Professor David Hornby
School of Biosciences
Professor of Biochemistry
d.hornby@sheffield.ac.uk
+44 114 222 4232
+44 114 222 4232
Firth Court
Full contact details
Professor David Hornby
School of Biosciences
Firth Court
Western Bank
Sheffield
S10 2TN
School of Biosciences
Firth Court
Western Bank
Sheffield
S10 2TN
- Profile
-
I started my research career interested in metabolic enzyme structure and function and along the way I have turned my attention to increasingly more complex enzymes and proteins, especially those involved in nucleic acid transactions.
This has led me to question the foundations of our understanding of enzyme catalysis.
My research currently involves a series of collaborations aimed at exploring the evolution of enzyme mechanism via random mutagenesis of several enzymes and proteins.
A more recent interest has arisen through collaboration with the Microbiology community at Sheffield and is the challenge of understanding the molecular basis of antibiotic resistance, in particular methicillin resistance.
Career history
- 2013 - 2015: Director of Innovation, Liverpool Life Sciences UTC
- 2012: Professor of Biochemistry Department of Molecular Biology and Biotechnology (on sabbatical leave at the Liverpool School of Tropical Medicine)
- 2007 - 2012: Head of the Department of Molecular Biology and Biotechnology
- 2008 - 2011: Director of Enterprise in Life Sciences
- 1999 - 2007: Professor of Biochemistry Department of Molecular Biology and Biotechnology
- 1999 - 2002: Director of the Transgenomic Research Laboratory
- 1998 - 1999: Reader Department of Molecular Biology and Biotechnology
- 1994 - 1998: Senior Lecturer Department of Molecular Biology and Biotechnology
- 1992 - 1993: Visiting Scientist Department Molecular Biology The Scripps Research Institute California
- 1990 - 1994: Lecturer Department of Molecular Biology and Biotechnology
- 1990: EMBO fellowship Gene Expression Program EMBL, Heidelberg
- 1986 - 1990: Lecturer Department of Biochemistry
- 1985 - 1986: Postdoctoral research associate Biozentrum der Universitat Basel, Switzerland
- 1984 - 1985: Postdoctoral research associate Departments of Biochemistry, Sheffield and Genetics, Leeds
- 1980 - 1984: PhD (Biochemistry) University of Sheffield
- Research interests
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DNA Modifying Enzymes: Cytosine-C5-specific DNA methyltransferases, in particular the monospecific enzyme, M.HhaI and the multi-specific enzyme M.SPRI. The aim is to identify essential residues involved in base flipping in the former and to determine the structural basis of multiple specificity in the latter.
RNA and DNA Polymerases present opportunities for developing a range of molecular biology methods and are in themselves key enzymes in cellular physiology. The former are of interest as targets for structure determination by new cryo-EM methods and the latter is a work horse for the development of in vitro mutagenesis methods in use in my lab.
Multi-enzyme complexes often contain components that are shared by other complexes. Using random mutagenesis methods, we are interested in the evolutionary pressures facing such promiscuous subunits, such as the E3 component of bacterial oxoacid dehydrogenases.
Enzymes are thought to bring substrates into precise alignment in order to stimulate product formation. Since many naturally occurring enzymes that catalyze the same reaction exhibit significant primary structural diversity, we are using random mutagenesis combined with screening and structural methods, to identify the sensitive and essential elements of primary structure in a range of enzyme catalyzed reactions and antibiotic resistance targets.
- Publications
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Show: Featured publications All publications
Featured publications
Journal articles
- Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions.. J Chromatogr A, 1216(9), 1377-1382.
All publications
Books
- RNA Purification and Analysis: Sample Preparation, Extraction, Chromatography. Wiley.
- DNA Chromatography. Wiley.
Journal articles
- Evolving MRSA : high-level β-lactam resistance in Staphylococcus aureus is associated with RNA Polymerase alterations and fine tuning of gene expression. PLoS Pathogens, 16(7). View this article in WRRO
- Charles McDonald 1953–2017. The Biochemist, 39(6), 51-51.
- Arginine methylation and citrullination of splicing factor proline- and glutamine-rich (SFPQ/PSF) regulates its association with mRNA. RNA, 21(3), 347-359. View this article in WRRO
- Affinity filtration coupled with capillary-based affinity purification for the isolation of protein complexes.. Anal Biochem, 439(1), 47-49.
- c-IAP1 binds and processes PCSK9 protein: linking the c-IAP1 in a TNF-α pathway to PCSK9-mediated LDLR degradation pathway.. Molecules, 17(10), 12086-12101. View this article in WRRO
- Quantum dot-conjugated anti-GRP78 scFv inhibits cancer growth in mice.. Molecules, 17(1), 796-808. View this article in WRRO
- Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions.. J Chromatogr A, 1216(9), 1377-1382.
- Enrichment and analysis of RNA centered on ion pair reverse phase methodology.. RNA, 12(4), 691-696.
- Micro-scale open-tube capillary separations of functional proteins. ANAL BIOCHEM, 350(1), 128-137.
- 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.
- Identification of nuclear protein complexes using open tube capillary chromatography. AIChE Annual Meeting, Conference Proceedings, 1917.
- Recognition of base-pairing by DNA polymerases during nucleotide incorporation: the properties of the mutagenic nucleotide dPTP alphaS.. Org Biomol Chem, 1(12), 2070-2074.
- A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.. Nucleic Acids Res, 31(7), 1805-1812.
- The effect of tautomeric constant on the specificity of nucleotide incorporation during DNA replication: support for the rare tautomer hypothesis of substitution mutagenesis.. J Mol Biol, 326(5), 1389-1401.
- The small subunit of M. AquI is responsible for sequence-specific DNA recognition and binding in the absence of the catalytic domain.. J Bacteriol, 185(4), 1284-1288.
- The RuvABC resolvasome.. Eur J Biochem, 269(22), 5492-5501.
- Use of fluorescent DNA-intercalating dyes in the analysis of DNA via ion-pair reversed-phase denaturing high-performance liquid chromatography.. Anal Biochem, 309(2), 248-252.
- An analytical method for the detection of methylation differences at specific chromosomal loci using primer extension and ion pair reverse phase HPLC.. Hum Mutat, 20(4), 305-311.
- Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.. J Mol Biol, 321(4), 591-599.
- Recombinant alpha and beta subunits of M.AquI constitute an active DNA methyltransferase.. J Biochem Mol Biol, 35(3), 348-351.
- Multidimensional differential display via ion-pair reversed-phase denaturing high-performance liquid chromatography.. Anal Biochem, 304(1), 47-54.
- Holliday junction binding and processing by the RuvA protein of Mycoplasma pneumoniae.. Eur J Biochem, 269(5), 1525-1533.
- High-throughput analysis of nucleic acid modification reactions using ion-pair reverse-phase high-performance liquid chromatography.. Anal Biochem, 301(2), 290-297.
- RNA footprinting analysis using ion pair reverse phase liquid chromatography.. RNA, 8(2), 247-251.
- DNA replication with the mutagenic nucleotide dPTP; Effects of tautomerism on nucleotide incorporation. CHEMISTRY OF NUCLEIC ACID COMPONENTS, 5, 215-220.
- Novel mutations in the BRCA1 and BRCA2 genes in Iranian women with early-onset breast cancer.. Breast Cancer Res, 4(4), R6. View this article in WRRO
- Rapid analysis of biochemical modifications in DNA fragments - Visualisation of phosphorylation and cytosine deamination in single 15 minute analyses.. AM J HUM GENET, 69(4), 462-462.
- Rapid, high precision analysis of DNA and RNA footprinting reactions utilising the WAVE (R) Nucleic Acid Fragment Analysis System.. AM J HUM GENET, 69(4), 468-468.
- Novel mutations in the BRCA1 and BRCA2 gene in Iranian women with early-onset Breast Cancer. J MED GENET, 38, S54-S54.
- Analysis of nucleic acid modification enzyme reactions using IP RP HPLC. J MED GENET, 38, S71-S71.
- Enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity.. Nucleic Acids Res, 29(7), 1565-1573.
- Tracing the origin of the RACTK1 K(+) channel.. Biochem Biophys Res Commun, 277(1), 147-151.
- The mechanism of DNA repair by uracil-DNA glycosylase: studies using nucleotide analogues.. Nucleosides Nucleotides Nucleic Acids, 19(10-12), 1505-1516.
- Isolation of single-stranded DNA using denaturing DNA chromatography.. Anal Biochem, 284(1), 164-167.
- A positive selection vector combining tetracycline resistance that eliminates the need for bacterial plating.. Anal Biochem, 278(1), 46-51.
- Synthesis of two stable nitrogen analogues of S-adenosyl-L-methionine. J ORG CHEM, 64(20), 7467-7473.
- Obituary: John Lacey (1937–1998). Mycologist, 13(2), 96-IBC.
- Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone.. J Mol Biol, 286(2), 389-401.
- MED3/343: Networked learner support in continuing medical education. Journal of Medical Internet Research, 1(SUPPL. 1).
- Studying the function of methyltransferases using nucleotide analogue based random mutagenesis. CHEMISTRY OF NUCLEIC ACID COMPONENTS, 2, 209-212.
- Tyrosine phosphorylation of a 95 kDa protein and induction of the acrosome reaction in human spermatozoa by recombinant human zona pellucida glycoprotein 3.. Mol Hum Reprod, 4(12), 1136-1144.
- Exploring the structural flexibility of 5m-cytosine-DNA methyltransferases.. Biochem Soc Trans, 26(4), S394.
- Novel splicing of ROMK K+ channel RNA generates new isoforms in rat kidney. JOURNAL OF PHYSIOLOGY-LONDON, 511P, 29P-29P.
- Protein-mediated base flipping.. Curr Opin Biotechnol, 9(4), 354-358.
- Regulation of distal nephron K+ channels (ROMK) mRNA expression by aldosterone in rat kidney.. J Physiol, 509 ( Pt 3), 629-634.
- Substitution of the conserved phenylalanine in the S-adenosyl-L-methionine binding site of M.MspI with tyrosine modifies the kinetic properties of the enzyme.. Biol Chem, 379(4-5), 591-594.
- The polypeptide backbone of recombinant human zona pellucida glycoprotein-3 initiates acrosomal exocytosis in human spermatozoa in vitro. BIOCHEM J, 330, 839-845.
- Quantification of ROMK mRNA expression in rat kidney by competitive polymerase chain reaction (PCR). JOURNAL OF PHYSIOLOGY-LONDON, 505P, 115P-115P.
- The polypeptide backbone of recombinant human ZP3 induces acrosomal exocytosis in human spermatozoa. HUM REPROD, 12(5), S13-S13.
- Biological activity of recombinant human ZP3 produced in vitro: potential for a sperm function test.. Mol Hum Reprod, 2(12), 911-919.
- Renal and extrarenal localization of the RACTK1 K+ channel by immunofluorescence. JOURNAL OF PHYSIOLOGY-LONDON, 497P, P94-P95.
- Atomic force microscopy used to image the inwardly-rectifying ATP-sensitive potassium channel protein, ROMK1.. KIDNEY INTERNATIONAL, 50(5), 1780-1780.
- Renal and extrarenal localisation of the RACTK and ROMK1 K+-channel proteins. JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY, 7(9), A0139-A0139.
- Imaging ROMK1 inwardly rectifying ATP-sensitive K+ channel protein using atomic force microscopy.. Proc Natl Acad Sci U S A, 93(16), 8756-8760.
- Recombinant human zona pellucida glycoprotein 3 induces calcium influx and acrosome reaction in human spermatozoa.. Mol Hum Reprod, 2(8), 583-589.
- Differential expression of ROMK1 and RACTK potassium channel mRNAs in cell lines. JOURNAL OF PHYSIOLOGY-LONDON, 493P, P92-P92.
- Activation of a yeast pseudo DNA methyltransferase by deletion of a single amino acid.. J Mol Biol, 257(4), 804-813.
- A ROMK1/GLUTATHIONE-S-TRANSFERASE FUSION PROTEIN IMAGED USING THE ATOMIC-FORCE MICROSCOPE. JOURNAL OF PHYSIOLOGY-LONDON, 489P, P90-P90.
- IMMUNOCYTOCHEMICAL LOCATION OF THE POTASSIUM CHANNEL ROMK1 IN RAT-KIDNEY CORTEX. JOURNAL OF PHYSIOLOGY-LONDON, 489P, P93-P94.
- Identification of direct-repeat-binding protein 1 (DRP-1), a DNA-binding protein that binds specifically to the 'malic' enzyme gene promoter direct repeat element.. Biochem J, 311 ( Pt 3), 901-904.
- The DNA recognition subunit of a DNA methyltransferase is predominantly a molten globule in the absence of DNA.. FEBS Lett, 355(1), 57-60.
- Component analysis and characterization of a nuclear deoxyribonucleotidase.. Biochem J, 298 Pt 3, 727-732.
- Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding.. Biochem J, 298 ( Pt 1), 107-113.
- Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2.. J Mol Biol, 235(2), 545-553.
- Modulation of human DNA methyltransferase activity and mRNA levels in the monoblast cell line U937 induced to differentiate with dibutyryl cyclic AMP and phorbol ester.. J Mol Endocrinol, 11(2), 191-200.
- Hydrogen bonding in biological structures. FEBS Letters, 323(3), 295-295.
- Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor.. Biochem J, 291 ( Pt 2), 493-504.
- Effects of co-factor and deoxycytidine substituted oligonucleotides upon sequence-specific interactions between MspI DNA methyltransferase and DNA.. J Mol Biol, 230(3), 779-786.
- Synthesis and biological evaluation of (S)-AzaAdoMet, a stahle isosteric and isoelectronic analogue of AdoMet, S-adenosyl L-methionine. Collection of Czechoslovak Chemical Communications, 58(s1), 116-119.
- DNA methyltransferases (EC 2.1.1.72 and EC 2.1.1.73).. Methods Mol Biol, 16, 201-211.
- The HsdS polypeptide of the type IC restriction enzyme EcoR124 is a sequence-specific DNA-binding protein.. Mol Microbiol, 6(21), 3251-3256.
- Characterization and purification of a novel dATP-binding protein in eukaryotes.. Biochem J, 287 ( Pt 3), 871-879.
- Purification of DNA binding proteins by affinity and ion exchange chromatography.. Methods Mol Biol, 11, 273-286.
- A laboratory guide for in vivo studies of DNA methylation and protein/DNA interactions. FEBS Letters, 287(1-2), 226-227.
- S1 nuclease transcript mapping using sequenase-derived single-stranded probes.. Biotechniques, 10(4), 426-428.
- Transcriptional analysis of the restriction and modification genes of bacteriophage P1.. Mol Microbiol, 5(3), 685-694.
- PURIFICATION, CHEMICAL MODIFICATION AND ANALYSIS OF PH-DEPENDENCE OF THE NADP+-DEPENDENT GLUTAMATE-DEHYDROGENASE OF ESCHERICHIA-COLI. BIOCHEM SOC T, 16(5), 876-877.
- Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutants.. J Mol Biol, 200(1), 23-29.
- ISOLATION OF 3 COMPONENTS OF THE HYDROXYGLUTARATE PATHWAY FROM CLOSTRIDIUM-SYMBIOSUM. BIOCHEM SOC T, 15(6), 1039-1040.
- CHARACTERIZATION OF ECOP1 DNA ADENINE METHYLASE. BIOCHEM SOC T, 15(6), 1039-1039.
- A rapid method for Bal31 deletion analysis.. Nucleic Acids Res, 15(20), 8564.
- A SIMPLE METHOD FOR THE CALIBRATION OF RECORDING FLUOROMETERS BY KINETIC MEANS IN THE STUDY OF NAD(P)+-DEPENDENT DEHYDROGENASES. BIOCHEM SOC T, 15(3), 386-387.
- The crystal structure of glutamate dehydrogenase from Clostridium symbiosum at 0.6 nm resolution.. Biochem J, 242(3), 789-795.
- High level expression of the EcoP1 modification methylase gene and characterisation of the gene product.. Gene, 54(2-3), 239-245.
- Crystallization of an NAD+-dependent glutamate dehydrogenase from Clostridium symbiosum.. J Mol Biol, 181(1), 147-149.
- Kinetic studies of ox-liver glutamate dehydrogenase oxidative deamination of two glutamate analogues, L-threo-gamma-methylglutamate and L-alpha-amino-gamma-nitraminobutyrate, in the presence of the allosteric effector ADP.. Int J Biochem, 17(7), 851-854.
- The kinetic mechanism of ox liver glutamate dehydrogenase in the presence of the allosteric effector ADP. The oxidative deamination of L-glutamate.. Biochem J, 223(1), 161-168.
- A kinetic study of the oxidative deamination of L-glutamate by Peptostreptococcus asaccharolyticus glutamate dehydrogenase using a variety of coenzymes.. Eur J Biochem, 143(3), 557-560.
- Characterization of Peptostreptococcus asaccharolyticus glutamate dehydrogenase purified by dye-ligand chromatography.. J Gen Microbiol, 130(9), 2385-2394.
- The coenzyme specificity of glutamate dehydrogenase from Peptococcus asaccharolyticus. Biochemical Society Transactions, 11(2), 175-176.
- Beef liver glutamate dehydrogenase: a study of the oxidation of various alternative amino acid substrates retaining the correct spacing of the two carboxylate groups.. Int J Biochem, 15(4), 495-500.
- ChemInform Abstract: Synthesis of Two Stable Nitrogen Analogues of S-Adenosyl-L-methionine.. ChemInform, 31(5), no-no.
Chapters
- A Nomenclature for Restriction Enzymes, DNA Methyltransferases, Homing Endonucleases, and Their Genes, Restriction Endonucleases (pp. 1-18). Springer Berlin Heidelberg
- Protein fusions as an aid to purification, Highly Selective Separations in Biotechnology (pp. 163-178). Springer Netherlands
- Overexpression and purification of eukaryotic transcription factors as glutathione-S-transferase fusions in E. coli. (pp. 185-197).
- Nucleic Acid Chromatography Wiley-VCH Verlag GmbH & Co. KGaA
- DNA Methylation John Wiley & Sons, Ltd
Conference proceedings papers
- Analysis of the RNA component of human telomerase and its associated activity.. AMERICAN JOURNAL OF HUMAN GENETICS, Vol. 71(4) (pp 333-333)
- A rapid, accurate and quantitative method for analysis of the methylation status of imprinted genes, using primer extension and IP RP HPLC.. EUROPEAN JOURNAL OF HUMAN GENETICS, Vol. 10 (pp 294-294)
- The signal transduction pathway of the acrosome reaction in human spermatozoa in response to purified recombinant human ZP3. HUMAN SPERM ACROSOME REACTION, Vol. 236 (pp 426-427)
- The production and purification of recombinant human ZP3 from E-6coli. HUMAN SPERM ACROSOME REACTION, Vol. 236 (pp 404-405)
- Induction of the human acrosome reaction by rhuZP3. HUMAN SPERM ACROSOME REACTION, Vol. 236 (pp 105-122)
- Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions.. J Chromatogr A, 1216(9), 1377-1382.
- Teaching activities
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Level 3 modules
- MBB308 Molecular Systems Biology and Synthetic Biology (Module Coordinator)
Level 2 modules
- FCP201 Molecules to Market (Module Coordinator)
- MBB267 Molecular Bioscience 2B
- Professional activities and memberships
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- 2015 Fellow of the Royal Society of Biology (FRSB)