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Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid.

ABSTRACT: The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the in vivo incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-defined metal-binding site. Here, we report a designed artificial metallohydratase, based on the transcriptional repressor lactococcal multidrug resistance regulator (LmrR), in which the non-canonical amino acid (2,2'-bipyridin-5yl)alanine is used to bind the catalytic Cu(ii) ion. Starting from a set of empirical pre-conditions, a combination of cluster model calculations (QM), protein-ligand docking and molecular dynamics simulations was used to propose metallohydratase variants, that were experimentally verified. The agreement observed between the computationally predicted and experimentally observed catalysis results demonstrates the power of the artificial metalloenzyme design approach presented here.

SUBMITTER: Drienovska I

PROVIDER: S-EPMC5633786 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid.

Drienovská Ivana I Alonso-Cotchico Lur L Vidossich Pietro P Lledós Agustí A Maréchal Jean-Didier JD Roelfes Gerard G

Chemical science 20170904 10

The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the <i>in vivo</i> incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-define ...[more]

PMID: 29081955

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Project description:Artificial metalloenzymes are unique as they combine the good features of homogeneous and enzymatic catalysts, and they can potentially improve some difficult catalytic assays. This study reports a method that can be used to create an artificial metal-binding site prior to proving it to be functional in a wet lab. Haloalkane dehalogenase was grafted into a metal-binding site to form an artificial metallo-haloalkane dehalogenase and was studied for its potential functionalities in silico. Computational protocols regarding dynamic metal docking were studied using native metalloenzymes and functional artificial metalloenzymes. Using YASARA Structure, a simulation box covering template structure was created to be filled with water molecules followed by one mutated water molecule closest to the metal-binding site to metal ion. A simple energy minimization step was subsequently run using an AMBER force field to allow the metal ion to interact with the metal-binding residues. Long molecular dynamic simulation using YASARA Structure was performed to analyze the stability of the metal-binding site and the distance between metal-binding residues. Metal ions fluctuating around 2.0 Å across a 20 ns simulation indicated a stable metal-binding site. Metal-binding energies were predicted using FoldX, with a native metalloenzyme (carbonic anhydrase) scoring 18.0 kcal/mol and the best mutant model (C1a) scoring 16.4 kcal/mol. Analysis of the metal-binding site geometry was performed using CheckMyMetal, and all scores for the metalloenzymes and mutant models were in an acceptable range. Like native metalloenzymes, the metal-binding site of C1a was supported by residues in the second coordination shell to maintain a more coordinated metal-binding site. Short-chain multihalogenated alkanes (1,2-dibromoethane and 1,2,3-trichloropropane) were able to dock in the active site of C1a. The halides of the substrate were in contact with both the metal and halide-stabilizing residues, thus indicating a better stabilization of the substrate. The simple catalytic mechanism proposed is that the metal ion interacted with halogen and polarized the carbon-halogen bond, thus making the alpha carbon susceptible to attack by nucleophilic hydroxide. The interaction between halogen in the metal ion and halide-stabilizing residues may help to improve the stabilization of the substrate-enzyme complex and reduce the activation energy. This study reports a modified dynamic metal-docking protocol and validation tests to verify the metal-binding site. These approaches can be applied to design different kinds of artificial metalloenzymes or metal-binding sites.

Project description:ObjectivesThis work aimed to design, synthesize and characterize replacement natural moisturizing factor (NMF) composed of modified hygroscopic linear amino acids to pre-empt or repair skin barrier dysfunction.MethodsFollowing synthesis and characterization, thermo-gravimetric analysis and quantum mechanics molecular modelling quantified and depicted water binding to the new compounds. Deliquescence relative humidity demonstrated the water-scavenging ability of the compounds, whereas snake skin moisturizing studies showed they increased water uptake into snake skin.ResultsFrom thermal analysis, N-hydroxyglycine showed greatest water-holding capacity followed by N-hydroxyserine, l-homoserine and ?-hydroxyglycine; coupled with quantum mechanics molecular modelling, between 8 and 12 molecules of water could associate with each molecule of either N-hydroxyglycine, N-hydroxyserine or l-homoserine. All of our modified amino acids were efficacious and induced similar or greater water uptake compared with the established moisturizing compounds hyaluronic acid, glycerine and urea in snake skin. Incorporated at 10% in Oilatum, N-hydroxyserine induced >200% greater moisture uptake into dry snake skin compared to treatment with water alone, with efficacy related to the molecule structure and ability to bind to 12 water molecules. Oilatum cream spiked with all our unnatural amino acid hydrotropes increased water uptake into snake skin compared with Oilatum alone. The compound series was designed to elucidate some structure - efficacy relationships. Amino acid chirality did not affect the water-holding capacity but did affect uptake into skin. Compounds with high melting points and bond energies tended to decrease water-holding capacity. With isosteric replacement, the more electronegative atoms gave greater water-holding capacities.ConclusionsThis work demonstrates the potential of unnatural amino acid hydrotropes as skin moisturizers and has developed some predictive 'rules' for further design and refinement of chemical structures.

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Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid.

Publications

Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid.

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