Literature DB >> 16581913

Protein stability promotes evolvability.

Jesse D Bloom1, Sy T Labthavikul, Christopher R Otey, Frances H Arnold.   

Abstract

The biophysical properties that enable proteins to so readily evolve to perform diverse biochemical tasks are largely unknown. Here, we show that a protein's capacity to evolve is enhanced by the mutational robustness conferred by extra stability. We use simulations with model lattice proteins to demonstrate how extra stability increases evolvability by allowing a protein to accept a wider range of beneficial mutations while still folding to its native structure. We confirm this view experimentally by mutating marginally stable and thermostable variants of cytochrome P450 BM3. Mutants of the stabilized parent were more likely to exhibit new or improved functions. Only the stabilized P450 parent could tolerate the highly destabilizing mutations needed to confer novel activities such as hydroxylating the antiinflammatory drug naproxen. Our work establishes a crucial link between protein stability and evolution. We show that we can exploit this link to discover protein functions, and we suggest how natural evolution might do the same.

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Year:  2006        PMID: 16581913      PMCID: PMC1458665          DOI: 10.1073/pnas.0510098103

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  43 in total

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Journal:  J Mol Biol       Date:  1992-06-05       Impact factor: 5.469

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Authors:  B K Shoichet; W A Baase; R Kuroki; B W Matthews
Journal:  Proc Natl Acad Sci U S A       Date:  1995-01-17       Impact factor: 11.205

3.  Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability.

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Journal:  J Mol Biol       Date:  1993-09-20       Impact factor: 5.469

Review 4.  Structural and genetic analysis of protein stability.

Authors:  B W Matthews
Journal:  Annu Rev Biochem       Date:  1993       Impact factor: 23.643

5.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins.

Authors:  A M Lesk; C Chothia
Journal:  J Mol Biol       Date:  1980-01-25       Impact factor: 5.469

6.  Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence.

Authors:  P Markiewicz; L G Kleina; C Cruz; S Ehret; J H Miller
Journal:  J Mol Biol       Date:  1994-07-29       Impact factor: 5.469

7.  Systematic mutation of bacteriophage T4 lysozyme.

Authors:  D Rennell; S E Bouvier; L W Hardy; A R Poteete
Journal:  J Mol Biol       Date:  1991-11-05       Impact factor: 5.469

Review 8.  Genetic analysis of protein stability and function.

Authors:  A A Pakula; R T Sauer
Journal:  Annu Rev Genet       Date:  1989       Impact factor: 16.830

9.  Expression and enzymatic activity of recombinant cytochrome P450 17 alpha-hydroxylase in Escherichia coli.

Authors:  H J Barnes; M P Arlotto; M R Waterman
Journal:  Proc Natl Acad Sci U S A       Date:  1991-07-01       Impact factor: 11.205

10.  The relation between the divergence of sequence and structure in proteins.

Authors:  C Chothia; A M Lesk
Journal:  EMBO J       Date:  1986-04       Impact factor: 11.598

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  389 in total

1.  Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme.

Authors:  Eric J Hayden; Evandro Ferrada; Andreas Wagner
Journal:  Nature       Date:  2011-06-02       Impact factor: 49.962

Review 2.  The role of robustness in phenotypic adaptation and innovation.

Authors:  Andreas Wagner
Journal:  Proc Biol Sci       Date:  2012-01-04       Impact factor: 5.349

3.  A method for multi-codon scanning mutagenesis of proteins based on asymmetric transposons.

Authors:  Jia Liu; T Ashton Cropp
Journal:  Protein Eng Des Sel       Date:  2011-12-18       Impact factor: 1.650

4.  Thermodynamic stability explains the differential evolutionary dynamics of cytochrome b and COX I in mammals.

Authors:  Juan Carlos Aledo; Héctor Valverde; Manuel Ruíz-Camacho
Journal:  J Mol Evol       Date:  2012-02-24       Impact factor: 2.395

Review 5.  Toward a systems biology perspective on enzyme evolution.

Authors:  Shelley D Copley
Journal:  J Biol Chem       Date:  2011-11-08       Impact factor: 5.157

6.  Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis.

Authors:  Brandon W Heimer; Brooke E Tam; Hadley D Sikes
Journal:  Protein Eng Des Sel       Date:  2015-09-18       Impact factor: 1.650

Review 7.  Enzyme (re)design: lessons from natural evolution and computation.

Authors:  John A Gerlt; Patricia C Babbitt
Journal:  Curr Opin Chem Biol       Date:  2009-02-23       Impact factor: 8.822

8.  Reflections on the catalytic power of a TIM-barrel.

Authors:  John P Richard; Xiang Zhai; M Merced Malabanan
Journal:  Bioorg Chem       Date:  2014-07-11       Impact factor: 5.275

9.  Codon misreading tRNAs promote tumor growth in mice.

Authors:  Mafalda Santos; Patricia M Pereira; A Sofia Varanda; Joana Carvalho; Mafalda Azevedo; Denisa D Mateus; Nuno Mendes; Patricia Oliveira; Fábio Trindade; Marta Teixeira Pinto; Renata Bordeira-Carriço; Fátima Carneiro; Rui Vitorino; Carla Oliveira; Manuel A S Santos
Journal:  RNA Biol       Date:  2018-06-07       Impact factor: 4.652

Review 10.  Directed polymerase evolution.

Authors:  Tingjian Chen; Floyd E Romesberg
Journal:  FEBS Lett       Date:  2013-11-05       Impact factor: 4.124

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