We use interdisciplinary methods to evaluate enzyme catalysts from various sources,
such as bacteria, plants, and yeast, with non-natural substrates. Our vision is to
transform natural compounds or synthetically-derived chemicals into novel products.
Transfer of the genes encoding native or bioengineered enzymes into a chassis organism
can potentially make various bioactive or commodity molecules in vivo or in vitro.
Semibiocatalysis of Ethyl Dimethylpyrazines from Hydroxyketones made via Carboligation
Chemistry Catalyzed by a Pyruvate Decarboxylase
A yeast pyruvate decarboxylase assembled regioisomerically enriched mixtures of hydroxyketones
that, when reacted with an alkyl diamine, a spontaneous coupling reaction produces
an ethyl mixture of dimethylpyrazines enriched in one isomer over the other.
More on the Biocatalysis of Arylserines and Arylisoserines from Epoxides by an MIO
α/β-Aminomutase and a Mild Amine-Group Donor
An MIO-dependent aminomutase from Taxus canadensis (TcPAM) was repurposed to transfer the amino group irreversibly from (2S)-styryl-α-alanine to exogenously supplied trans-3-phenylglycidate enantiomers. TcPAM converted (2S,3R)-3-phenylglycidate to (2S)-anti-phenylserine predominantly (89%) and (2R,3S)-3-phenylglycidate to (2R)-anti-phenylserine (88%) over their antipodes, with inversion of the configuration at Cα in each case.
Recycling CoA in the Biocatalysis of Surrogate Taxanes to Access New Generation Bioactive
Compounds
We diverged from a fixed program of using MIO-aminomutase/lyases to aminate cinnamic
acids and describe a first account of employing an MIO-aminomutase (TcPAM) from Taxus plants to convert previously untested epoxy acid substrates to bifunctional hydroxy
amino acids. Arylserines were made more abundantly over the arylisoserines when styrylalanine
was used instead of ammonium salts, to selectively transaminate the MIO group of TcPAM. This mild amine-group delivery to the oxirane avoided nonenzymatic ring-opening
of the epoxides.
Taxane analogues (docetaxel, paclitaxel, cabazitaxel, paclitaxel C, and tesetaxel) are used 1) for breast, ovarian, and prostate cancers, 2) to stem complications from stent implants in heart surgery, and 3) to work potentially as neuroprotectants against stroke. Current methods to make
docetaxel still use an 11 to 12-step semisynthesis, which involves protecting group
chemistry that compromises yields and reduces atom economy.
We use regioselective biocatalysts (Taxus Acyltransferases (AT) and Bacterial CoA Ligases) to bypass protecting group chemistry to make the drug docetaxel.
Streamlined 3-Step Biocatalysis of Docetaxel: An alternative to make docetaxel:
Coupling acyltransferases with CoA ligases (above) provides a Green source of docetaxel
and its drug analogues.
A Taxus phenylalanine aminomutase (TcPAM) converts (2S)-α-phenylalanine ((2S)-α-Phe) to (3R)-β-Phe and lies on the paclitaxel (Taxol™) biosynthetic pathway in Taxus plants.
To understand how to use TcPAM chemistry to biocatalyze β-amino acids, it is necessary to understand the subtleties
of its mechanism.
The aminomutase forms a transient MIO-NH2 adduct with a finite lifetime. The lifetime of adduct was unknown for TcPAM or any of the several enzymes in this family until we used stopped-flow monitoring
of product release to measure the exponential burst phase at presteady state.
Andrimid Pathway Aminomutase
TcPAM converts (2S)-α-Phe to (3R)-β-Phe, while PaPAM on the andrimid biosynthetic pathway converts the same substrate to (3S)-β- Phe. We used the TcPAM structure in complex with (E)-cinnamate, which functions as both a substrate and an intermediate, and the PaPAM structure to account for the distinct β-amino acid stereochemistries. TcPAM must rotate/flip the cinnamate skeleton 180° before exchange and PaPAM must hold the intermediate stationary before rebinding of the NH2/H pair to the cinnamate.
Phe455 (spheres) in PaPAM shown displacing the phenylpropanoate ligand (green), preventing
a bidentate linkage (magenta) with Arg323. This trajectory may explain the different
product stereochemistries of the two enzymes—TcPAM forms a bidentate complex with
its substrate.
In vivo Biocatalysis of β-Amino Acids
Our goal is to use this mechanistic information to repurpose these aminomutases to
produce value-added phenylpropanoids.
PaPAM biocatalyzed various phenyl- (and heteryl-) β-amino acids from their corresponding
α-amino acids.
A new graduate student can embark on studies involving organic chemistry synthesis
of novel surrogate substrates. Other areas of training include molecular cloning techniques,
expression of various enzymes in E. coli, and assay development. Included are basic biochemical applications and molecular
engineering approaches related to enzyme kinetics, enzyme purification and characterization,
and various analytical techniques (such as NMR, GC/ MS, LC-MS(/MS), and X-ray crystallography).
For Complete Listing of Publications and Patents (click here)
Assessing Alkyl Methoxypyrazines as Predictors of the Potato Taste Defect in Coffee, Shingiro, J.B.; Shee, P.K.; Beaudry, R.M.; Thiagarajan, D.; Bourquin, L.D.; Walker,
K.D. ACS Food Sci. Technol. 2022, accepted.
Biocatalysis of precursors to new-generation SB-T-taxanes effective against paclitaxel-resistant
cancer cells, A. Al-Hilfi; K.D. Walker. Arch. Biochem. Biophys.2022, 719, online. DOI: 10.1016/j.abb.2022.109165
A Semibiocatalytic Approach toward Regioisomerically Enriched Ethyl Dimethylpyrazines
Important in Flavor Industries, G. Attanayake; G. Mao; K.D. Walker. J. Agric. Food Chem. 2021, 69 (50) 15314–15324. DOI: 10.1021/acs.jafc.1c05786.
PATENT:Developing a Semibiocatalytic Process toward Regioisomerically Enriched Alkyl Pyrazines, G. Attanayake; G. Mao; K.D. Walker. Filed, July 13, 2021.
Intermolecular amine transfer to enantioenriched trans-3-phenylglycidates by an α/β-aminomutase
to access both anti-phenylserine isomers, P.K. Shee; H. Yan; K.D. Walker. ACS Catal. 2020, 10, 15071-15082. DOI: 10.1021/acscatal.0c03977
CoA Recycling by a Benzoate Coenzyme A Ligase in Cascade Reactions with Aroyltransferases
to Biocatalyze Paclitaxel Analogs, S.A. Sullivan, ; I.N. Nawarathne; K.D. Walker. Arch. Biochem. Biophys. 2020, Arch. Biochem. Biophys. 2020, 683, 108276. DOI:10.1016/j.abb.2020.108276
Exploring the Scope of an α/β-Aminomutase for the Amination of Cinnamate Epoxides
to Arylserines and Arylisoserines, P.K. Shee; N.D. Ratnayake; T. Walter; O. Goethe; E.N. Onyeozili; K.D. Walker. ACS Catal.2019, 9, 7418-7430. DOI: 10.1021/acscatal.9b01557
Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase
Define its Mutase and Lyase Activities, G. Attanayake; T. Walter; K. D. Walker. Biochemistry (ACS), 2018, 57 (25), 3503–3514. DOI: 10.1021/acs.biochem.8b00269 inSpecial Issue: Current Topics in Mechanistic Enzymology
Biocatalysis of a Paclitaxel Analogue: Conversion of Baccatin III to N-Debenzoyl-N-(2-furoyl)paclitaxel
and Characterization of an Amino Phenylpropanoyl CoA Transferase. C.K. Thornburg; T. Walter; K.D. Walker. Biochemistry (ACS) 2017, 56 (44), 5920–5930. DOI: 10.1021/acs.biochem.7b00912.
Paclitaxel Biosynthesis: Adenylation and Thiolation Domains of an NRPS TycA PheAT
Module Produce Various Arylisoserine CoA Thioesters. R. Muchiri; K.D. Walker. 2017, Biochemistry (ACS) 56 (10), 1415–1425: DOI: 10.1021/acs.biochem.6b01188.
Identification and characterization of the missing phosphatase on the riboflavin biosynthesis
pathway in Arabidopsis thaliana. N. Sa; R. Rawat; C.K. Thornburg; K.D. Walker; S. Roje. 2016, Plant J. 88(5), 705–716 DOI: 10.1111/tpj.13291Featured Article.
Mutation of aryl binding-pocket residues results in an unexpected activity switch
in an Oryza sativa tyrosine aminomutase. T. Walter; D. Wijewardena; K.D. Walker, Biochemistry, 2016, 55 (25), 3497–3503 DOI:10.1021/acs.biochem.6b00331.
Layer-by-layer deposition with polymers containing nitrilotriacetate, a convenient
route to fabricate metal- and protein-binding films. S. Wijeratne; W. Liu; J. Dong; W. Ning; N.D. Ratnayake; K.D. Walker; M.L. Bruening, ACS Appl. Mater. Interfaces, 2016, 8, 10164–10173 DOI: 10.1021/acsami.6b00896
A Tyrosine Aminomutase from Rice (Oryza sativa) Isomerizes (S)-α- to (R)-β-Tyrosine
with Unique High Enantioselectivity and Retention of Configuration. T. Walter; Z. King; K. D. Walker, Biochemistry, 2016, 55 (1), 1–4 DOI: 10.1021/acs.biochem.5b01331
Whole-cell biocatalytic production of variously substituted β-aryl- and β-heteroaryl-β-amino
acids, N. D. Ratnayake; C. Theisen.; T. Walter; K. D. Walker, J. Biotechnol.,2016, 217, 12–21. DOI: 10.1016/j.jbiotec.2015.10.012
Kinetically and crystallographically guided mutations of a benzoate CoA ligase (BadA)
elucidate mechanism and expand substrate permissivity, C. K. Thornburg; S. Wortas-Strom; M. Nosrati; J. H. Geiger; K. D. Walker, Biochemistry,2015, 54(40), 6230–6242. DOI: 10.1021/acs.biochem.5b00899
Ring‑substitutedα‑arylalaninesforprobing substituenteffectsontheisomerizationreaction catalyzedbyanaminomutase, N.D. Ratnayake; N. Liu; L. A. Kuhn; K. D. Walker, ACS Catalysis,2014, 4(9), 3077.
Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum, Y. Yang; H. Zhao; R. A. Barrero; B. Zhang; G. Sun; I.
W. Wilson; F. Xie; K. D. Walker; J. W. Parks; R. Bruce; et al., BMC Genomics,2014, 15(1):69.
A bacterial tyrosine aminomutase proceeds through retention or inversion of stereochemistry
to catalyze its isomerization reaction, U. Wanninayake; K.D. Walker, J.Am.Chem.Soc.,2013, 135(30), 11193.
Assessingthe deamination rate of a covalent aminomutase adduct by burst phase analysis, U. Wanninayake; K.D. Walker, Biochemistry,2012, 51(26), 5226.
Taxolbiosynthesis:TyrocidinesynthetaseA catalyzes the production ofphenylisoserinylCoAand otheraminophenylpropanoyl thioesters, R. Muchiri; K.D. Walker, Chem. Biol., 2012, 19(6), 679.
Insights into the mechanistic pathway of the Pantoea agglomerans phenylalanine aminomutase, S. Strom; U. Wanninayake; N. D. Ratnayake; K. D. Walker; J. H. Geiger, Ang. Chem. Int. Ed., 2012, 51(12), 2898.
(S)-Styryl-α-alanine used to probe the intermolecular mechanism of an intramolecular
MIO-aminomutase, U. Wanninayake; Y. Deporre; M. Ondari; K. D. Walker, Biochemistry,2011, 50(46), 10082.
CV
Chemistry, Biochemistry, Molecular Biology, and Biocatalysis
B.S., 1988, Univ. of Washington
Research Chemist, 1988-1990, FDA (Bothell, WA)
Ph.D., 1997, Univ. of Washington
NIH Postdoc. Research Fellow, 1997-2000, Institute of Biological Chemistry, Washington
State Univ.
Research Assistant Professor, 2000-2003, Institute of Biological Chemistry, Washington
State Univ.