Dr Shaun Lott - InvitrogenTM Life Science Award 2006

Dr Shaun Lott School of Biological Sciences University of Auckland

In my research I aim to combine structural, biophysical and computational investigations into an integrated experimental approach to the determination and analysis of protein structure and to understand this information in the light of its biological context. The evolution of high-throughput structural biology means that the determination of protein structure can now more often be the origin of functional hypotheses, rather than play its more traditional role as the explicative end of protein analysis. In pioneering a higher throughput platform for structural biology in New Zealand, I have been aiming to make the structural analysis of proteins a routine endeavour in molecular biology.

Structural genomics, perhaps more correctly called structural proteomics, sets out to apply genomic-scale technologies to the determination of three-dimensional protein structure, with the aim of increasing the output of structural biology. An important outcome of this approach is to increase the availability of protein structural analysis to the molecular biology community. The development of this technological platform also enables several fundamental questions about the relationship between protein sequence and protein structure to be addressed: How many distinct protein structural types exist in nature? Is it possible to model the structures of all protein families? Can we use structural information to determine or predict the functions of otherwise uncharacterised gene products? One of the ongoing challenges is the experimental exploitation of structure-derived predictions about protein function.

I have used a combination of structural and computational analyses to identify a deeply conserved but previously uncharacterised family of proteins as adenosine-specific binding proteins with a likely kinase activity (Lott et al., 2006), illustrating the kind of biochemical knowledge that can be deduced from structural information.

This structure-first approach can also be applied to problems of medical relevance. I have also had success with proteins from the pathogen Mycobacterium tuberculosis which are either validated targets for the design of new anti-bacterial agents or proteins likely to be important to the bacterium in its unique niche. Anthranilate phosphoribosyl transferase catalyses the second step in tryptophan biosynthesis, and has been identified by genetic knock-out as essential for pathogenesis. Its structure identified conformational changes associated with the binding of one substrate which enabled the correct prediction of how the second substrate binds and how the reaction is likely to occur - essential information for the identification and future design of inhibitors (Lee et al., 2006).

I also have an ongoing collaboration with Fiona McDonald at the University of Otago in which structural and biophysical analyses are being used to investigate mechanisms of regulation of the human epithelial sodium channel, in particular by the ubiquitin ligases of the Nedd4 family, and by the so far poorly understood protein Murr1/COMMD1. Current work includes the determination by NMR of the high affinity interaction between the binding domain of Nedd4 and its target sequence in the channel, and biophysical characterisation of Murr1/COMMD1 and related proteins.

Recent Publications

2006

ANTHONY HARRISON, ROCHELLE RAMSAY, EDWARD N. BAKER & J. SHAUN LOTT
"Crystal Structure of Isochorismate Synthase from Mycobacterium tuberculosis, the First Enzyme in the Biosynthesis of the Siderophore Mycobactin"
Journal of Bacteriology In Press

J. SHAUN LOTT, BLAKE PAGET, JODIE M. JOHNSTON, LOUIS T. J. DELBAERE, JILL A. SIMON-SIGRELL, MARK J. BANFIELD, AND EDWARD N. BAKER
"The structure of an ancient conserved domain establishes a structural basis for stable histidine phosphorylation and identifies a new family of adenosine specific kinases."
Journal of Biological Chemistry, 281, 22131-22141

VICKERY L. ARCUS, J. SHAUN LOTT, JODIE M. JOHNSTON & EDWARD N. BAKER
"The potential impact of structural genomics on Mycobacterium tuberculosis drug discovery."
Drug Discovery Today, 11, 28-34

CLARE LEE, CATHERINE GOODFELLOW, FARAH JAVID-MAJD, EDWARD N. BAKER & J. SHAUN LOTT
"The crystal structure of TrpD, a metabolic enzyme essential for lung colonization by Mycobacterium tuberculosis, in complex with its substrate phosphoribosylpyrophosphate."
Journal of Molecular Biology, 355, 784-797

2005

CELIA J. WEBBY, HEATHER M. BAKER, J. SHAUN LOTT, EDWARD N. BAKER & EMILY J. PARKER.
"The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for Type I and Type II enzymes."
Journal of Molecular Biology, 354, 927-939

NICOLE MORELAND, RACHAEL ASHTON, HEATHER M. BAKER, IVAN IVANOVIC, SEAN PATTERSON, VICKERY L. ARCUS, EDWARD N. BAKER & J. SHAUN LOTT
"A Flexible and Economical Medium-Throughput Strategy for Protein Production and Crystallization."
Acta Crystallographica Section D, 61, 1378-1385

MIRIAM L. SHARPE, EDWARD N. BAKER & J. SHAUN LOTT
"Crystallization of Hypoxic Response Protein I (HRPI) from Mycobacterium tuberculosis Using Dehydration."
Acta Crystallographica Section F: Structural Biology and Crystallization Communications 61, 565-568

CELIA J. WEBBY, J. SHAUN LOTT, HEATHER M. BAKER, EDWARD N. BAKER & EMILY J. PARKER
"Crystallization and preliminary X-ray crystallographic analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Mycobacterium tuberculosis."
Acta Crystallographica Section F: Structural Biology and Crystallization Communications 61, 403-406

ANTHONY J. HARRISON, ROCHELLE J. RAMSAY, EDWARD N. BAKER & J. SHAUN LOTT
"Crystallization and preliminary X-ray crystallographic analysis of MbtI, a protein essential for siderophore biosynthesis in Mycobacterium tuberculosis."
Acta Crystallographica Section F: Structural Biology and Crystallization Communications 61, 121-123

SIMON LI, NEIL A. PETERSON, MIN-YOUNG KIM, CHANG-YUB KIM, LI-WEI HUNG, MINMIN YU, TIMOTHY LEKIN, BRENT W. SEGELKE, J. SHAUN LOTT & EDWARD N. BAKER
"Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin."
Journal of Molecular Biology 346, 1035-1046

2004

J. SHAUN LOTT & EDWARD N. BAKER
"Using structural genomics to understand Mycobacterium tuberculosis"
IUBMB Life, 56, 113-117

2003

J. SHAUN LOTT, MARK J. BANFIELD, JILL A. SIGRELL, EDWARD N. BAKER.
"Making the most of two crystals: structural analysis of a conserved hypothetical protein using native gel screening and SAD phasing."
Acta Crystallographica Section D 59, 2242-2246

EDWARD N. BAKER, VICKERY L. ARCUS AND J. SHAUN LOTT
"Protein structure prediction and analysis as a tool for functional genomics"
Applied Bioinformatics, 2, S3-S10