Dr. Shaun Lott

Lecturer in Structural Bioinformatics

Structural Biology

Phone: 373-7599 ext 87074
Fax: 373-7414
Room 403
Email: s.lott@auckland.ac.nz

Research Interests

I have research expertise in the areas of recombinant DNA technology, bioinformatics, recombinant protein expression and X-ray crystallography. In my current research I am aiming to combine my expertise in these areas into an integrated approach to the analysis of protein structure and function. 

Structural Genomics

The use of protein structure to functionally annotate completed genomes is one of the major post-genomic challenges facing structural biology. 

I have responsibility in the Laboratory of Structural Biology for the organisation of our Structural Genomics programme. This programme is part of the Mycobacterium tuberculosis Structural Genomics Consortium (http://www.doe-mbi.ucla.edu/TB/), a collaboration of over 70 other structural biology groups in twelve countries. I am an Objective Leader on the New Enterprise Research Fund programme grant that partially funds this work. 

One overall aim of this programme is to translate the information present in fully sequenced genomes into protein structures, and hence functions. A second aim is to develop systems and methodologies for increasing the throughput of macromolecular structure determination. The target organisms are Pyrobaculum aerophilum, a hyperthermophilic archaeon, and Mycobacterium tuberculosis, the causative agent of TB. We aim to discover relationships between protein sequence, structure and function that are hidden at the sequence level and to establish hitherto unknown relationships between protein families that will only be apparent at the level of three-dimensional structure. The structures solved will also reveal potential targets for new tuberculosis therapies - to this end we have targeted proteins with known involvement in bacterial survival in lung colonisation and antibiotic response and resistance. 

Sodium channel regulation by WW domain-containing proteins

WW domains are small protein domains that bind to proline-rich and phosphoserine-containing target amino acid sequences. Proteins of the Nedd4 family contain multiple WW domains that mediate binding to the human epithelial sodium channel (ENaC), thereby regulating channel activity by the ubiquitination and subsequent endocytosis of the channel subunits. This interaction is important in sodium and water homeostasis and the consequent regulation of blood pressure in the body. 

I have used Surface Plasmon Resonance (BIAcore) analysis to demonstrate that a single WW domain (WW3) predominantly mediates the binding of Nedd4 to the human ENaC. Further SPR measurements coupled with mutational and molecular modelling studies have begun to establish the structural reasons for the differential binding affinities between the four WW domains of human Nedd4 and the channel (Lott et al., 2002). I am now extending this analysis to other members of the Nedd4 protein family and their regulators in order to create a comprehensive model of the roles of these proteins in ENaC regulation. Also, the structure of the complex of Nedd4 WW3 with its cognate ligand is currently being studied using NMR spectroscopy, in order to understand the relatively high affinity of this interaction. This work is carried out in collaboration with Dr Fiona McDonald at the University of Otago. 

Phylogenetic profiling

With the availability of whole-genome sequences, a number of techniques have been developed for assigning gene function by non-homology or ‘guilt by association’ methods. One such method is phylogenetic profiling, which predicts gene function based on co-inheritance between species. A major problem with phylogenetic profiling is the overprediction of functional linkages i.e. a high false positive rate. I am interested in establishing a rigorous confidence estimate to improve the reliability of functional predictions made using this technique. This work is being carried out in collaboration with Dr Vic Arcus, Dr Pat Riddle (Computer Science) and A. Prof Chris Triggs (Statistics).

Selected Recent Publications