title: Extending enzyme molecular recognition with an expanded amino acid alphabet.
abstract: Natural enzymes are constructed from the 20 proteogenic amino acids, which may then require posttranslational modification or the recruitment of coenzymes or metal ions to achieve catalytic function. Here, we demonstrate that expansion of the alphabet of amino acids can also enable the properties of enzymes to be extended. A chemical mutagenesis strategy allowed a wide range of noncanonical amino acids to be systematically incorporated throughout an active site to alter enzymic substrate specificity. Specifically, 13 different noncanonical side chains were incorporated at 12 different positions within the active site ofN-acetylneuraminic acid lyase (NAL), and the resulting chemically modified enzymes were screened for activity with a range of aldehyde substrates. A modified enzyme containing a 2,3-dihydroxypropyl cysteine at position 190 was identified that had significantly increased activity for the aldol reaction of erythrose with pyruvate compared with the wild-type enzyme. Kinetic investigation of a saturation library of the canonical amino acids at the same position showed that this increased activity was not achievable with any of the 20 proteogenic amino acids. Structural and modeling studies revealed that the unique shape and functionality of the noncanonical side chain enabled the active site to be remodeled to enable more efficient stabilization of the transition state of the reaction. The ability to exploit an expanded amino acid alphabet can thus heighten the ambitions of protein engineers wishing to develop enzymes with new catalytic properties.
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.|School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Claire L
authors.initials: CL
authors.lastname: Windle
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.|School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Katie J
authors.initials: KJ
authors.lastname: Simmons
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.|School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: James R
authors.initials: JR
authors.lastname: Ault
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.|School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Chi H
authors.initials: CH
authors.lastname: Trinh
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; a.berry@leeds.ac.uk a.s.nelson@leeds.ac.uk.|School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Adam
authors.initials: A
authors.lastname: Nelson
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Arwen R
authors.identifier: 0000-0001-8499-7490
authors.initials: AR
authors.lastname: Pearson
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; a.berry@leeds.ac.uk a.s.nelson@leeds.ac.uk.|School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Alan
authors.identifier: 0000-0003-3502-0426
authors.initials: A
authors.lastname: Berry
mesh_terms: D002384:Catalysis; D020134:Catalytic Domain / Q000235:genetics*; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry / Q000235:genetics; D004795:Enzyme Stability / Q000235:genetics; D007700:Kinetics; D016297:Mutagenesis, Site-Directed; D007652:Oxo-Acid-Lyases / Q000737:chemistry / Q000235:genetics*; D013379:Substrate Specificity / Q000235:genetics*
chemical_list: D007652:Oxo-Acid-Lyases; C018728:N-acetylneuraminate lyase; D003545:Cysteine
keywords: aldolases; chemical modification; protein engineering