Gail Bartlett's Research Page

Structural Bioinformatics

My main interest is in the relationship between protein sequence, structure and function, and the rules which link the folding of a protein sequence into a three dimensional structure.

Plugging Protein-Protein Interactions

Coiled coil proteins provide us with a basic set of rules which we can use to design proteins with a specific structure whose function can be potentially modified. My current work involves using the CCPLUS coiled coil database as a knowledge-base from which we can try to identify arrays of orphan holes on the surfaces of proteins which may be targets for a designed coiled coil interaction.

Non-covalent interactions in proteins

I also work in collaboration with Professor Ron Raines at the University of Madison, Wisconsin, looking at non-covalent interactions in protein structures. Recently, we have been looking at an interaction called the n-->pi* interaction, which is abundant in protein structures. It is roughly analogous to a hydrogen bond, but is much lower in energy.

Previous Work

2005-2006 — I worked on ab initio protein structure prediction with Willie Taylor at the National Institute of Medical Research, looking at ways of filtering correct and incorrect predictions.

2004-2005 — I worked as a Computational Biologist for the Bioinformatics Support Service at Imperial College London, assisting researchers with a range of bioinformatics problems, including microarray analysis, protein and nucleic acid sequence analysis, genome tiling and structure analysis.

2000-2004 — My PhD was an analysis of catalytic residues and enzyme active sites from a structural and evolutionary perspective, carried out at UCL and the European Bioinformatics Institute under the supervision of Professor Janet Thornton CBE FRS. The work resulted in the establishment of two major databases, the Catalytic Site Atlas, and MACiE (Mechanism and Catalysis in Enzymes)

Publications:

19

A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

Fletcher JM, Boyle AL, Bruning M, Bartlett GJ, Vincent TL, Zaccai NR, Armstrong CT, Bromley EHC, Booth PJ, Brady RL, Thomson AR, Woolfson DN

ACS Synthetic Biology (2012) 6:240-250

18

Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils

Steinkruger JD, Bartlett GJ, Woolfson DN, Gellman SH

J Am Chem Soc (2012) 134(38): 15652-5

17

Squaring the circle in peptide assembly: from fibers to discrete nanostructures by de novo design.

Boyle AL, Bromley EH, Bartlett GJ, Sessions RB, Sharp TH, Williams CL, Curmi PM, Forde NR, Linke H, Woolfson DN

J Am Chem Soc (2012) 134(37): 15457-67

16

New currency for old rope: from coiled-coil assemblies to alpha-helical barrels.

Woolfson DN, Bartlett GJ, Bruning M, Thomson AR

Curr Opin Struct Biol (2012) 22(4): 432-41

15

The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif.

Steinkruger JD, Bartlett GJ, Hadley EB, Fay L, Woolfson DN, Gellman SH

J Am Chem Soc (2012) 134(5):2626-33

14

A de novo peptide hexamer with a mutable channel

Zaccai NR, Chi B, Thomson AR, Boyle AL, Bartlett GJ, Bruning M, Linden N, Sessions RB, Booth PJ, Brady RL, Woolfson DN

Nat Chem Biol (2011) 7(12):935-41

13

Designed coiled coils promote folding of a recombinant bacterial collagen

Yoshizumi A, Fletcher JM, Yu Z, Persikov AV, Bartlett GJ, Boyle AL, Vincent TL, Woolfson DN, Brodsky B

J Biol Chem (2011) 286(20):17512-20

12

n-->pi* interactions in proteins

Bartlett GJ, Choudhary A, Raines RT, Woolfson DN

Nat Chem Biol 6(8):615-20 (2010)

11

Prediction of protein structure from ideal forms

Taylor WR, Bartlett GJ, Chelliah V, Klose D, Lin K, Sheldon T, Jonassen I.

Proteins January 3 (2008 Epub ahead of print)

10

Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de-novo protein structure prediction

Bartlett GJ, Taylor WR.

Proteins November 14 (2007 Epub ahead of print)

09

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM.

Nucleic Acids Res. 2007 Jan;35(Database issue):D515-20. Epub 2006 Nov 1.

08

MACiE: a database of enzyme reaction mechanisms

Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB.

Bioinformatics 2005 Dec 1;21(23):4315-6. Epub 2005 Sep 27.

07

Effective function annotation through catalytic residue conservation

George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB.

Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12299-304. Epub 2005 Jul 21.

06

Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families

Torrance JW, Bartlett GJ, Porter CT, Thornton JM.

J Mol Biol. 2005 Apr 1;347(3):565-81.

05

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.

Porter CT, Bartlett GJ, Thornton JM.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D129-33.

04

Catalysing new reactions during evolution: economy of residues and mechanism.

Bartlett GJ, Borkakoti N, Thornton JM.

J Mol Biol. 2003 Aug 22;331(4):829-60.

03

Using a neural network and spatial clustering to predict the location of active sites in enzymes.

Gutteridge A, Bartlett GJ, Thornton JM.

J Mol Biol. 2003 Jul 18;330(4):719-34.

02

Inferring protein function from structure.

Bartlett GJ, Todd AE, Thornton JM.

Methods Biochem Anal. 2003;44:387-407.

01

Analysis of catalytic residues in enzyme active sites.

Bartlett GJ, Porter CT, Borkakoti N, Thornton JM.

J Mol Biol. 2002 Nov 15;324(1):105-21.