结构 | http://tksamc.df.ibilce.unesp.br | [ |
PHEPS | 结构 | http://pheps.orgchm.bas.bg/home.html | [ | |
基于温度因子 | B-FITTER | 结构 | Windows系统本地安装 | [ |
设计二硫键 | Disulfide By Design | 结构 | http://cptweb.cpt.wayne.edu/DbD2 | [ |
DISULFIDE | 结构 | http://disulfind.disi.unitn.it | [ | |
破坏表面大面积疏水区域 | AGGRESCAN3D | 结构/序列 | http://biocomp.chem.uw.edu.pl/A3D2 | [ |
基于进化分析 | ||||
同源序列比对 | 3DM | 序列 | https://3dm.bio-prodict.com | [ |
Consensus Finder | 序列 | http://kazlab.umn.edu | [ | |
祖先酶重构 | Ancestors 1.0 | 序列 | http://ancestors.bioinfo.uqam.ca/ancestorWeb | [ |
FireProt ASR | 序列 | https://loschmidt.chemi.muni.cz/fireprotasr | [ | |
基于折叠自由能计算 | ||||
单纯ΔΔG计算 | FoldX | 结构 | 全平台本地安装 | [ |
Rosetta | 结构 | Linux系统本地安装 | [ | |
PoPMuSiC | 结构 | http://babylone.ulb.ac.be/popmusic | [ | |
组合其他策略的ΔΔG计算 | PROSS | 结构 | http://pross.weizmann.ac.il/step/pross-terms | [ |
FireProt | 结构/序列 | https://loschmidt.chemi.muni.cz/fireprot | [ | |
基于机器学习 | ||||
支持向量机 | I-mutant | 结构/序列 | http://gpcr.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi | [ |
SRP神经网络 | DeepDDG | 结构 | http://protein.org.cn/ddg.html | [ |
卷积神经网络 | MutCompute | 结构 | https://mutcompute.com | [ |
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