Research

Directed evolution

The evolution of enzymes with synthetically-useful activity

Nature has evolved spectacularly efficient catalysts - enzymes - which are tailored to specific biochemical reactions.  The synthetic chemist, however, requires catalysts which may be applied to a broad range of problems in synthetic chemistry, allowing complete control of stereochemistry.  In collaboration with Dr Alan Berry, we have used directed evolution to generate enzymes with synthetically useful activities.  For example, we have broadened the substrate specificity of sialic acid aldolase sufficiently that the variant enzyme may be applied in the synthesis of a wide range of sialic acid mimetics.

We have also used directed evolution to modify the stereochemical course of enzyme-catalysed carbon-carbon bond formation for the first time.  Critically, this approach allows diastereoisomeric products to be prepared enzymatically from the same starting materials. Tagatose 1,6-bisphosphate aldolase was engineered to attack the opposite diastereotopic face of its aldehyde substrate to yield the diastereomeric product, fructose 1,6-bisphosphate.  Similarly, from the relatively unslective sialic acid aldolase, a pair of complementary aldolases were created for the synthesis of 4R and 4S sialic acid mimetics.

Publications in this area:

143 Adam  Nelson , "Catalytic machinery of enzymes expanded", Nature 2019, 570, 172-173
Keywords: "Directed evolution"

127 James  Ault , Alan  Berry , Adam  Nelson , Arwen  Pearson , Katie  Simmons, Chi  Trinh and Claire  Windle , "Extending enzyme molecular recognition with an expanded amino acid alphabet", Proc. Natl. Acad. Sci. USA 2017, 114, 2610-1615
Keywords: "Directed evolution"

125 Alan  Berry , Adam  Nelson and Claire  Windle , "Aldolase-catalysed stereoselective synthesis of fluorinated small molecules", Curr. Opin. Chem. Biol. 2017, 37, 33-38
Keywords: "Directed evolution"

121 Alan  Berry , James  Howard , Marion  Muller and Adam  Nelson , "An enantio- and diastereoselective chemoenzymatic synthesis of alpha-fluoro beta-hydroxy carboxylic esters", Angew. Chem. Int. Ed. 2016, 55, 6767-6770
Keywords: "Directed evolution"

117 Alan  Berry , Adam  Daniels , Tom  Harman , Tomas  Lebl, Keith   Mullholland, Adam  Nelson , Arwen  Pearson, Jennifer  Stockwell , Chi  Trinh , Claire  Windle and Thomas  Woodhall , "Evaluation of fluoropyruvate as nucleophile in reactions catalysed by N-acetyl neuraminic acid lyase variants: scope, limitations and stereoselectivity", Org. Biomol. Chem. 2015, , in press
Keywords: "Directed evolution"

103 Alan  Berry , Marion  Muller , Adam  Nelson and Claire  Windle , "Engineering aldolases as biocatalysts", Curr. Opin. Chem. Biol. 2014, 19, 25-33
Keywords: "Directed evolution"

101 Alan  Berry , Amanda  Bolt , Ivan  Campeotto , Adam  Daniels , Adrian   Mulholland , Adam  Nelson , Arwen  Pearson , Simon  Phillips and Marc  van der Kamp , "The reaction mechanism of N-acetylneuraminic acid lyase revealed by a combination of crystallography, QM/MM simulation and mutagenesis", ACS Chem. Biol. 2014, 9, 1025-1032
Keywords: "Directed evolution"

97 James  Ault , Alan  Berry , Adam  Nelson , Arwen  Pearson, Anna  Polyakova , Nicole  Timms , Chi  Trinh and Claire  Windle , "Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with gamma-thialysine by using a chemical mutategenesis strategy", ChemBioChem 2013, 13, 474-481
Keywords: "Directed evolution"

93 Alan  Berry , Tilly  Bingham , Tom  Harman , Angela  Kinnell and Adam  Nelson , "Development of an organo- and enzyme-catalysed one-pot, sequential three-component reaction", Tetrahedron 2012, 68, 7719-7722
Keywords: "Directed evolution"

92 Alan  Berry , Adam  Daniels , Adam  Nelson and Nicole  Timms , "Directed Evolution and (Semi-) Rational Design Strategies for the Creation of Synthetically Useful, Stereoselective Biocatalysts", Comprehensive Chirality 2012, , in press
Keywords: "Directed evolution"

83 Alan  Berry , Amanda  Bolt , Ivan  Campeotto , Catriona  Dennis, Tom  Harman , Adam  Nelson , Arwen  Pearson and Simon  Phillips, "Structural Insights into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution", J. Mol. Biol. 2010, 404, 56-69
Keywords: "Directed evolution"

80 Alan  Berry , Louise  Horsfall and Adam  Nelson , "Identification and characterization of important residues in the catalytic mechanism of CMP-Neu5Ac synthetase from Neisseria meningitides", FEBS J. 2010, 277, 2779-2790
Keywords: "Directed evolution"

78 Alan  Berry , Ivan  Campeotto , Stephen  Carr , Adam  Nelson , Arwen  Pearson , Simon  Phillips and Chi  Trinh , "Structure of an Escherichia coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 A resolution", Acta Cryst. F 2009, F65, 1088-1090
Keywords: "Directed evolution"

68 Alan  Berry , Amanda  Bolt and Adam  Nelson , "Directed evolution of aldolases for exploitation in synthetic organic chemistry", Arch. Biochem. Biophys. 2008, 474, 318-330
Keywords: "Directed evolution"

61 Alan  Berry , Lorna  Farnsworth , Adam  Nelson , Gavin  Williams and Thomas  Woodhall , "Creation of a Pair of Stereochemically Complementary Biocatalysts", J. Am. Chem. Soc. 2006, 128, 16238-16247
Keywords: "Stereochemically diverse libraries" "Directed evolution"

51 Alan  Berry , Adam  Nelson , Gavin  Williams and Thomas  Woodhall , "Structure-guided saturation mutagenesis of N-acetylneuraminic acid lyase for the synthesis sialic acid mimetics", Prot. Eng. Des. Sel. 2005, 18, 239-246
Keywords: "Stereochemically diverse libraries" "Directed evolution"

49 Alan  Berry , Adam  Nelson , Gavin  Williams and Thomas  Woodhall , "Creation of an aldolase for the parallel synthesis of sialic acid mimetics", Angew. Chem., Int. Ed. 2005, 44, 2109-2112
Open Access Version
Keywords: "Stereochemically diverse libraries" "Directed evolution"

46 Alan  Berry , Adam  Nelson , Gavin  Williams and Thomas  Woodhall , "Synthesis of screening substrates for the directed evolution of sialic acid aldolase: Towards tailored enzymes for the preparation of influenza A sialidase inhibitor analogues", Org. Biomol. Chem. 2005, 3, 1795-1800
Open Access Version - provided courtesy of the RSC
Keywords: "Stereochemically diverse libraries" "Directed evolution"

43 Alan  Berry , Adam  Nelson and Gavin  Williams , "Directed Evolution of Enzymes for Biocatalysis and the Life Sciences", Cell. Mol. Life Sci. 2004, 61, 3034-3046
Keywords: "Directed evolution"

33 Alan  Berry , Silvie  Domann , Adam  Nelson and Gavin  Williams , "Modifying the stereochemistry of an enzyme-catalysed reaction by directed evolution", Proc. Natl. Acad. Sci. USA 2003, 100, 3143-3148
Keywords: "Directed evolution"

30 Alan  Berry , Adam  Nelson and Venti  Suryanti, "Cloning, over-expression, purification and chacterisation of N-acetylneuraminate synthase from Streptococcus agalactiae", Prot. Express. Purif. 2003, 27, 346-356
Keywords: "Directed evolution"

People currently working in this research area:

Alan Berry

Adam Nelson

Katie Simmons

Emily Turri