raffertyj

Dr John Rafferty

Reader in Structural Biology


Tel: 0114 222 2809
Email: j.rafferty@sheffield.ac.uk

Research

Research Precis

fig1My research interests centre on the structural study of proteins and DNA primarily by X-ray crystallography but also utilizing other biophysical techniques such as NMR, SAXS and electron microscopy. The work provides detailed 3-dimensional insights into biological macromolecules and their assemblies that can be combined with biochemical and genetic investigations to provide a better understanding of how they function.

Currently my work covers a number of areas and includes determining structural details of proteins involved in processing DNA Holliday junctions, of proteins from bacterial membranes & periplasm and of human kinase enzymes. In addition, I have a longstanding interest in the enzymes of fatty acid biosynthesis which has evolved to include the control of lipid production by cyanobacteria.

DNA metabolism

Drawing originally from work on E.coli DNA recombination protein RuvA and its DNA junction complex, my group has focussed on the cutting of the junction catalysed by various DNA sequence specific resolvase enzymes. This has led to the structures of the bacterial enzymes RusA, RecU and phage RuvC and their DNA complexes. In parallel with the crystallography, we have been examining their DNA bound structures in solution by small angle X-ray scattering (SAXS).
In a second area of DNA metabolism, my group has been investigating proteins that are critical to initiation of replication in Gram-positive organisms. These proteins form part of the large multi-subunit systems that permit the bacteria to establish and maintain the replication machinery.

Host-pathogen interface proteins

Recently we have carried out successful and exciting studies of proteins from the pathogen Campylobacter jejuni, which is the major cause of food poisoning worldwide. This work has seen structures determined for proteins from the bacterial periplasm responsible for metabolite transport, protein folding & establishment of the outer membrane and mechanisms for avoiding the host immune system. The work has been extended to examine proteins from the periplasm of other organisms such as Rhodopseudomonas palustris, which is of interest because of its potential biotechnological role in lignin processing.

Drug target kinases

Human kinase enzymes are major anti-cancer and anti-heart disease drug targets. I have ongoing collaborations with groups in the university medical school to study the structures of certain of these enzymes in complex with inhibitor molecules.

Research Keywords

Structural biology, X-ray crystallography, macromolecules, structure-function relationships

Teaching

Level 3 Modules

MBB344 Genomic Science
MBB362 Biochemistry Data Handling

Level 2 Modules

MBB261 Biochemistry 2
MBB265 Practical Molecular Bioscience 2
MBB266 Biostructures, Energetics and Synthesis

Level 1 Modules

MBB161 Biochemistry (Module Coordinator)
MBB165 Practical Molecular Bioscience 1

Career History

Career History

  • 2005 - present: Reader in Structural Biology, Mol.Biol.&Biotech.Dept, Sheffield Univ
  • 1999 - 2004: Royal Society Olga Kennard Fellow, Mol.Biol.&Biotech.Dept, Sheffield Univ
  • 1996 - 1999: BBSRC David Phillips Research Fellow, Mol.Biol.&Biotech.Dept, Sheffield Univ.
  • 1992 - 1996: PDRA, Mol.Biol. & Biotech. Dept, Sheffield Univ.
  • 1990 - 1991: PDRA, Biochem. & Mol.Biol. Dept, Leeds Univ.
  • 1989 - 1990: PDRA, Biophysics Dept, Leeds Univ.
  • 1986 - 1990: PhD, Biophysics Dept, Leeds Univ.








































Publications

Journal articles

Chapters

Conference proceedings papers

  • Roujeinikova A, Simon WJ, Gilroy J, Rice DW, Rafferty JB & Slabas AR (2007) Structures of fatty acyl-( acyl carrier protein) thioesters reveal a binding cavity that expands to fit longer substrates. FEBS JOURNAL, Vol. 274 (pp 223-223) RIS download Bibtex download
  • Bailey S, Abdelghany HM, Sedelnikova SE, Blackburn GM, Baker PJ, Rafferty JB & McLennan AG (2002) Crystal structure and mutational analysis of the diadenosine tetraphosphate (Ap4A) 'Nudix' hydrolase from Caenorhabditis elegans. DRUG DEVELOPMENT RESEARCH, Vol. 56(4) (pp 567-567) RIS download Bibtex download
  • Slabas AR, Hanley ZAC, Schierer TED, Rice D, Turnbull A, Rafferty J, Simon B & Brown A (2001) Acyltransferases and their role in the biosynthesis of lipids - opportunities for new oils. Journal of Plant Physiology, Vol. 158(4) (pp 505-513) RIS download Bibtex download