Literature DB >> 15879217

Computational thermostabilization of an enzyme.

Aaron Korkegian1, Margaret E Black, David Baker, Barry L Stoddard.   

Abstract

Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.

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Year:  2005        PMID: 15879217      PMCID: PMC3412875          DOI: 10.1126/science.1107387

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  31 in total

Review 1.  Challenges in enzyme mechanism and energetics.

Authors:  Daniel A Kraut; Kate S Carroll; Daniel Herschlag
Journal:  Annu Rev Biochem       Date:  2003-04-10       Impact factor: 23.643

Review 2.  The role of dynamics in enzyme activity.

Authors:  R M Daniel; R V Dunn; J L Finney; J C Smith
Journal:  Annu Rev Biophys Biomol Struct       Date:  2002-12-02

3.  Assessment of progress over the CASP experiments.

Authors:  Ceslovas Venclovas; Adam Zemla; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2003

Review 4.  Energy estimation in protein design.

Authors:  Joaquim Mendes; Raphael Guerois; Luis Serrano
Journal:  Curr Opin Struct Biol       Date:  2002-08       Impact factor: 6.809

5.  Computer-aided design of a PDZ domain to recognize new target sequences.

Authors:  Jose Reina; Emmanuel Lacroix; Scott D Hobson; Gregorio Fernandez-Ballester; Vladimir Rybin; Markus S Schwab; Luis Serrano; Cayetano Gonzalez
Journal:  Nat Struct Biol       Date:  2002-08

6.  Computational design of receptor and sensor proteins with novel functions.

Authors:  Loren L Looger; Mary A Dwyer; James J Smith; Homme W Hellinga
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

7.  Design of a novel globular protein fold with atomic-level accuracy.

Authors:  Brian Kuhlman; Gautam Dantas; Gregory C Ireton; Gabriele Varani; Barry L Stoddard; David Baker
Journal:  Science       Date:  2003-11-21       Impact factor: 47.728

8.  A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.

Authors:  Gautam Dantas; Brian Kuhlman; David Callender; Michelle Wong; David Baker
Journal:  J Mol Biol       Date:  2003-09-12       Impact factor: 5.469

9.  Engineering the proteolytic specificity of activated protein C improves its pharmacological properties.

Authors:  David T Berg; Bruce Gerlitz; Jing Shang; Tommy Smith; Paula Santa; Mark A Richardson; Ken D Kurz; Brian W Grinnell; Ken Mace; Bryan E Jones
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-01       Impact factor: 11.205

10.  The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.

Authors:  Gregory C Ireton; Margaret E Black; Barry L Stoddard
Journal:  Structure       Date:  2003-08       Impact factor: 5.006

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  128 in total

1.  Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins.

Authors:  Yunqi Li; Jianwen Fang
Journal:  Biochem Biophys Res Commun       Date:  2010-05-06       Impact factor: 3.575

2.  Automated selection of stabilizing mutations in designed and natural proteins.

Authors:  Benjamin Borgo; James J Havranek
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-17       Impact factor: 11.205

3.  A collaborative environment for developing and validating predictive tools for protein biophysical characteristics.

Authors:  Michael A Johnston; Damien Farrell; Jens Erik Nielsen
Journal:  J Comput Aided Mol Des       Date:  2012-04-04       Impact factor: 3.686

4.  Effect of codon message on xylanase thermal activity.

Authors:  Liangwei Liu; Linmin Wang; Zhang Zhang; Suya Wang; Hongge Chen
Journal:  J Biol Chem       Date:  2012-06-15       Impact factor: 5.157

Review 5.  Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.

Authors:  Bram Stynen; Hélène Tournu; Jan Tavernier; Patrick Van Dijck
Journal:  Microbiol Mol Biol Rev       Date:  2012-06       Impact factor: 11.056

6.  Protein thermostability calculations using alchemical free energy simulations.

Authors:  Daniel Seeliger; Bert L de Groot
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

7.  Increasing protein stability: importance of DeltaC(p) and the denatured state.

Authors:  Hailong Fu; Gerald Grimsley; J Martin Scholtz; C Nick Pace
Journal:  Protein Sci       Date:  2010-05       Impact factor: 6.725

Review 8.  Bacterial cocaine esterase: a protein-based therapy for cocaine overdose and addiction.

Authors:  Diwahar Narasimhan; James H Woods; Roger K Sunahara
Journal:  Future Med Chem       Date:  2012-02       Impact factor: 3.808

9.  Rapid Bioinformatic Identification of Thermostabilizing Mutations.

Authors:  David B Sauer; Nathan K Karpowich; Jin Mei Song; Da-Neng Wang
Journal:  Biophys J       Date:  2015-10-06       Impact factor: 4.033

10.  Amino-acid mutations to extend the biological half-life of a therapeutically valuable mutant of human butyrylcholinesterase.

Authors:  Lei Fang; Shurong Hou; Liu Xue; Fang Zheng; Chang-Guo Zhan
Journal:  Chem Biol Interact       Date:  2014-02-25       Impact factor: 5.192

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