Literature DB >> 34280872

Advances in optimizing enzyme electrostatic preorganization.

Matthew R Hennefarth1, Anastassia N Alexandrova2.   

Abstract

Utilizing electric fields to catalyze chemical reactions is not a new idea, but in enzymology it undergoes a renaissance, inspired by Warhsel's concept of electrostatic preorganization. According to this concept, the source of the immense catalytic efficiency of enzymes is the intramolecular electric field that permanently favors the reaction transition state over the reactants. Within enzyme design, computational efforts have fallen short in designing enzymes with natural-like efficacy. The outcome could improve if long-range electrostatics (often omitted in current protocols) would be optimized. Here, we highlight the major developments in methods for analyzing and designing electric fields generated by the protein scaffolds, in order to both better understand how natural enzymes function, and aid artificial enzyme design.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Electric fields; Electrostatic preorganization; Enzymatic catalysis; Enzyme design; Theory

Mesh:

Substances:

Year:  2021        PMID: 34280872      PMCID: PMC8761209          DOI: 10.1016/j.sbi.2021.06.006

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  47 in total

1.  How much do enzymes really gain by restraining their reacting fragments?

Authors:  A Shurki; M Strajbl; J Villà; A Warshel
Journal:  J Am Chem Soc       Date:  2002-04-17       Impact factor: 15.419

2.  From chemistry to biochemistry to catalysis to movement.

Authors:  W P Jencks
Journal:  Annu Rev Biochem       Date:  1997       Impact factor: 23.643

3.  Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid Isomerase.

Authors:  Valerie Vaissier Welborn; Teresa Head-Gordon
Journal:  J Am Chem Soc       Date:  2019-08-02       Impact factor: 15.419

4.  Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site.

Authors:  Lu Wang; Stephen D Fried; Thomas E Markland
Journal:  J Phys Chem B       Date:  2017-10-11       Impact factor: 2.991

5.  Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework.

Authors:  David J Reilley; Jian Wang; Nikolay V Dokholyan; Anastassia N Alexandrova
Journal:  J Chem Theory Comput       Date:  2021-06-24       Impact factor: 6.006

6.  Oriented electric fields accelerate Diels-Alder reactions and control the endo/exo selectivity.

Authors:  Rinat Meir; Hui Chen; Wenzhen Lai; Sason Shaik
Journal:  Chemphyschem       Date:  2010-01-18       Impact factor: 3.102

7.  Extreme electric fields power catalysis in the active site of ketosteroid isomerase.

Authors:  Stephen D Fried; Sayan Bagchi; Steven G Boxer
Journal:  Science       Date:  2014-12-19       Impact factor: 47.728

8.  Current status of the AMOEBA polarizable force field.

Authors:  Jay W Ponder; Chuanjie Wu; Pengyu Ren; Vijay S Pande; John D Chodera; Michael J Schnieders; Imran Haque; David L Mobley; Daniel S Lambrecht; Robert A DiStasio; Martin Head-Gordon; Gary N I Clark; Margaret E Johnson; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2010-03-04       Impact factor: 2.991

Review 9.  Selective CH bond functionalization with engineered heme proteins: new tools to generate complexity.

Authors:  Ruijie K Zhang; Xiongyi Huang; Frances H Arnold
Journal:  Curr Opin Chem Biol       Date:  2018-10-18       Impact factor: 8.822

10.  Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

Authors:  Garrett B Goh; Benjamin S Hulbert; Huiqing Zhou; Charles L Brooks
Journal:  Proteins       Date:  2014-01-15
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