Publications

Haoran Yu, Yihan Yan, Cheng Zhang, Paul A. Dalby (2017) Two strategies to engineer flexible loops for improved enzyme thermostability. Scientific Reports, 7, 41212

Affaticati PE, Dai SB, Payongsri D, Hailes HC, Tittmann K, Dalby PA. (2016) Structural analysis of an evolved transketolase reveals divergent binding modes. Scientific Reports, 6, 35716

Barata T.S., Zhang C., Dalby P.A., Brocchini S., Zloh M. (2016) Int J. Mol. Sci. 17(6):853. Identification of Protein–Excipient Interaction Hotspots Using Computational Approaches. doi:10.3390/ijms17060853

P. Morris, L. Rios-Solis, R. García-Arrazola, G. J. Lye, P. A. Dalby. (2016) Enzyme and Microbial Technology IN PRESS Mutagenesis of E. coli transketolase cofactor-binding loops towards those of Thermus thermophilus: Impact on thermotolerance and activity

F. Subrizi, M. Cardenas-Fernandez, G. J. Lye, J. M. Ward, P. A. Dalby, T. D. Sheppard, H. C. Hailes (2016) Green Chemistry. IN PRESS Transketolase catalysed upgrading of L-arabinose: the one-step stereoselective synthesis of L-gluco-heptulose. DOI: 10.1039/C5GC02660A

Chakroun N, Hilton D, Ahmad S, Platt G, Dalby P. (2016) Molecular Pharmaceutics. 13(2):307-319. Mapping the aggregation kinetics of Fab.DOI: 10.1021/acs.molpharmaceut.5b00387

Dawid Deszcz, Pierre Affaticati, Nadine Ladkau, Alex Gegel, John M. Ward, Helen C. Hailes, Paul A. Dalby. (2015). FEBS J. 13:2512-2526. Single active-site mutants are sufficient to enhance serine:pyruvate a-transaminase activity in an w-transaminase. DOI: 10.1111/febs.13293

Payongsri P, Steadman D, Hailes HC, Dalby PA. (2015) Enzyme Microb Technol 71:45-52. Second generation engineering of transketolase for polar aromatic aldehyde substrates. 10.1016/j.enzmictec.2015.01.008

Lucy E. Rayner, Gar Kay Hui, Jayesh Gor, Richard K. Heenan, Paul A. Dalby, Stephen J. Perkins (2015) J Biol Chem The solution structures of two human IgG1 antibodies show conformational stability and accommodate their C1q and FCgR ligands.

Rios-Solis L, Morris P, Grant C, Odeleye A, Hailes HC, Ward JM, Dalby PA, Baganz F, Lye GJ (2015) Chem Eng Sci 122:360-372. Modelling and optimisation of the one-pot, multi-enzymatic synthesis of chiral amino-alcohols based on microscale kinetic parameter determination

Du CJ, Rios-Solis L, Ward JM, Dalby PA, Lye GJ (2014) Biocatalysis and Biotransformation 32, 302-313. Evaluation of CV2025 w-transaminase for the bioconversion of lignin breakdown products into value-added chemicals: synthesis of vanillylamine from vanillin

Grant, C., Deszcz, D., Wei, Y. C., Martínez-Torres, R. J., Morris, P., Folliard, T., Sreenivasan, R., Ward, J.M., Dalby, P.A., Woodley, J.M., Baganz, F. (2014). Identification and use of an alkane transporter plug-in for applications in biocatalysis and whole-cell biosensing of alkanes. Sci Rep, 4, 5844. doi:10.1038/srep05844

Rayner, L. E., Hui, G. K., Gor, J., Heenan, R. K., Dalby, P. A., & Perkins, S. J. (2014). The Fab conformations in the solution structure of human IgG4 restricts access to its Fc region: implications for functional activity. J Biol Chem. doi:10.1074/jbc.M114.572404

Sagar, D.M., Aoudjane, S., Gaudet, M., Aeppli, G., Dalby, P.A. (2013) Scientific Reports 3:2130. Optically Induced Thermal Gradients for Protein Characterization in Nanolitre-scale Samples In Microfluidic Devices. DOI:10.1038/srep02130

Lucy E. Rayner, Nilufar Kadkhodayi-Kholghi, Jayesh Gor, Paul A. Dalby, Stephen J. Perkins, (2013) J. Mol. Biol. 425:506-523. The solution structure of rabbit IgG accounts for its interactions with the Fc receptor and complement C1q and its conformational stability.

Dalby, P. A., Ward, J. M., & Hailes, H. C. (2012). 7.17 C-X Bond Formation: C-C Bond Formation using TDP-Dependent Enzymes. Comprehensive Chirality, 7, 372-389. doi:10.1016/B978-0-08-095167-6.00722-9

Polykarpou, E.M., Dalby, P.A., Papageorgiou, L.G. (2012) Biochemical Engineering Journal 67:186-193. Novel efficient optimisation systems for purification process synthesis.

Polykarpou, E.M., Dalby, P.A., Papageorgiou, L.G. (2012) Chemical Engineering Research and Design. 90(9):1262-1270. An MILP formulation for the synthesis of protein purification processes.

Grant, Y., Dalby, P.A., Matejtschuk, P. (2012) American Pharmaceutical Review. 15(2):75-80. Use of Design of Experiment and Micro-scale Down Strategies in Formulation and Cycle Development for Lyophilization.

Robert Patterson, Jessica Nerren, Michael Kogut, Pinar Court, Bernardo Villarreal-Ramos, Hans-Martin Seyfert, Paul A. Dalby, Dirk Werling (2012) Developmental & Comparative Immunology 37(1):107-114. Yeast-surface expressed BVDV E2 protein induces a Th1/Th2 response in naïve T cells.

Ordidge G.C., Mannall, G., Liddell, J., Dalby, P.A., Micheletti, M. (2012) Biotechnology Progress. 28(2):435-444. A generic hierarchical screening method for the analysis of microscale refolds using an automated robotic platform.

Grant, Y., Matejtschuk, P., Bird, C., Wadhwa, M., Dalby, P.A. (2012) Biotechnol. Letts. 34(4):641-648. Rapid Identification and Optimisation of Freeze Drying Formulation using Microscale and Design of Experiment approaches: A Case Study using Granulocyte Colony Stimulating Factor (G-CSF).

John Strafford, Panwajee Payongsri, Edward G. Hibbert, Phattaraporn Morris, Sukhjeet S. Batth, David Steadman, Mark E. B. Smith, John Ward, Helen C. Hailes, Paul A. Dalby (2012) J. Biotechnol. 157(1): 237-245. Directed evolution to re-adapt a co-evolved network within an enzyme.

L. Rios-Solis, M. Halim, A. Cázares, P. Morris, J. M. Ward, H.C. Hailes, P.A. Dalby, F. Baganz, G. J. Lye (2011) Biocatalysis and Biotransformation. 29(5):192-203. A microscale toolbox for rapid evaluation of multi-step enzymatic syntheses comprising a mix and match E. coli expression system.

Parker, B.M., Taylor, I., Woodley, J.M., Ward, J.M., Dalby, P.A. (2011) J. Biotechnol. 155(4):396-405. Directed evolution of a thermostable L-aminoacylase biocatalyst.

Polykarpou, E.M., Dalby, P.A., Papageorgiou, L.G. (2011) Biotechnology Progress. 27(6): 1653-1660. Optimal Synthesis of Chromatographic Trains for Downstream Protein Processing.

Lye, G.J., Dalby, P.A., Baganz, F., Ward, J.M and Hailes, H.C. (2011). Biocatalysis is the future… the future is now! The Chemical Engineer, issue 839 (May), 36-38.

Dalby, P.A. (2011) Current Opinion in Structural Biology 21:1-8. Strategy and success for the directed evolution of enzymes.

Jahromi, R.R.F., Morris, P., Martinez-Torres, R.J., Dalby, P.A. (2011) J. Biotechnology. 155:209-216. Structural stability of E. coli transketolase to temperature and pH denaturation.

Mahendrarajah, K., Dalby, P.A., Wilkinson, B. Jackson, S.E. & Main, E.R.G. (2011) Anal Biochem 411:155-157. A high throughput fluorescence chemical denaturation assay as a general screen for protein-ligand binding.

Ahmad, S.S., Dalby, P.A. (2011) Biotechnol. Bioeng. 108(2):322-332. Thermodynamic parameters for salt-induced reversible protein precipitation from automated microscale experiments.

Abe, Y., Gor, J., Bracewell, D.G., Perkins, S.J., Dalby, P.A. (2010) Biochem. J. 432(1), 101-111. Masking of the Fc region in human IgG4 by constrained X-ray scattering modelling: implications for antibody function and therapy.

James L. Galman, David Steadman, Sarah Bacon, Phattaraporn Morris, Lydia G. Crago, Mark E.B. Smith, John Ward, Paul A. Dalby, Helen C. Hailes (2010) ChemComm. 46(4), 7608-7610. alpha,alpha'-Dihydroxyketone formation using aromatic and heteroaromatic aldehydes with evolved transketolase enzymes.

Gaudet, M., Remtulla, N., Jackson, S.E., Main, E.R.G., Bracewell, D.G., Aeppli, G., Dalby, P.A. (2010) Protein Science. 19, 1544-1554. Protein denaturation and protein:drug interactions from intrinsic protein fluorescence measurements at the nanolitre scale. (DOI: 10.1002/pro.433)

Hailes, H.C, Dalby, P.A., Lye, G. J., Baganz, F., Micheletti, M., Szita, N., Ward, J.M. (2010) Current Organic Chemistry. 14(17):1883-1893. alpha,alpha'-Dihydroxy Ketones and 2-Amino-1,3-diols: Synthetic and Process Strategies using Biocatalysts.

Cázares, A., Galman, J.L., Crago, L.G., Smith, M.E.B., Strafford, J., Ríos-Solís, L., Lye, G.J., Dalby, P.A., Hailes, H.C. (2010) Organic & Biomolecular Chemistry. 8(6), 1301-1309. Non-alpha-hydroxylated aldehydes with evolved transketolase enzymes DOI: 10.1039/b924144b
Cover issue of 8(6) 2010, March 21.

Smith, M.E.B., Chen, B.H., Hibbert, E.G., Kaulmann, U., Smithies, K., Galman, J.L., Baganz, F., Dalby, P.A., Hailes, H.C., Lye, G.J., Ward, J.M., Woodley, J.M., Micheletti, M. (2009) Org. Proc. Res. Dev. 14(1), 99-107. A Multi-Disciplinary Approach Toward the Rapid and Preparative Scale Biocatalytic Synthesis of Chiral Amino Alcohols: A Concise Transketolase / alpha-Transaminase-Mediated Synthesis of (2S,3S)-2-Aminopentane-1,3-diol.

Hailes, H.C., Dalby. P.A., Lye, G.J., Ward, J.M. (2009) Chim Oggi. 27(4), 28-31. Biocatalytic Approaches to Ketodiols and Aminodiols.

Grant, Y., Matejtschuk, P., Dalby, P.A. (2009) Biotechnol. Bioeng. 104(5), 957-964. Rapid optimisation of protein freeze-drying formulations using ultra scale-down and factorial design of experiment in microplates. (DOI 10.1002/bit.22448)

Dalby. P.A., Baganz, F.B., Lye, G.J., Ward, J.M. (2009) Chim Oggi. 27(4), 18-22. Protein and pathway engineering in biocatalysis.

Dalby, P. (2009) J. Biomolecular Screening 14(7), 900-900. High-Throughput Characterization of Proteins From Microtiter Plates to Microfluidics. 15th Annual Conference and Exhibition of the Society-of-Biomolecular-Sciences, APR 26-30, 2009 Lille, France.

Paramesvaran, J., Hibbert, E.G., Russell, A.J., Dalby, P.A. (2009) Protein Engineering Design and Selection. 22(7), 401-411. Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies. (DOI 10.1093/protein/gzp020)

Mannall, G.J, Myers, J.P., Liddell J., Titchener-Hooker, N.J., Dalby, P.A. (2009) Biotech. Bioeng. 103(2), 329-340. Ultra scale-down of protein refold screening in microwells: Challenges, solutions and application. (DOI 10.1002/bit.22245)

Smith, M.E.B., Hibbert, E.G., Jones, A.B., Dalby, P.A, and Hailes, H.C. (2008) Adv Syn Catal 350, 2631-2638. Enhancing and reversing the enantioselectivity of E. coli transketolase via single point mutations. (DOI 10.1002/adsc.200800489)

Chen, B.H., Hibbert, E.G., Dalby, P.A., and Woodley, J.M. (2008) AIChE J. 58, 2155-2163. A new approach to bioconversion reaction kinetic parameter identification. (DOI 10.1002/aic.11545)

Hibbert, E.G., Senussi, T., Smith, M.E.B., Costelloe, S.J., Ward, J.M., Hailes, H.C., and Dalby, P.A. (2008) J. Biotechnol. 134, 240-245. Directed evolution of transketolase substrate specificity towards an aliphatic aldehyde. (DOI 10.1016/j.jbiotec.2008.01.018)

Aucamp, J.P., Martinez-Torres, R.J., Hibbert, E.G. and Dalby, P.A. (2008) Biotech. Bioeng. 99, 1303-1310. A microplate-based evaluation of complex denaturation pathways: Structural stability of E. coli transketolase. (DOI 10.1002/bit.21705)
Cover of issue 99(6) 2008, April 15.

Costelloe, S.J., Ward, J.M., and Dalby, P.A. (2008) J. Mol. Evol. 66, 36-49. Evolution of the TPP-dependent enzyme family. DOI 10.1007/s00239-007-9056-2)

Dimitriadou, E.K., Lye, G.J., Dalby, P.A. (2007) Redesign and altered ion-binding of a natural calcium regulated biosensor, photoprotein aequorin. Amino Acids 33 (3): XLVI-XLVI.

Baganz, F., Chen, B., Dalby, P., Hibbert, E., Lye, G., Micheletti, M., Woodley, J., Kaulmann U., Ward, J., Hailes, H., Smith, M. and Smithies, K. (2007) Accelerating biocatalytic process design: Integrating new tools from biology, chemistry and engineering. J. Biotechnol. 131 S78-S78.

Dalby, P.A., Aucamp, J.P., George, R. and Martinez-Torres, R.J. (2007) Biochem. Soc. Transact. 35, 1606-1609. Structural stability of an enzyme biocatalyst. DOI:10.1042/BST0351606

Hibbert, E.G., Senussi, T., Costelloe, S.J., Lei, W., Smith, M.E.B., Ward, J.M., Hailes, H.C., and Dalby, P.A. (2007) Journal of Biotechnology 131, 425-432. Directed evolution of transketolase activity on non-phosphorylated substrates.

Hailes, H.C., Dalby, P.A. and Woodley, J.M. (2007) J. Chem. Technol. Biotechnol. 82, 1063–1066. Integration of biocatalytic conversions into chemical syntheses.

Miller, O.J., Hibbert, E.G., Ingram, C.U., Lye, G.J. and Dalby, P.A. (2007) Biotechnol. Letts. 29, 1759-1770. Optimisation and evaluation of a generic microplate-based HPLC screen for transketolase.

Martinez-Torres, R.J., Aucamp, J.P., George, R. and Dalby, P.A. (2007) Enzyme Microb. technol. 41, 653-662. Structural stability of E. coli transketolase to urea denaturation.

Mannall, G. J., Titchener-Hooker, N. J. and Dalby, P. A. (2007) Biotech. Bioeng. 97, 1523-1534. Factors affecting protein refolding yields in a fed-batch and batch-refolding system.

Dalby, P. A. (2007) Recent Patents Biotechnol. 1 (1), 1-9. Engineering enzymes for biocatalysis.

Ingram, C. U., Bommer, M., Smith, M. E. B., Dalby, P. A., Ward, J. M., Hailes, H.C., Lye, G. J. (2007) Biotech. Bioeng. 96, 559-569. One-pot synthesis of amino-alcohols using a de-novo transketolase and -alanine:pyruvate transaminase pathway in Escherichia coli.

Chen, B. H., Sayar, A., Kaulmann, U., Dalby, P. A., Ward, J. M. and Woodley, J. M. (2006) Biocatal. Biotrans. 24, 449-457. Reaction modelling and simulation to assess the integrated use of transketolase and ω-transaminase for the synthesis of an aminotriol.

Mannall, G. J., Titchener-Hooker, N. J., Chase, H. A. and Dalby, P. A. (2006) Biotech. Bioeng. 93, 955-963. A critical assessment of the impact of mixing on dilution refolding.

Smith, M. E. B., Smithies, K., Senussi, T., Dalby, P. A. and Hailes, H. C. (2006) Eur J. Org. Chem. 1121-1123. The First Mimetic of the Transketolase Reaction.

Hibbert, E. G. and Dalby, P. A. (2005) Microbial cell factories. 4, 29. Directed evolution strategies for improved enzymatic performance.

Hibbert, E. G., Baganz, F., Hailes, H. C., Ward, J. M., Lye, G. J., Woodley, J. M. and Dalby, P. A. (2005) Biomolecular Engineering 22 (1-3), 11-19. Directed evolution of biocatalytic processes.

Aucamp, J. P., Cosme, A. M., Lye, G. J. and Dalby, P. A. (2005) Biotech Bioeng. 89 (5), 599-607. High-throughput measurement of protein stability in microtiter plates.

Miller, O. J. and Dalby, P. A. (2004) Trends Biotech. 22 (5), 203-205. Exposing hidden relationships using directed evolution.

Dalby, P. A. (2003) Curr. Opin. Struct. Biol. 13 (4), 500-505. Optimising enzyme function by directed evolution.

Lye, G. J., Ayazi-Shamlou, P., Baganz, F., Dalby, P. A., and Woodley, J. M. (2003) Trends Biotech. 21 (1), 29-37. Accelerated design of bioconversion processes using automated microscale processing techniques.

Lye, G. J., Dalby, P. A., and Woodley, J. M. (2002) Org. Process Res. Dev. 6 (4), 434-440. Better biocatalytic processes faster: New tools for the implementation of biocatalysis in organic synthesis

Dalby, P. A., Hoess, R. H., and DeGrado, W. F., (2000) Protein Sci. 9, 2366-2376. Evolution of binding affinity in a WW domain probed by phage display.

Dalby, P. A., Oliveberg, M. O., and Fersht, A. R., (1998) J. Mol. Biol. 276, 625-646. Folding Intermediates of Wild-type and Mutants of Barnase. I. Use of phi-value Analysis and m-values to Probe the Cooperative Nature of the Folding Pre-equilibrium.

Dalby, P. A., Clarke, J., and Fersht, A. R., (1998) J. Mol. Biol. 276, 647-656. Folding Intermediates of Wild-type and Mutants of Barnase. II. Correlation of Changes in Equilibrium Amide Exchange Kinetics, with the Population of the Folding Intermediate.

Dalby, P. A., Oliveberg, M. O., and Fersht, A. R., (1998) Biochemistry. 37, 4674-4679. Movement of the Intermediate and Rate Determining Transition State of Barnase on the Energy Landscape with Changing Temperature.

Book Chapters

Dalby PA, Lye GJ and Woodley JM (2005) One-pot synthesis and the integration of chemical and biocatalytic conversions. In Handbook of Chiral Chemicals (2nd Edn)(Ed D J Ager), CRC Press, Boca Raton, pp 419-428.

Wohlgemuth R, Smith MEB, Dalby PA and Woodley JM (2010) Transketolases. In Encyclopedia of Industrial Biotechnology: Bioprocess, Bioseparation and Cell Technology, Ed, Michael C. Flickinger, Vol. 7 pp 4746-4752. John Wiley and Sons, Inc, Hoboken.