Protein Structure Bioinformatics Group
The Protein Structure Bioinformatics Group is part of a Bioinformatics Laboratory set up in the School of Biological Sciences.

Research
 

Analysis and evolution of snake venom serine proteases

Details to follow

Bacterial Adhesins

New project. Details to follow

Residue Pairings in Beta sheets

Our understanding of how beta sheets fold is limited. There are many analyses of the propensities of individual amino acids to be in beta sheets. Our research focusses on the next level of complexity, namely how do these residues come together to form the hydrogen bonded beta sheet structure. Analysis of intrastrand residue pairs in antiparallel beta sheets has shown that only a subset of possible pairs is favoured and that the preferences are different at the hydrogen bonded and non-hydrogen bonded sites. Helen Fooks is currently extending this to look at parallel beta sheet structures.

Analysis of Protein Structural Motifs

We are developing methods to automatically identify, classify and analyse a number of supersecondary structural motifs in proteins. Any resulting patterns will be useful in prediction of protein structure from amino acid sequence. Motifs analysed include beta turns, gamma turns, Greek keys, beta hairpins and beta bulges. Many of the methods have been incorporated into a publicly available package PROMOTIF , which will identify a number of motifs from a protein coordinate file. This includes a program, HERA, for drawing schematic hydrogen bnding diagrams of protein structures. Data from PROMOTIF analyses are included in the PDBsum web site, which provides information derived from all currently available protein coordinate files. We have also analysed TIM barrels, and the common motifs involved in Superfolds

Structural Motif Prediction

This project attempts to predict the structures of supersecondary motifs from amino acid sequence. We are initially concentrating on beta hairpins. We have derived an energy function which scores sequences based on secondary structure propensity, turn propensity etc. This function is used to scan a sequence through a database of beta hairpins,looking for the site which is most likely to form a hairpin structure. New developments inlcude the application of neural networks to this problem.

Protein Design

We are attempting to use the information derived from analyses of known protein structures (beta sheet residue pairings, beta turn propensities) etc to design novel peptides with a particular three dimensional structure.


 
 

Return to top

Available Software
To obtain any of the following programs (supplied as gzipped tar files click the "download' button next to the program name. Included in the set of files is a confidentiality agreement which I would be grateful if you would complete and return to me. If you have any problems, please e-mail me at e.g.hutchinson@reading.ac.uk
Click to download promotif3.tar.gzPROMOTIF a program to identify structural motifs in proteins (version 3.01 Aug 2002)
Click to download promotif2.tar.gzPROMOTIF a program to identify structural motifs in proteins (version 2.0)

Return to top

Recent Publications
1)E. G. Hutchinson, W. Tichelaar, G. Hofhaus, H. Weiss & K. R. Leonard "Identification and electron microscopic analysis of a chaperonin oligomer from Neurospora crassa mitochondria" EMBO J. 8: 1485-1490 (1989)..
2)E. G. Hutchinson & J. M. Thornton "HERA - A Program to Draw Schematic Diagrams of Protein Secondary Structures" PROTEINS: Structure, Function and Genetics 8:203-212 (1990). .
3)J. M. Thornton, M. W. MacArthur, D. K. Smith, S. P. Gardner, E. G. Hutchinson, A. L. Morris, B. L. Sibanda "Analysis of Errors found in Protein Structure Coordinates in the Brookhaven Data Bank" Proceedings of CCP4 meeting on Accuracy and Reliability of Macromolecular Crystal Structures, Daresbury, 1990.
4)E. G. Hutchinson, W. Tichelaar, H. Weiss & K. R. Leonard "Electron microscopic characterisation of helical filaments formed by subunits I and II (core proteins) of ubiquinol: cytochrome c reductase from Neurospora mitochondria" J. Structural Biology 103: 75-88 (1990)..
5))E. G. Hutchinson, A. L. Morris & J. M. Thornton " Structural Patterns in Globular Proteins " In " Structure Correlation " (Editor J. Dunitz) (1992).
6)J. M. Thornton, S. P. Gardner & E. G. Hutchinson "Protein Structure Databases: Design & Applications ".; In " Computer Modelling of Biomolecular Processes" (Editors J. Goodfellow & D. Moss) (1992).
7)H. J. Stirk, D. N. Woolfson, E. G. Hutchinson & J. M. Thornton "Depicting topology and handedness in jelly roll structures" FEBS Lett. 308: 1-3 (1992).
8)A. L. Morris, M. W. MacArthur, E. G. Hutchinson & J. M. Thornton "Assessing the Accuracy of Protein Structural Coordinates" PROTEINS: Structure, Function and Genetics 12: 345-364 (1992).
9)A. W. E. Chan, E. G. Hutchinson, D. Harris & J. M. Thornton "Identification, Classification and Analysis of beta-bulges in proteins" Protein Science 2: 1574-1590 (1993). .
10)D. N. Woolfson, P. A. Evans, E. G. Hutchinson & J. M. Thornton "Topological and Stereochemical Restrictions in beta-sandwich protein structures" Protein Engineering Vol. 6 No. 5: 461-470 (1993).
11)E. G. Hutchinson & J. M. Thornton "The Greek Key Motif - Extr action, Classification and Analysis" Protein Engineering Vol. 6 No. 3: 233-245 (1993).
12)E. G. Hutchinson & J. M. Thornton " A revised set of potentia ls for beta-turn formation in proteins" Protein Science 3:2207-2216 (1994).
13)E. G. Hutchinson & J. M. Thornton "PROMOTIF - A program to id entify structural motifs in proteins" Protein Science 5:212-220 (1996).
14)R. A. Laskowski, E. G. Hutchinson, A. D. Michie, A. C. Wallace & J. M. Thornton "PDBsum: Summaries and structural analyses of PDB data files" PDB Newsletter, January 1997.
15)R. A. Laskowski, E. G. Hutchinson, A. D. Michie, A. C. Wallace, M. L. Jones & J. M. Thornton "PDBsum: a Web-based database of summaries and analyses of all PDB structures" TIBS 22 No 12: 488-490 (1997).
16)Swindells, M. B, Orengo, C. A., Jones, D. T., Hutchinson, E. G. & Thornton, J. M. "Contemporary approaches to protein structure classification" Bioessays Vol 20 No 11, 884-891 (1998).
17)Orengo, C. A., Martin, A. C. R., Hutchinson, E. G., Jones, S., Jones, D. T., Michie, A. D., Swindells, M. B. & Thornton, J. M. "Classifying a protein in the CATH database of Domain Structures" Acta Cryst Vol D54, 1155-1167 (1998).
18)E. G Hutchinson, R. B. Sessions, J. M. Thornton & D. N. Woolfson "Determinants of strand register in antiparallel beta sheets of proteins" Protein Science 7, 2287-2300 (1998).
19)A. C. R. Martin, C. A. Orengo, E. G. Hutchinson, S. Jones, M. K armirantzou, R. A. Laskowski, J. B. O. Mitchell, C. Taroni & J. M. Thornton "Protein Folds and Functions" Structure 6: 875-884 (1998).
20)F. Peelman, N. Vinaimont, A. Verhee, B. Vanloo, J.-L Verschelde, C. La beur, S. Seguret-Mace, N. Duverger, G. Hutchinson, J. Vanderkerckhove, J. Tavernier & M. Rosseneu "A proposed architecture for lecithin cholesterol acyl transferase (LCAT). Identification of the catalytic triad and molecular modelling" Protein Science 7: 587-599 (1998).
21)Salem, G., Hutchinson, E. G., Orengo, C. A. & Thornton, J. M. "Correlation of observed fold frequency with the occurrence of local structural motifs" J. Mol. Biol. 287,969-981 (1999).
22)Nagano, N., Hutchinson, E. G. & Thornton, J. M. "Barrel st ructures in proteins - Automatic identification and classification including a sequence analysis of TIM barrels" Protein Science 8, 2072-2084 (1999).
23)Bicknell, A. B., Lomthaisong, K., Woods, R. J., Hutchinson, E. G., Bennett, P. J., Gladwell, R. T. & Lowry, P. J., 'Characterisation of serine protease that cleaves pro-gamma melanotropin at the adrenal to stimulat growth" Cell 105, 903-912 (2001)
24)Ciani, B., Hutchinson, E. G.,, Sessions, R. B. & Woolfson, D. N. "Designing Alpha to Beta conformational transitions in peptides" J. Biol. Chem. 277 (12), 10150-10155 (2002)
25)de la Cruz, X., Hutchinson, E. G.,, Shepherd, A. D.& Thornton, J. M. "Towards predicting protein topology: An approach to identifying Beta-Hairpins" Proc. Natl. Acad Sci 99, 11157-11162 (2002)
26)Fooks, H. M., Martin, A. C. R., Woolfson, D. N., Sessions, R. B. &Hutchinson, E. G. "Amino Acid Pairing Preferences in Parallel Beta Sheets in Proteins" Journal of Molecular Biology 356, 32-44 (2006)

Return to top

Current Research Opportunities
Unless a specific job opportunity is advertised in this section, please contact Dr Gail Hutchinson at the address given below if you are interested in exploring the possibility of working within our research group:
Return to top

Contacts
Dr Gail Hutchinson
School of Animal and Microbial Sciences
University of Reading
Whiteknights
PO Box 228
Reading
Berks.
RG6 6AJ
Tel: -44-(0)118-987-5123 x7022
Fax: -44(0)118-931-0180
E-mail: E.G.Hutchinson@reading.ac.uk

Return to top
 

This page was created by Gail March 2001.