... understanding life in molecular detail

Prof Alan Berry

Protein engineering; Directed evolution; Biocatalysis; Enzymology


We have a wide range of interests in synthetic biology and its applications in generating novel proteins and enzymes using rational design and directed evolution. Our work spans biochemistry and chemistry with an emphasis on the enzymes that make and break carbon-carbon bonds, particularly aldolases. We have used the modern methods of protein engineering to alter the specificity of enzyme reactions, the stability of enzymes and their stereochemistry, and structural techniques such as X-ray crystallography and NMR spectroscopy with enzyme kinetics to characterise the resulting enzymes.

Current major projects include:
  • Creating new enzymes containing non-natural amino acids
  • Enzymology of polyketide and polyether synthases
  • Selection of novel enzymes via mRNA display
  • Synthetic biology and construction of orthogonal organelles

We have a wide range of interests in synthetic biology and enzymology and their applications in generating novel proteins and enzymes using rational design and directed evolution. Our work spans biochemistry and chemistry with an emphasis on the enzymes that make and break carbon-carbon bonds, particularly aldolases.

Engineering and evolving new aldolases.  Aldolases catalyse the condensation of an aldehyde and a ketone to generate a new carbon-carbon bond.  The enzymes therefore offer great potential in biotechnology as efficient, green catalysts but their properties can also cause problems - for example their limited substrate range and their stability.  We have demonstrated that it is possible to alter the stability and specificity of a number of aldolases.  Excitingly we have also been able to engineer/evolve aldolases to alter and control their stereochemistry - thereby giving the possibility of tailoring the specificity and the stereochemical outcome of the reaction.  On-going work aims to engineer aldolases with simultaneous stereochemical control over two carbon centres (see Fig 1). 

 

Fig. 2 The active site of the aldolase NAL engineered to contain a novel amino acid (gamma-thia-lysine) in the active site.  This modified enzyme is active in the normal enzyme reaction.

Other recent work has shown that unnatural amino acids can be inserted into the enzyme active site and that activity can still be retained.  We are now searching for new activities that are dependent on the location of an unnatural amino acid in the aldolase active site (Fig. 2).

 

Characterising and engineering polyketide synthases / non-ribosomal peptide synthases.  The modular PKS/NRPSs offer great potential to engineer the specificity of product production by altering the individual modules in the enzyme.  We are investigating the structure and mechanism of the NRPS responsible for the biosynthesis of indanomycin.

Directed evolution using mRNA display.  We are extending our interest in enzymes that make carbon-carbon bonds to evolve new enzyme activities.  These directed evolution experiments will require the screening of very large libraries of variants to select for novel, interesting enzymes and we are using mRNA display to select for the active enzymes.

Engineering / evolving new protein - protein interactions.  As well as using these techniques of protein engineering and evolution to create new enzymes we are also altering the recognition of the proteins associated with protein import into the peroxisome (with Prof Alison Baker).

In all our projects we use the modern methods of molecular biology to alter the enzymes and a wide range of methods (including structural techniques such as X-ray crystallography and NMR spectroscopy with enzyme kinetics) to characterise the resulting enzymes.

Detailed research programme                  Close ▲
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Professor of Molecular Enzymology
BSc (Soton) PhD (Soton)
FRSC FSB

Royal Society University Research Fellow (Cambridge) 1987-1994
Lecturer (Leeds) 1994-1997
Senior Lecturer (Leeds) 1997-2006
Reader of Enzymology (Leeds) 2006-9

Astbury 10.108
School of Molecular and Cellular Biology
0113 343 3158
a.berry@leeds.ac.uk
http://bmbsgi10.leeds.ac.uk

Selected Publications

  1. Timms N; Windle CL; Polyakova A; Ault JR; Trinh CH; Pearson AR; Nelson A; Berry A Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine withγ-thialysine by using a chemical mutagenesis strategy. Chembiochem 14 474-481, 2013 DOI:10.1002/cbic.201200714

  2. Howard JK, Müller M, Berry A, Nelson A An Enantio- and Diastereoselective Chemoenzymatic Synthesis ofα-Fluoro β-Hydroxy Carboxylic Esters Angewandte Chemie - International Edition 55 6767-6770, 2016

  3. Williams GJ; Woodhall T; Farnsworth LM; Nelson A; Berry A Creation of a pair of stereochemically complementary biocatalysts. J Am Chem Soc 128 16238-16247, 2006 DOI:10.1021/ja065233q

  4. Daniels, A.D., Campeotto, I., van der Kamp, M.W., Bolt, A.H., Trinh, C.H., Phillips, S.E., Pearson, A.R., Nelson, A., Mulholland, A.J. and Berry, A. (2014) Reaction Mechanism of N-Acetylneuraminic acid lyase revealed by a combination of crystallography, QM/MM simulation, and mutagenesis. ACS Chem Biol. 9, 1025-1032