Protein Crystallography and Bioinformatics

Prof P J Artymiuk

Sheffield 222 4190
P.Artymiuk@sheffield.ac.uk

Career History

My laboratory works on both experimental and theoretical aspects of macromolecular structure analysis:

X-ray crystallography is used experimentally to determine macromolecular structures and to study the relationship between structure and function in proteins of biological and medical interest. Projects underway include the DNA-binding flap endonuclease enzymes and members of a novel family of pore-forming toxins from E. coli and Bacillus cereus. The structure of the E. coli toxin hemolysin E revealed the molecular architecture of a new family of toxins and suggested a novel mode of membrane interaction. Recently collaborations on therapeutic macromolecules (see below) have led to the first structure determination of the leptin binding domain of the human obesity receptor (Figure 1) which is important in energy homeostasis and in regulation of the immune system.

Figure 1. Leptin binding domain (LBD) of the human obesity receptor. Our crystal structure reveals the interaction of the LBD with the Fab fragment of a neutralizing antibody. (A) Overview of the structure which contains two LBD domains (one in blue and the other in purple) and two antibody Fab fragments (yellow and green). (B) Atomic detail of interactions between LBD and the antibody (yellow). (C) The binding of the antibody (yellow and green) to the LBD (blue) partially blocks the predicted binding site of the hormone leptin (pink).

Therapeutic biomolecules with enhanced characteristics. Protein molecules are now used therapeutically in medicine but many of these molecules are cleared from the circulation by the kidneys or by proteolysis within hours or minutes of administration. In collaboration with scientists in the University of Sheffield Medical School , our start-up company Asterion Ltd has been developing methods to extend the lifetimes in the circulation of a variety of therapeutic biomolecules including cyrokine hormones such as human growth hormone, erythropoietin and GCSF (see www.asterion.co.uk).

Bioinformatics and theoretical techniques. There is a vast amount of information now available on biological macromolecules. This information can only be exploited to its full potential if methods are developed to help detect and clarify the complex relationships between these molecules. In collaboration with the Information Studies School at Sheffied University, we are developing algorithms to: (a) compare the 3-dimensional folds of protein structures; (b) identify patterns of sidechains; (c) investigate the rapidly expanding database of complex RNA 3-dimensional structures; and (d) devise new methods for representing protein surfaces. With collaborators at the Universiti Kebangsaan Malaysia we have recently produced novel web servers (www.grafss.org) for searching for patterns in proteins (Figure 2A) and nucleic acids (Figure 2B.)

Figure 2. 3D searching of protein and RNA molecules. (A) An unusual amino acid side chain motif consisting of two arginines and two glutamates found in two different proteins (a sucrose specific porin shown with green and black carbons, and a DNA polymerase with cyan and white carbons) found using our ASSAM server. (B) Use of NASSAM to identify GRNA tetraloop structures in the 23S rRNA chain of the Haloarcula marismortui large ribosomal subunit.

Selected Publications

Structure of the NheA component of the Nhe toxin from Bacillus cereus: implications for function. M. Ganash, D. Phung, S. Sedelnikova, T. Lindbäck, P.E. Granum and P.J.Artymiuk. PLoS One (in press)
Novel metal-binding sites in E. coli ExoIX – implications for DNA binding and catalysis in flap endonucleases. C.S. Anstey-Gilbert, G.R. Hemsworth, C.S. Flemming, M.R.G. Hodskinson, S.E. Sedelnikova, T.J. Stillman, J.R. Sayers and P.J. Artymiuk. Nucleic Acids Research doi:10.1093/nar/gkt591
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. N. Nadzirin, P. Willett, P.J. Artymiuk & M. Firdaus-Raih. Nucleic Acids Research 41: W432-W440 (2013) doi:10.1093/nar/gkt431
Structure-function dissection of the Frizzled receptor in Drosophila melanogaster suggests different mechanisms of action in planar polarity and canonical Wnt signaling. D. Strutt, D. Madder, V. Chaudhary, P.J. Artymiuk. Genetics 192: 1295-1313 (2012)
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. H.Y. Hamdani, S.D. Appasamy, P. Willett, P.J. Artymiuk & M. Firdaus-Raih. Nucleic Acids Research 40: W35-W41 doi: 10.1093/nar/gks513 (2012)
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures from the PDB. N. Nadzirin, E.J. Gardiner, P. Willett, P.J. Artymiuk & M. Firdaus-Raih. Nucleic Acids Research 40: W380-W386 doi: 10.1093/nar/gks401 (2012)
Structure of the leptin-binding domain of the human obesity receptor in complex with a neutralizing monoclonal antibody. B. Carpenter, G.R. Hemsworth, Z. Wu, M. Maamra, C.J. Strasburger, R.J. Ross & P.J. Artymiuk. Structure 20: 487-497 (2012)
Novel base triples in RNA structures revealed by graph theory. M. Firdaus-Raih, A.M. Harrison, P. Willett & P.J. Artymiuk. BMC Bioinformatics, 12(Suppl 13):S2 (2011)
A Burkholderia pseudomallei glutamine deamidase inhibits helicase activity of translation factor eIF4A. A. Cruz, G.M. Hautbergue, P.J. Artymiuk, P.J. Baker, M. Bokori-Brown, C.-T. Chang., M.J. Dickman., A. Essex-Lopresti, S.V. Harding, N.M. Mahadi, L.E. Marshall, G.W. Mobbs, R. Mohamed, S. Nathan, S.A. Ngugi, C. Ong, W.F. Ooi, L.J. Partridge, H.L. Phillips, M. Firdaus-Raih, S. Ruzhenikov, M. Sarkar-Tyson, S.E. Sedelnikova, S.J. Smither., P. Tan, R.W. Titball, S.A. Wilson & D.W. Rice. Science 334: 821-824 (2011)
Assessing the role of Asp 194 in the transmembrane domains of the α-chain of the high-affinity receptor complex for Immunoglobulin E in signal transduction. A. Rashid, M.W. Iodice, K.M. Carroll, J.E.M. Housden, P.J. Artymiuk, B.A. Helm. Molecular Immunology 48: 128-136 (2010)
Immunogenicity, toxicology, pharmacokinetics and pharmacodynamics of growth hormone ligand-receptor fusions. E Ferrandis, S.L. Pradhananga, C. Touvay, C. Kinoshita, I.R. Wilkinson, K. Stafford, Z. Wu, C.J. Strasburger, J.R. Sayers, P.J. Artymiuk, and R. J. Ross. Clinical Science 119: 483-491 (2010)
Mycobacterium tuberculosis cAMP receptor protein (Rv3676) differs from the Escherichia coli paradigm in its cAMP-binding, DNA-binding and transcription activation properties. M. Stapleton, I. Haq, D.M. Hunt, K.B. Arnvig, P.J. Artymiuk, R.S. Buxton, J. Green. J Biol Chem. 285:7016-7027(2009)
The O2 sensitivity of the transcription factor FNR is controlled by Ser24 modulating the kinetics of [4Fe-4S] to [2Fe-2S] conversion. A.J. Jervis, J.C. Crack, G. White, P.J. Artymiuk, M.R. Cheesman, A.J. Thomson, N.E. Le Brun, J. Green. Proc Natl Acad Sci USA. 106: 4659-64 (2009)
The formation and structure of Escherichia coli K-12 haemolysin E pores. S. Hunt, A.J. Moir, S. Tzokov, P.A. Bullough, P.J. Artymiuk, J. Green. Microbiology. 154: 633-42 (2008)
A ligand-receptor fusion of growth hormone forms a dimer and is a potent long-acting agonist. I.R. Wilkinson, E. Ferrandis, P.J. Artymiuk, M. Teillot, C. Soulard, C. Touvay, S.L. Pradhananga , S. Justice, Z. Wu, K.C. Leung, C.J. Strasburger, J.R. Sayers , R.J. Ross. Nature Medicine 13: 1108-13 (2007)
Structure of the hemolysin E (HlyE, ClyA, and SheA) channel in its membrane-bound form. S.B. Tzokov, N.R. Wyborn, T.J. Stillman, S. Jamieson, N. Czudnochowski, P.J. Artymiuk, J. Green, P.A. Bullough. J Biol Chem. 281:23042-9 (2006)
The double life of aconitase. P.J. Artymiuk, J. Green. Structure. 14: 2-4 (2006)
E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy. A.J. Wallace, T.J. Stillman, A. Atkins, S.J. Jamieson, P.A. Bullough, J. Green, & P.J. Artymiuk. Cell 100: 265-276 (2000)
Crystal structure of manganese catalase from Lactobacillus plantarum. V.V. Barynin, M.M. Whittaker, S.V. Antonyuk, V.S. Lamzin, P.M. Harrison, P.J. Artymiuk & J.W. Whittaker. Structure 9: 725-738 (2001)
E. coli aconitase B structure reveals a HEAT-like domain with implications for protein-protein recognition. C.H.Williams, T.J.Stillman, V.V.Barynin, S.E.Sedelnikova, Y.Tang, J.Green, J.R.Guest & P.J.Artymiuk. Nature Struct. Biol. 9: 447-452 (2002)
Interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of DNA binding. J.J.Dervan, M.Feng, D.Patel, J.A.Grasby, P.J.Artymiuk, C.A.Ceska and J.R.Sayers. Proc. Natl. Acad. Sci. USA 99: 8542-8547 (2002)
Protein Structures and Information Extraction from Biological Texts: The PASTA System. G.Demetriou, R.Gaizauskas, P.Artymiuk and P.Willett. Bioinformatics 19: 135-143 (2003)
GAPDOCK: A genetic algorithm approach to protein docking in Capri round 1. E.J.Gardiner, P.Willett and P.J.Artymiuk Proteins 53: 10-14 (2003)

For electronic links to publications, see HERE