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理性与半理性蛋白质设计

Rational and Semirational Protein Design.

作者信息

Korendovych Ivan V

机构信息

Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.

出版信息

Methods Mol Biol. 2018;1685:15-23. doi: 10.1007/978-1-4939-7366-8_2.

Abstract

This mini review gives an overview over different design approaches and methodologies applied in rational and semirational enzyme engineering. The underlying principles for engineering novel activities, enantioselectivity, substrate specificity, stability, and pH optimum are summarized.

摘要

本综述概述了合理和半合理酶工程中应用的不同设计方法和策略。总结了工程化新活性、对映选择性、底物特异性、稳定性和最适pH值的基本原理。

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本文引用的文献

1
Insights from molecular dynamics simulations for computational protein design.
Mol Syst Des Eng. 2017 Feb 1;2(1):9-33. doi: 10.1039/C6ME00083E. Epub 2017 Jan 9.
2
Installing hydrolytic activity into a completely de novo protein framework.
Nat Chem. 2016 Sep;8(9):837-44. doi: 10.1038/nchem.2555. Epub 2016 Jul 4.
3
Abiological catalysis by artificial haem proteins containing noble metals in place of iron.
Nature. 2016 Jun 23;534(7608):534-7. doi: 10.1038/nature17968. Epub 2016 Jun 13.
4
Thermostability of Enzymes from Molecular Dynamics Simulations.
J Chem Theory Comput. 2016 Jun 14;12(6):2489-92. doi: 10.1021/acs.jctc.6b00120. Epub 2016 May 6.
5
New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities.
J Am Chem Soc. 2015 Dec 2;137(47):14905-11. doi: 10.1021/jacs.5b07812. Epub 2015 Nov 20.
6
Enantioselective enzymes by computational design and in silico screening.
Angew Chem Int Ed Engl. 2015 Mar 16;54(12):3726-30. doi: 10.1002/anie.201411415. Epub 2015 Feb 4.
7
Design of an allosterically regulated retroaldolase.
Protein Sci. 2015 Apr;24(4):561-70. doi: 10.1002/pro.2622. Epub 2015 Jan 13.
8
Catalytic efficiency of designed catalytic proteins.
Curr Opin Struct Biol. 2014 Aug;27:113-21. doi: 10.1016/j.sbi.2014.06.006. Epub 2014 Jul 19.
9
Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations.
J Chem Inf Model. 2014 Jul 28;54(7):2079-92. doi: 10.1021/ci500126x. Epub 2014 Jun 30.
10
Computationally designed libraries for rapid enzyme stabilization.
Protein Eng Des Sel. 2014 Feb;27(2):49-58. doi: 10.1093/protein/gzt061. Epub 2014 Jan 8.

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