P lab

E3 Lab Publications

Newton, M.S., Arcus, V.L., Gerth, M.L. and Patrick, W.M. (2018). Enzyme evolution: innovation is easy, optimization is complicated. Current Opinion in Structural Biology, 48, 110-116. [PDF and link]
Maddock, D.J., Gerth, M.L. and Patrick, W.M. (2017). An engineered glycerol dehydratase with improved activity for the conversion of meso-2,3-butanediol to butanone. Biotechnology Journal, 12, 1700480. [PDF]
Oulavallickal, T., Brewster, J.L., McKellar, J.L.O., Fairhurst, M.J., Tenci, N.A. and Gerth, M.L. (2017). The Pseudomonas syringae pv. actinidiae chemoreceptor protein F (PscF) periplasmic sensor domain: cloning, purification and X-ray crystallographic analysis. Acta Crystallographica Section F, 73, 701-705. [PDF and link]
Ferla, M.P., Brewster, J.L., Hall, K.R., Evans, G.B. and Patrick, W.M. (2017). Primordial-like enzymes from bacteria with reduced genomes. Molecular Microbiology, 105, 508-524. [PDF; and see the associated MicroCommentary by Burckhard Seelig here]
Gerth, M.L., Liu, Y., Jiao, W., Zhang, X.-X., Baker, E.N., Lott, J.S., Rainey, P.B. and Johnston, J.M. (2017). Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas. Proteins: Structure, Function, and Bioinformatics, 85, 1580-1588. [PDF]
Patrick, W.M. (2017). Biochemical evolution: the pursuit of perfection (second edition). Quarterly Review of Biology, 92, 332-333. [Invited book review; PDF]
Lawrence, S.A., Armstrong, C.B., Patrick, W.M. and Gerth, M.L. (2017). High-throughput chemical screening identifies compounds that inhibit different stages of the Phytophthora agathidicida and Phytophthora cinnamomi life cycles. Frontiers in Microbiology, 8, 1340. [PDF]
Newton, M.S., Guo, X., Söderholm, A., Näsvall, J., Lundström, P., Andersson, D.I., Selmer, M. and Patrick, W.M. (2017). Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes. Proceedings of the National Academy of Sciences USA, 114, 4727-4732. [PDF]
Mesarich, C.H., Rees-George, J., Gardner, P.P., Ghomi, F.A., Gerth, M.L., Andersen, M.T., Rikkerink, E.H.A., Fineran, P.C. and Templeton, M.D. (2017). Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS ONE, 12, e0172790. [PDF]
Brewster, J.L., McKellar, J.L.O., Finn, T.J., Newman, J., Peat, T.S. and Gerth, M.L. (2016). Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Scientific Reports, 6, 35198. [PDF]
Soo, V.W.C., Yosaatmadja, Y., Squire, C.J. and Patrick, W.M. (2016). Mechanistic and evolutionary insights from the reciprocal promiscuity of two pyridoxal phosphate-dependent enzymes. Journal of Biological Chemistry, 291, 19873-19887. [PDF]
Brewster, J.L., Finn, T.J., Ramirez, M.A. and Patrick, W.M. (2016). Whither life? Conjectures on the future evolution of biochemistry. Biology Letters, 12, 20160269. [PDF]
Read, H.M., Mills, G., Johnson, S., Tsai, P., Dalton, J., Barquist, L., Print, C.G., Patrick, W.M. and Wiles, S. (2016). The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium. PeerJ, 4, e2130. [PDF]
Söderholm, A., Guo, X., Newton, M.S., Evans, G.B., Näsvall, J., Patrick, W.M. and Selmer, M. (2015). Two-step ligand binding in a (βα)8 barrel enzyme – substrate-bound structures shed new light on the catalytic cycle of HisA. Journal of Biological Chemistry, 290, 24657-24668. [PDF]
Maddock, D.J., Patrick, W.M. and Gerth, M.L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design and Selection, 28, 251-258. [PDF]
Chambers, C.R. and Patrick, W.M. (2015). Archaeal nucleic acid ligases and their potential in biotechnology. Archaea, 2015, 170571. [PDF]
McKellar, J.L.O., Minnell, J.J. and Gerth, M.L. (2015). A high-throughput screen for ligand binding reveals the specificities of three amino acid chemoreceptors from Pseudomonas syringae pv. actinidiae. Molecular Microbiology, 96, 694-707. [PDF; and see the associated MicroCommentary by Tino Krell here]
Newton, M.S., Arcus, V.L. and Patrick, W.M. (2015). Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. Journal of the Royal Society Interface, 12, 20150036. [PDF]
Patrick, W.M. and Gerth, M.L. (2014). ITCHY: Incremental truncation for the creation of hybrid enzymes. Methods in Molecular Biology, 1179, 225-244. [PDF]
Copp, J.N., Hanson-Manful, P., Ackerley, D.F. and Patrick, W.M. (2014). Error-prone PCR and effective generation of gene variant libraries for directed evolution. Methods in Molecular Biology, 1179, 3-22. [PDF]
Ferla, M.P. and Patrick, W.M. (2014). Bacterial methionine biosynthesis. Microbiology, 160, 1571-1584. [PDF]
Bernhardt, H.S. and Patrick, W.M. (2014). Genetic code evolution started with the incorporation of glycine, followed by other small hydrophilic amino acids. Journal of Molecular Evolution, 78, 307-309. [PDF]
Köpke, M., Gerth, M.L., Maddock, D.J., Mueller, A.P., Liew, F., Simpson, S.D. and Patrick, W.M. (2014). Reconstruction of an acetogenic 2,3-butanediol pathway involving a novel NADPH-dependent primary-secondary alcohol dehydrogenase. Applied and Environmental Microbiology, 80, 3394-3403. [PDF; and check out the Spolight from the Editors here]
Ferla, M.P., Thrash, J.C., Giovannoni, S.J. and Patrick, W.M. (2013). New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS ONE, 8, e83383. [PDF]
Wilson, R.H., Morton, S.K., Deiderick, H., Gerth, M.L., Paul, H.A., Gerber, I., Patel, A., Ellington, A.D., Hunicke-Smith, S.P. and Patrick, W.M. (2013). Engineered DNA ligases with improved activities in vitro. Protein Engineering, Design and Selection, 26, 471-478. [PDF]
Saraswat, M., Grand, R.S. and Patrick, W.M. (2013). Desalting DNA by drop dialysis increases library size upon transformation. Bioscience, Biotechnology and Biochemistry, 77, 402-404. [PDF]
Hanson-Manful, P. and Patrick, W.M. (2013). Construction and analysis of randomized protein-encoding libraries using error-prone PCR. Methods in Molecular Biology, 996, 251-267. [PDF]
Gerth, M.L., Ferla, M.P. and Rainey, P.B. (2012). The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1. Environmental Microbiology, 14, 1929-1940. [PDF]
Gerth, M.L., Nigon, L.V. and Patrick, W.M. (2012). Characterization of the indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa PAO1. The Protein Journal, 31, 359-365. [PDF]
Setiyaputra, S., Mackay, J.P. and Patrick, W.M. (2011). The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold. Journal of Molecular Biology, 408, 291-303. [PDF]
Soo, V.W.C., Hanson-Manful, P. and Patrick, W.M. (2011). Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proceedings of the National Academy of Sciences USA, 108, 1484-1489. [PDF]
Patrick, W.M., Nakatani, Y., Cutfield, S.M., Sharpe, M.L., Ramsay, R.J. and Cutfield, J.F. (2010). Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe ‘clamp’ at the active site entrance. FEBS Journal, 277, 4549-4561. [PDF]
Firth, A.E. and Patrick, W.M. (2008). GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Research, 36, W281-W285. [PDF]
Patrick, W.M. and Matsumura, I. (2008). A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase. Journal of Molecular Biology, 377, 323-336. [PDF]
Gerth, M.L. and Lutz, S. (2007). Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities. Journal of Molecular Biology, 370, 742-751. [PDF]
Patrick, W.M., Quandt, E.M, Swartzlander, D.B. and Matsumura, I. (2007). Multicopy suppression underpins metabolic evolvability. Molecular Biology and Evolution, 24, 2716-2722. [PDF]
Gerth, M.L. and Lutz, S. (2007). Mutagenesis of non-conserved active site residues improves the activity and narrows the specificity of human thymidine kinase 2. Biochemical and Biophysical Research Communications, 354, 802-807. [PDF]
O’Loughlin, T.L., Patrick, W.M. and Matsumura, I. (2006). Natural history as a predictor of protein evolvability. Protein Engineering, Design and Selection, 19, 439-442. [PDF]
Firth, A.E. and Patrick, W.M. (2005). Statistics of protein library construction. Bioinformatics, 21, 3314-3315. [PDF]
Patrick, W.M. and Blackburn, J.M. (2005). In vitro selection and characterization of a stable subdomain of phosphoribosylanthranilate isomerase. FEBS Journal, 272, 3684-3697. [PDF]
Patrick, W.M. and Firth, A.E. (2005). Strategies and computational tools for improving randomized protein libraries. Biomolecular Engineering, 22, 105-112. [PDF]
Gerth, M.L., Patrick, W.M. and Lutz, S. (2004). A second-generation system for unbiased reading frame selection. Protein Engineering, Design and Selection, 17, 595-602. [PDF]
Lutz, S. and Patrick, W.M. (2004). Novel methods for directed evolution of enzymes: quality, not quantity. Current Opinion in Biotechnology, 15, 291-297. [PDF]
Patrick, W.M., Firth, A.E. and Blackburn, J.M. (2003). User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Engineering, 16, 451-457. [PDF]
Patrick, W.M., Weisner, J. and Blackburn, J.M. (2002). Site-directed mutagenesis of Tyr354 of Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance. ChemBioChem, 3, 789-792. [PDF]