Dr John Rafferty

School of Biosciences

Reader in Structural Biology

Principal Admissions Tutor

j.rafferty@sheffield.ac.uk
+44 114 222 2809

Firth Court

Full contact details

Dr John Rafferty
School of Biosciences
Firth Court
Western Bank
Sheffield
S10 2TN

Profile

Career history

2005 - present: Reader in Structural Biology, School of Biosciences, 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.

Research interests

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.

The structure of MatC, with its helices and strands shown as cartoon coils and arrows, and a bound D-malate substrate, shown in stick form.

The protein has a hinged “Venus-flytrap-like” structure, with a cleft where the substrate is coordinated, separating two globular domains (the helices and strands for the first domain are shown in cyan and magenta and for the second domain in red and orange). (Rosa et al. (2019) J. Mol. Biol. 431, 351-367)

DNA & 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.

Publications

Show: Featured publications All publications

Featured publications

Journal articles

Phansopa C, Roy S, Rafferty JB, Douglas CWI, Pandhal J, Wright PC, Kelly DJ & Stafford GP (2014) Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species.. Biochem J, 458(3), 499-511. View this article in WRRO
Green V, Curtis FA, Sedelnikova S, Rafferty JB & Sharples GJ (2013) Mutants of phage bIL67 RuvC with enhanced Holliday junction binding selectivity and resolution symmetry.. Mol Microbiol, 89(6), 1240-1258. View this article in WRRO
Afonso JP, Chintakayala K, Suwannachart C, Sedelnikova S, Giles K, Hoyes JB, Soultanas P, Rafferty JB & Oldham NJ (2013) Insights into the structure and assembly of the Bacillus subtilis clamp-loader complex and its interaction with the replicative helicase.. Nucleic Acids Res, 41(9), 5115-5126. View this article in WRRO
Salmon RC, Cliff MJ, Rafferty JB & Kelly DJ (2013) The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates.. PLoS One, 8(3), e59844. View this article in WRRO
Canas C, Carrasco B, Garcia-Tirado E, Rafferty JB, Alonso JC & Ayora S (2011) The Stalk Region of the RecU Resolvase Is Essential for Holliday Junction Recognition and Distortion. J MOL BIOL, 410(1), 39-49.
Kale A, Phansopa C, Suwannachart C, Craven CJ, Rafferty JB & Kelly DJ (2011) The virulence factor PEB4 (Cj0596) and the periplasmic protein Cj1289 are two structurally related SurA-like chaperones in the human pathogen Campylobacter jejuni.. J Biol Chem, 286(24), 21254-21265.
Roujeinikova A, Simon WJ, Gilroy J, Rice DW, Rafferty JB & Slabas AR (2007) Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates.. J Mol Biol, 365(1), 135-145.
Macmaster R, Sedelnikova S, Baker PJ, Bolt EL, Lloyd RG & Rafferty JB (2006) RusA Holliday junction resolvase: DNA complex structure--insights into selectivity and specificity.. Nucleic Acids Res, 34(19), 5577-5584. View this article in WRRO
Thaw P, Sedelnikova SE, Muranova T, Wiese S, Ayora S, Alonso JC, Brinkman AB, Akerboom J, van der Oost J & Rafferty JB (2006) Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.. Nucleic Acids Res, 34(5), 1439-1449. View this article in WRRO
Rafferty JB, Bolt EL, Muranova TA, Sedelnikova SE, Leonard P, Pasquo A, Baker PJ, Rice DW, Sharples GJ & Lloyd RG (2003) The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold.. Structure, 11(12), 1557-1567.
Kehoe LE, Snidwongse J, Courvalin P, Rafferty JB & Murray IA (2003) Structural basis of Synercid (quinupristin-dalfopristin) resistance in Gram-positive bacterial pathogens.. J Biol Chem, 278(32), 29963-29970.
Bailey S, Sedelnikova SE, Mesa P, Ayora S, Waltho JP, Ashcroft AE, Baron AJ, Alonso JC & Rafferty JB (2003) Structural analysis of Bacillus subtilis SPP1 phage helicase loader protein G39P.. J Biol Chem, 278(17), 15304-15312.
Abdelghany HM, Bailey S, Blackburn GM, Rafferty JB & McLennan AG (2003) Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis. J BIOL CHEM, 278(7), 4435-4439.

All publications

Journal articles

Alrafaie AM, Pyrzanowska K, Smith EM, Partridge DG, Rafferty J, Mesnage S, Shepherd J & Stafford GP (2024) A diverse set of Enterococcus-infecting phage provides insight into phage host-range determinants. Virus Research, 347, 199426-199426.
Curry E, Sedelnikova S, Rafferty J, Hulley M, Pohle M, Muir G & Brown A (2024) Expanding the RNA polymerase biocatalyst solution space for mRNA manufacture. Biotechnology Journal, 19(6).
Bennison DJ, Nakamoto JA, Craggs TD, Milón P, Rafferty JB & Corrigan RM (2021) The stringent response inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions. mBio.
Churchill-Angus AM, Schofield THB, Marlow TR, Sedelnikova SE, Wilson JS, Rafferty JB & Baker PJ (2021) Characterisation of a tripartite α-pore forming toxin from Serratia marcescens. Scientific Reports, 11(1).
Wilson JS, Churchill-Angus AM, Davies SP, Sedelnikova SE, Tzokov SB, Rafferty JB, Bullough PA, Bisson C & Baker PJ (2019) Identification and structural analysis of the tripartite α-pore forming toxin of Aeromonas hydrophila. Nature Communications, 10(1). View this article in WRRO
Ji S, Dix SR, Aziz AA, Sedelnikova SE, Baker PJ, Rafferty JB, Bullough PA, Tzokov SB, Agirre J, Li F-L & Rice DW (2019) The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PL39. Journal of Biological Chemistry, 294(48), 18077-18091.
Rosa LT, Dix SR, Rafferty JB & Kelly DJ (2019) A New Mechanism for High-Affinity Uptake of C4-Dicarboxylates in Bacteria Revealed by the Structure of Rhodopseudomonas palustris MatC (RPA3494), a Periplasmic Binding Protein of the Tripartite Tricarboxylate Transporter (TTT) Family. Journal of Molecular Biology, 431(2), 351-367.
Rosa LT, Dix SR, Rafferty JB & Kelly DJ (2017) Structural basis for high-affinity adipate binding to AdpC (RPA4515), an orphan periplasmic-binding protein from the tripartite tricarboxylate transporter (TTT) family in Rhodopseudomonas palustris. FEBS Journal. View this article in WRRO
Khavnekar S, Dantu SC, Sedelnikova S, Ayora S, Rafferty J & Kale A (2017) Structural insights into dynamics of RecU–HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state. Nucleic Acids Research, 45(2), 975-986. View this article in WRRO
AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR & Artymiuk PA (2016) Direct observation of DNA threading in flap endonuclease complexes. Nature Structural and Molecular Biology, 23, 640-646. View this article in WRRO
Phansopa C, Roy S, Rafferty JB, Douglas CWI, Pandhal J, Wright PC, Kelly DJ & Stafford GP (2014) Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species.. Biochem J, 458(3), 499-511. View this article in WRRO
Green V, Curtis FA, Sedelnikova S, Rafferty JB & Sharples GJ (2013) Mutants of phage bIL67 RuvC with enhanced Holliday junction binding selectivity and resolution symmetry.. Mol Microbiol, 89(6), 1240-1258. View this article in WRRO
Afonso JP, Chintakayala K, Suwannachart C, Sedelnikova S, Giles K, Hoyes JB, Soultanas P, Rafferty JB & Oldham NJ (2013) Insights into the structure and assembly of the Bacillus subtilis clamp-loader complex and its interaction with the replicative helicase.. Nucleic Acids Res, 41(9), 5115-5126. View this article in WRRO
Salmon RC, Cliff MJ, Rafferty JB & Kelly DJ (2013) The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates.. PLoS One, 8(3), e59844. View this article in WRRO
Abd Aziz AG, Sedelnikova SE, Ruzheinikov SN, Thorpe S, Mohamed R, Nathan S, Rafferty JB, Baker PJ & Rice DW (2012) Crystallization and preliminary X-ray analysis of the receiver domain of a putative response regulator, BPSL0128, from Burkholderia pseudomallei.. Acta Crystallogr Sect F Struct Biol Cryst Commun, 68(Pt 8), 917-922.
Canas C, Carrasco B, Garcia-Tirado E, Rafferty JB, Alonso JC & Ayora S (2011) The Stalk Region of the RecU Resolvase Is Essential for Holliday Junction Recognition and Distortion. J MOL BIOL, 410(1), 39-49.
Kale A, Phansopa C, Suwannachart C, Craven CJ, Rafferty JB & Kelly DJ (2011) The virulence factor PEB4 (Cj0596) and the periplasmic protein Cj1289 are two structurally related SurA-like chaperones in the human pathogen Campylobacter jejuni.. J Biol Chem, 286(24), 21254-21265.
Fahy E, Carroll J, Rafferty J, Roantree V, Reid C, Norman M & Clarke S (2011) OBSERVATIONS ON THE LOCAL DISTRIBUTION, BIOLOGY AND ECOLOGY OF PALOURDE TAPES DECUSSATUS (L.) OF RELEVANCE TO ITS EXPLOITATION IN THE REPUBLIC OF IRELAND. Biology & Environment: Proceedings of the Royal Irish Academy, 110(2), 95-108.
Muench SP, Prigge ST, McLeod R, Rafferty JB, Kirisits MJ, Roberts CW, Mui EJ & Rice DW (2007) Studies of Toxoplasma gondii and Plasmodium falciparum enoyl acyl carrier protein reductase and implications for the development of antiparasitic agents.. Acta Crystallogr D Biol Crystallogr, 63(Pt 3), 328-338. View this article in WRRO
Roujeinikova A, Simon WJ, Gilroy J, Rice DW, Rafferty JB & Slabas AR (2007) Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates.. J Mol Biol, 365(1), 135-145.
Macmaster R, Sedelnikova S, Baker PJ, Bolt EL, Lloyd RG & Rafferty JB (2006) RusA Holliday junction resolvase: DNA complex structure--insights into selectivity and specificity.. Nucleic Acids Res, 34(19), 5577-5584. View this article in WRRO
Thaw P, Sedelnikova SE, Muranova T, Wiese S, Ayora S, Alonso JC, Brinkman AB, Akerboom J, van der Oost J & Rafferty JB (2006) Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.. Nucleic Acids Res, 34(5), 1439-1449. View this article in WRRO
McGregor N, Ayora S, Sedelnikova S, Carrasco B, Alonso JC, Thaw P & Rafferty J (2005) The Structure of Bacillus subtilis RecU Holliday Junction Resolvase and Its Role in Substrate Selection and Sequence-Specific Cleavage. Structure, 13(9), 1341-1351.
Dickman MJ, Sedelnikova SE, Rafferty JB & Hornby DP (2004) Rapid analysis of protein-nucleic acid complexes using MALDI TOF mass spectrometry and ion pair reverse phase liquid chromatography.. J Biochem Biophys Methods, 58(1), 39-48.
Rafferty JB, Bolt EL, Muranova TA, Sedelnikova SE, Leonard P, Pasquo A, Baker PJ, Rice DW, Sharples GJ & Lloyd RG (2003) The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold.. Structure, 11(12), 1557-1567.
Muranova TA, Sedelnikova SE, Leonard PM, Pasquo A, Bolt EL, Lloyd RG & Rafferty JB (2003) Crystallization of RusA Holliday junction resolvase from Escherichia coli.. Acta Crystallogr D Biol Crystallogr, 59(Pt 12), 2262-2264.
Santos-Sierra S, Lemonnier M, Nuñez B, Hargreaves D, Rafferty J, Giraldo R, Andreu JM & Dı́az-Orejas R (2003) Non-cytotoxic variants of the Kid protein that retain their auto-regulatory activity. Plasmid, 50(2), 120-130.
Kehoe LE, Snidwongse J, Courvalin P, Rafferty JB & Murray IA (2003) Structural basis of Synercid (quinupristin-dalfopristin) resistance in Gram-positive bacterial pathogens.. J Biol Chem, 278(32), 29963-29970.
Muench SP, Rafferty JB, McLeod R, Rice DW & Prigge ST (2003) Expression, purification and crystallization of the Plasmodium falciparum enoyl reductase.. Acta Crystallogr D Biol Crystallogr, 59(Pt 7), 1246-1248.
Bailey S, Sedelnikova SE, Mesa P, Ayora S, Alonso JC & Rafferty JB (2003) Crystallization of the Bacillus subtilis SPP1 bacteriophage helicase loader protein G39P.. Acta Crystallogr D Biol Crystallogr, 59(Pt 6), 1090-1092.
Bailey S, Sedelnikova SE, Mesa P, Ayora S, Waltho JP, Ashcroft AE, Baron AJ, Alonso JC & Rafferty JB (2003) Structural analysis of Bacillus subtilis SPP1 phage helicase loader protein G39P.. J Biol Chem, 278(17), 15304-15312.
Abdelghany HM, Bailey S, Blackburn GM, Rafferty JB & McLennan AG (2003) Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis. J BIOL CHEM, 278(7), 4435-4439.
Slabas AR, Kroon JTM, Scheirer TP, Gilroy JS, Hayman M, Rice DW, Turnbull AP, Rafferty JB, Fawcett T & Simon WJ (2002) Squash glycerol-3-phosphate (1)-acyltransferase - Alteration of substrate selectivity and identification of arginine and lysine residues important in catalytic activity. J BIOL CHEM, 277(46), 43918-43923.
Dickman MJ, Ingleston SM, Sedelnikova SE, Rafferty JB, Lloyd RG, Grasby JA & Hornby DP (2002) The RuvABC resolvasome.. Eur J Biochem, 269(22), 5492-5501.
Ettema TJG, Brinkman AB, Tani TH, Rafferty JB & van der Oost J (2002) A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes. J BIOL CHEM, 277(40), 37464-37468.
Hargreaves D, Santos-Sierra S, Giraldo R, Sabariegos-Jareño R, de la Cueva-Méndez G, Boelens R, Díaz-Orejas R & Rafferty JB (2002) Structural and functional analysis of the kid toxin protein from E. coli plasmid R1.. Structure, 10(10), 1425-1433.
Roujeinikova A, Baldock C, Simon WJ, Gilroy J, Baker PJ, Stuitje AR, Rice DW, Slabas AR & Rafferty JB (2002) X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site.. Structure, 10(6), 825-835.
Bailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, Baker PJ, McLennan AG & Rafferty JB (2002) The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms.. Structure, 10(4), 589-600.
Bailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, McLennan AG & Rafferty JB (2002) Crystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and a non-hydrolysable substrate analogue, AppCH2ppA.. Acta Crystallogr D Biol Crystallogr, 58(Pt 3), 526-528.
Roujeinikova A, Baldock C, Simon WJ, Gilroy J, Baker PJ, Stuitje AR, Rice DW, Rafferty JB & Slabas AR (2002) Crystallization and preliminary X-ray crystallographic studies on acyl-(acyl carrier protein) from Escherichia coli.. Acta Crystallogr D Biol Crystallogr, 58(Pt 2), 330-332.
Hargreaves D, Giraldo R, Santos-Sierra S, Boelens R, Rice DW, Díaz Orejas R & Rafferty JB (2002) Crystallization and preliminary X-ray crystallographic studies on the parD-encoded protein Kid from Escherichia coli plasmid R1.. Acta Crystallogr D Biol Crystallogr, 58(Pt 2), 355-358.
Abdelghany HM, Gasmi L, Cartwright JL, Bailey S, Rafferty JB & McLennan AG (2001) Cloning, characterisation and crystallisation of a diadenosine 5 ',5 '''-P-1,P-4-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans. BBA-PROTEIN STRUCT M, 1550(1), 27-36.
Showell C, Rafferty JB & Cunliffe VT (2001) Functional studies of the Xenopus Polycomb-group proteins Xeed and XEz.. DEV BIOL, 235(1), 262-263.
Sedelnikova SE, Smits SH, Leonard PM, Brinkman AB, van der Oost J, Rafferty JB & Rice DW (2001) Crystallization and quaternary structure analysis of an Lrp-like regulatory protein from the hyperthermophile Pyrococcus furiosus.. Acta Crystallogr D Biol Crystallogr, 57(Pt 6), 886-888.
Levy CW, Baldock C, Wallace AJ, Sedelnikova S, Viner RC, Clough JM, Stuitje AR, Slabas AR, Rice DW & Rafferty JB (2001) A study of the structure-activity relationship for diazaborine inhibition of Escherichia coli enoyl-ACP reductase.. J Mol Biol, 309(1), 171-180.
Turnbull AP, Rafferty JB, Sedelnikova SE, Slabas AR, Schierer TP, Kroon JT, Simon JW, Fawcett T, Nishida I, Murata N & Rice DW (2001) Analysis of the structure, substrate specificity, and mechanism of squash glycerol-3-phosphate (1)-acyltransferase.. Structure, 9(5), 347-353.
Turnbull AP, Rafferty JB, Sedelnikova SE, Slabas AR, Schierer TP, Kroon JT, Nishida I, Murata N, Simon JW & Rice DW (2001) Crystallization and preliminary X-ray analysis of the glycerol-3-phosphate 1-acyltransferase from squash (Cucurbita moschata).. Acta Crystallogr D Biol Crystallogr, 57(Pt 3), 451-453.
Leonard PM, Smits SH, Sedelnikova SE, Brinkman AB, de Vos WM, van der Oost J, Rice DW & Rafferty JB (2001) Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus.. EMBO J, 20(5), 990-997.
McLeod R, Muench SP, Rafferty JB, Kyle DE, Mui EJ, Kirisits MJ, Mack DG, Roberts CW, Samuel BU, Lyons RE , Dorris M et al (2001) Triclosan inhibits the growth of Plasmodium falciparum and Toxoplasma gondii by inhibition of apicomplexan Fab I. INT J PARASITOL, 31(2), 109-113.
Slabas AR, Simon WR, Schierer T, Kroon J, Fawcett T, Hayman M, Gilroy J, Nishida I, Murata N, Rafferty J , Turnbull A et al (2000) Plant glycerol-3-phosphate-l-acyltransferase (GPAT): structure selectivity studies. Biochemical Society Transactions, 28(6), 677-679.
Hayman MW, Fawcett T, Schierer TF, Simon JW, Kroon JTM, Gilroy JS, Rice DW, Rafferty J, Turnbull AP, Sedelnikova SE & Slabas AR (2000) Mutagenesis of squash (Cucurbita moschata) glycerol-3-phosphate acyltransferase (GPAT) to produce an enzyme with altered substrate selectivity. Biochemical Society Transactions, 28(6), 680-681.
Hayman MW, Fawcett T, Schierer TF, Simon JW, Kroon JTM, Gilroy JS, Rice DW, Rafferty J, Turnbull AP, Sedelnikova SE & Slabas AR (2000) Mutagenesis of squash (Cucurbita moschata) glycerol-3-phosphate acyltransferase (GPAT) to produce an enzyme with altered substrate selectivity. Biochemical Society Transactions, 28(6), 680-680.
Slabas AR, Simon WR, Schierer T, Kroon J, Fawcett T, Hayman M, Gilroy J, Nishida I, Murata N, Rafferty J , Turnbull A et al (2000) Plant glycerol-3-phosphate-1-acyltransferase (GPAT): structure selectivity studies. Biochemical Society Transactions, 28(6), 677-677.
Fisher M, Kroon JT, Martindale W, Stuitje AR, Slabas AR & Rafferty JB (2000) The X-ray structure of Brassica napus beta-keto acyl carrier protein reductase and its implications for substrate binding and catalysis.. Structure, 8(4), 339-347.
Fisher M, Sedelnikova SE, Martindale W, Thomas NC, Simon JW, Slabas AR & Rafferty JB (2000) Crystallization of the NADP-dependent beta-keto acyl-carrier protein reductase from Brassica napus.. Acta Crystallogr D Biol Crystallogr, 56(Pt 1), 86-88.
Roujeinikova A, Levy CW, Rowsell S, Sedelnikova S, Baker PJ, Minshull CA, Mistry A, Colls JG, Camble R, Stuitje AR , Slabas AR et al (1999) Crystallographic analysis of triclosan bound to enoyl reductase.. J Mol Biol, 294(2), 527-535.
Roujeinikova A, Sedelnikova S, de Boer GJ, Stuitje AR, Slabas AR, Rafferty JB & Rice DW (1999) Inhibitor binding studies on enoyl reductase reveal conformational changes related to substrate recognition.. J Biol Chem, 274(43), 30811-30817.
Levy CW, Roujeinikova A, Sedelnikova S, Baker PJ, Stuitje AR, Slabas AR, Rice DW & Rafferty JB (1999) Molecular basis of triclosan activity. NATURE, 398(6726), 383-384.
de Boer GJ, Pielage GJA, Nijkamp HJJ, Slabas AR, Rafferty JB, Baldock C, Rice DW & Stuitje AR (1999) Molecular genetic analysis of enoyl-acyl carrier protein reductase inhibition by diazaborine. MOL MICROBIOL, 31(2), 443-450.
Hargreaves D, Rafferty JB, Sedelnikova SE, Lloyd RG & Rice DW (1999) Crystallization of Escherichia coli RuvA complexed with a synthetic Holliday junction.. Acta Crystallogr D Biol Crystallogr, 55(Pt 1), 263-265.
Baldock C, Rafferty JB, Stuitje AR, Slabas AR & Rice DW (1998) The X-ray structure of Escherichia coli enoyl reductase with bound NAD+ at 2.1 A resolution.. J Mol Biol, 284(5), 1529-1546.
Hargreaves D, Rice DW, Sedelnikova SE, Artymiuk PJ, Lloyd RG & Rafferty JB (1998) Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.. Nat Struct Biol, 5(6), 441-446.
Baldock C, de Boer GJ, Rafferty JB, Stuitje AR & Rice DW (1998) Mechanism of action of diazaborines.. Biochem Pharmacol, 55(10), 1541-1549.
Rafferty JB, Fisher M, Langridge SJ, Martindale W, Thomas NC, Simon JW, Bithell S, Slabas AR & Rice DW (1998) Crystallization of the NADP-dependent beta-keto acyl carrier protein reductase from Escherichia coli.. Acta Crystallogr D Biol Crystallogr, 54(Pt 3), 427-429.
Rafferty JB, Ingleston SM, Hargreaves D, Artymiuk PJ, Sharples GJ, Lloyd RG & Rice DW (1998) Structural similarities between Escherichia coli RuvA protein and other DNA-binding proteins and a mutational analysis of its binding to the holliday junction.. J Mol Biol, 278(1), 105-116.
Rice DW, Rafferty JB, Artymiuk PJ & Lloyd RG (1997) Insights into the mechanisms of homologous recombination from the structure of RuvA.. Curr Opin Struct Biol, 7(6), 798-803.
Sedelnikova SE, Rafferty JB, Hargreaves D, Mahdi AA, Lloyd RG & Rice DW (1997) Crystallization of E. coli RuvA gives insights into the symmetry of a Holliday junction/protein complex.. Acta Crystallogr D Biol Crystallogr, 53(Pt 1), 122-124.
Baldock C, Rafferty JB, Sedelnikova SE, Baker PJ, Stuitje AR, Slabas AR, Hawkes TR & Rice DW (1996) A mechanism of drug action revealed by structural studies of enoyl reductase.. Science, 274(5295), 2107-2110.
Slabas AR, Brown AP, Rafferty JB, Rice DW, Baldock C, Kroon JTM, Simon W, Stuitje AR & Brough CL (1996) Soluble and membrane bound components of plant lipid synthesis. CR ACAD SCI III-VIE, 319(11), 1043-1047.
Baldock C, Rafferty JB, Sedelnikova SE, Bithell S, Stuitje AR, Slabas AR & Rice DW (1996) Crystallization of Escherichia coli enoyl reductase and its complex with diazaborine.. Acta Crystallogr D Biol Crystallogr, 52(Pt 6), 1181-1184.
Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG & Rice DW (1996) Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction.. Science, 274(5286), 415-421.
Rafferty JB, Simon JW, Baldock C, Artymiuk PJ, Baker PJ, Stuitje AR, Slabas AR & Rice DW (1995) Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase.. Structure, 3(9), 927-938.
SOMERS WS, RAFFERTY JB, PHILLIPS K, STRATHDEE S, HE Y-Y, McNALLY T, MANFIELD I, NAVRATIL O, OLD IG, SAINT-GIRONS I , STOCKLEY PG et al (1994) The Met Repressor-Operator Complex: DNA Recognition by ?-Strands. Annals of the New York Academy of Sciences, 726(1 DNA Damage), 105-117.
Rafferty JB, Simon JW, Stuitje AR, Slabas AR, Fawcett T & Rice DW (1994) Crystallization of the NADH-specific enoyl acyl carrier protein reductase from Brassica napus.. J Mol Biol, 237(2), 240-242.
Wright CE, Raffertya JB, Flower DR, Groom CR, Findlay JBC, North ACT, Phillips SEV & Zagalsky PF (1992) Crystallization and initial X-ray analysis of the C2-subunit of crustacyanin. Journal of Molecular Biology, 224(1), 283-284.
Phillips SEV, Manfield I, Parsons I, Davidson BE, Rafferty JB, Somers WS, Margarita D, Cohen GN, Saint-Girons I & Stockley PG (1989) Cooperative tandem binding of met repressor of Escherichia coli. Nature, 341(6244), 711-715.
Rafferty JB, Somers WS, Saint-Girons I & Phillips SEV (1989) Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor. Nature, 341(6244), 705-710.
Rafferty JB, Phillips SEV, Rojas C, Boulot G, Saint-girons I, Guillou Y & Cohen GN (1988) Crystallization of the met repressor from Escherichia coli. Journal of Molecular Biology, 200(1), 217-219.
Kaushik A, Than T, Petela NJ, Voulgaris M, Percival C, Daniels P, Rafferty JB, Nasmyth KA & Hu B () Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding. Nature Communications, 14(1).
Satur MJ, Urbanowicz P, Spencer DR, Rafferty JB & Stafford GP () Structural and functional characterisation of a stable, broad-specificity multimeric sialidase from the oral pathogen Tannerella forsythia. Biochemical Journal.
Bisson C, Salmon RC, West L, Rafferty JB, Hitchcock A, Thomas GH & Kelly DJ () The structural basis for high‐affinity uptake of lignin‐derived aromatic compounds by proteobacterial TRAP transporters. The FEBS Journal.

Chapters

Brown AP, Slabas AR & Rafferty JB (2009) Fatty Acid Biosynthesis in Plants — Metabolic Pathways, Structure and Organization, Lipids in Photosynthesis (pp. 11-34). Springer Netherlands
Simon JW, Gilroy J, Roujenikova A, Rafferty J, Baldock C, Baker PJ, Rice DW, Stuitje AR & Slabas AR (2003) Determination of the X-Ray Crystallographic Structure of E.coli Butyryl-ACP, Advanced Research on Plant Lipids (pp. 139-142). Springer Netherlands
Slabas AR, Rafferty J, Rice D, Baldock C, Simon JW, Thomas N, Bithell S & Stuitje AR (1997) Structural Studies on Plant and Bacterial Reductases Involved in Lipid Biosynthesis, Physiology, Biochemistry and Molecular Biology of Plant Lipids (pp. 38-41). Springer Netherlands
Slabas AR, Brough C, Kroon J, Simon W, Swinhoe R, Rice D, Rafferty J, Winz R, Stuitjet AR & Elborough K (1995) Towards a Structural Understanding of Enzymes of Lipid Biosynthesis, Plant Lipid Metabolism (pp. 55-57). Springer Netherlands

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)
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)
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)
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)

Preprints

Curry E, Sedelnikova S, Rafferty J, Hulley M & Brown A (2024) Expanding the RNA polymerase biocatalyst solution space for mRNA manufacture, Cold Spring Harbor Laboratory.
Hu B, Kaushik A, Than T, Petela N, Voulgaris M, Percival C, Daniels P, Rafferty J & Nasmyth K (2022) Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding, Research Square Platform LLC.
Kaushik A, Than T, Petela NJ, Voulgaris M, Percival C, Daniels P, Rafferty JB, Nasmyth KA & Hu B (2022) Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding, Cold Spring Harbor Laboratory.
Bennison DJ, Nakamoto JA, Craggs TD, Milón P, Rafferty JB & Corrigan RM () (p)ppGpp inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions, Cold Spring Harbor Laboratory.

Teaching activities

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