raffertyj

Dr John Rafferty

Reader in Structural Biology
Principal Admissions Tutor


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

Research

Research Precis

My research interests centre on structural studies of proteins and nucleic acids 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 research includes determining structural details of proteins involved in DNA or RNA binding; proteins from bacterial membrane transport systems; toxin & antitoxin proteins; and glycosidic enzymes.

MatCDNA & RNA metabolism

Drawing originally from work on E.coli DNA recombination protein RuvA and its DNA junction complex, my group has focussed on the recognition and processing of junction points in DNA. The work has involved studies of proteins from a diverse range of bacterial and viral sources. It has also expanded into structural studies of RNA binding proteins from bacterial pathogens and simple eukaryotes that regulate the assembly of the ribosome. In parallel with the crystallography, we have examined the solution structures by SAXS.

Host-pathogen interactions

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 across the inner membrane, 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.

Glycoside recognition and processing

The carbohydrate coat on many cells provides both a protective role but also a nutrient source for invading organisms. We have been studying the structural determinants that control the way key enzymes and associated binding domains recognize specific targets and process them. These proteins in pathogenic organisms provide potentially excellent targets for inhibition and the development of antibacterial compounds.

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

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
  • Fisher M, Martindale W, Slabas AR, Rice DW & Rafferty JB (1999) CRYSTALLOGRAPHIC STUDIES OF THE NADP-DEPENDENT beta-KETO ACP REDUCTASE FROM ESCHERICHIA COLI. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, Vol. 55 (pp 293-294) RIS download Bibtex download