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Yr Athro Dafydd Jones
PhD Cantab FLSW
- Sylwebydd y cyfryngau
- Ar gael fel goruchwyliwr ôl-raddedig
Timau a rolau for Dafydd Jones
Athro
Ysgol y Biowyddorau
Trosolwyg
Trosolwg o'r ymchwil
Prif ffocws y grŵp Jones yw plastigrwydd strwythurol a swyddogaethol proteinau. Mae ein hymchwil yn cynnwys astudio a pheirianneg amrywiaeth o systemau protein, gyda ffocws ar broteinau fflwroleuol a systemau ymwrthedd i wrthfiotigau. Mae llawer o waith y grŵp yn gorwedd ar y rhyngwyneb rhwng bioleg, cemeg a ffiseg ac mae ganddo sail ar ochr protein bioleg synthetig lle rydym yn adeiladu cydrannau proteinau newydd, sgaffaldiau newydd a systemau bionanohybrid. Mae gennym ddiddordeb arbennig mewn cyflwyno cemeg newydd i broteinau trwy ddefnyddio dulliau cod genetig estynedig a rhyngwynebu proteinau mewn modd wedi'i gynllunio â nano-ddeunyddiau i gynhyrchu ar gyfer nanoddyfeisiau a electroneg biomoleciwlaidd. Rydym hefyd wedi datblygu sawl dull sy'n seiliedig ar transposon ar gyfer esblygiad cyfeiriedig proteinau gan ddefnyddio ailgyfuniad nad yw'n homolog. Mae'r grwpiau yn defnyddio amrywiaeth o ddulliau gan gynnwys dylunio cyfrifiadurol, peirianneg protein rhesymegol ac esblygiad wedi'i gyfeirio gyda bioleg strwythurol, dadansoddi moleciwl sengl, dynameg moleciwlaidd, bioffiseg a thechnegau biocemegol a ddefnyddir i ymchwilio i briodweddau'r proteinau newydd hyn.
Adnoddau
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Newyddion
Mae Dafydd wedi cael ei ethol yn gymrawd Cymdeithas Ddysgedig Cymru am ei gyfraniad i fiocemeg.
Yn ddiweddar, rydym wedi peiriannu system rhyngweithio protein-protein sy'n seiliedig ar brotein fflwroleuol sy'n ymateb i'r copr metel olrhain biolegol pwysig. Mae sail strwythurol gweithredu (gallwch ddod o hyd i'r strwythurau o dan godau PDB 8c1x ac 8bxp) yn datgelu mecanwaith cyffredinol y gellir defnyddio proteinau fluroesecent i fonitro rhyngweithiadau heblaw FRET. Mae'r papur wedi'i gyhoeddi yn Chemical Science ac mae'n ymdrech gydweithredol wych arall sy'n cynnwys Pete Watson a Karma Albalawi o'r Adran Cemeg, Prifysgol Tabuk, Saudi Arabia. Hefyd, gwych i weld Kieran o'n rhaglen MRes ardderchog, gan gael y gydnabyddiaeth y mae'n ei derseves am ei fewnbwn. Mwy i ddod ar y pwnc hwn... Gallaf eich sicrhau.
Da cael ein papur ar beirianneg protein dan arweiniad MD o GFP i gynhyrchu chwiliedydd mwy disglair a hirhoedlog. Rydyn ni'n ei alw'n YuzuFP ar ôl lliw y protein. Ymdrech gydweithredol wych ym Mhrifysgol Caerdydd gan gynnwys Oliver Castell a Pete Watson. Mae'r papur wedi'i gyhoeddi yn Nature's Communications Chemistry. Mwy i ddod ar ein hymchwil peirianneg GFP.
Cydweithrediad gwych rhwng Sébastien Côté (U o Montreal, Canada), Chang-Seuk Lee (Prifysgol Menywod Seoul, De Korea) ac eto gyda Matteo Palma (QMUL) ar sut y gwnaethom ddefnyddio efelychiadau a modelu cyfrifiadurol i ragweld sut y bydd proteinau yn electrostatig yn gatio transistorau effaith maes nanotiwb carbon. Mae'r papur wedi'i gyhoeddi yn Nature Communications.
Mae gennym grant TRT BBSRC newydd i weithio ar ddatblygu offer protein fflwroleuol newydd i fonitro ffurfio cymhlethdod protein. Cydweithrediad gwych gyda chydweithwyr Richard Clarkson, Georgina Menzies a Pete Watson.
Felly roeddech chi'n meddwl eich bod chi'n gwybod sut mae glycosylation yn effeithio ar brotein? Mae ein papur newydd yn FEBS J gyda'r cydweithwyr Georgina Menzies , Stephen Wells, a Chris Pudney yn dangos bod gylcans wedi gwneud yr ensym masnachol pwysig ceffylau radish peroxidase yn fwy anhyblyg - ie yn fwy anhyblyg - a'i wneud yn llawer mwy egnïol a sefydlog o'i gymharu â'i ffurf nad yw'n glycosylated. Defnyddiwyd cymysgedd da o arbrawf ac efelychu i ddangos sut roedd yr effeithiau strwythurol a'r ddeinameg yn cael eu manfested.
Roedd gennym lawer o ddiddordeb yn ein papur diweddar yn Advanced Functional Materials ynghylch y defnydd o broteinau ffloresol i gatio dargludedd nanotiwbiau carbon yn optegol, gan gynnwys erthyglau wedi'u hamlygu yn Phys.org, AAS EurekAlert, Technology Networks ymhlith eraill. Yn y bôn, rydym yn dangos y gall GFP alluogi naill ai transistor optegol gated neu swyddogaeth cof yn seiliedig ar sut rydym yn atodi'r protein i'r CNT. Mae hyn i gyd wedi'i alluogi gan gemeg ffenyl azide wedi'i hamgodio'n enetig.
Cyhoeddiad
2026
- Regan, D. et al. 2026. Genetically encoding stimulated raman-scattering probes for cell imaging using infrared fluorescent proteins. The Journal of Physical Chemistry Letters 17 (34), pp.9862-9868. (10.1021/acs.jpclett.6c02085)
- Stevenson, C. J. et al., 2026. Genetic encoding of 3-cyano-tyrosine and its use in controlling the chromophore isomeric state of the fluorescent protein mKate. International Journal of Molecular Sciences 27 (16) 7184. (10.3390/ijms27167184)
- Wirawan, R. et al., 2026. Structural basis for independent pore function of Vpb4 from Bacillus thuringiensis. Nature Communications 17 8198. (10.1038/s41467-026-74567-y)
- Kurttila, M. et al., 2026. Environmental dipolar relaxation during excited-state proton transfer in green fluorescent protein. Journal of the American Chemical Society 148 (7), pp.7544-7551. (10.1021/jacs.5c21097)
2025
- Zitti, A. et al. 2025. Structure, function and dynamics of mCoral, a pH-responsive engineered variant of the mCherry fluorescent protein with improved hydrogen peroxide tolerance. International Journal of Molecular Sciences 27 (1) 154. (10.3390/ijms27010154)
- Ahmed, R. D. et al. 2025. Chromophore charge-state switching through copper-dependent homodimerisation of an engineered green fluorescent protein. Chemical Science 16 (46), pp.22136-22146. (10.1039/D5SC06589E)
- Regan, D. et al. 2025. Genetically encoding stimulated Raman-scattering probes for cell imaging using infrared fluorescent proteins. null (10.48550/arXiv.2511.08564)
- Ahmed, R. D. et al. 2025. Molecular dynamics guided identification of a brighter variant of superfolder Green Fluorescent Protein with increased photobleaching resistance. Communications Chemistry 8 174. (10.1038/s42004-025-01573-4)
2024
- Gwyther, R. E. A. et al. 2024. Optimising CNT-FET biosensor design through modelling of biomolecular electrostatic gating and its application to β-lactamase detection. Nature Communications 15 7482. (10.1038/s41467-024-51325-6)
- Grigorenko, B. L. et al., 2024. Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in the GFP-like fluorescent proteins. Organic and Biomolecular Chemistry 22 , pp.337-347. (10.1039/D3OB01450A)
2023
- Mack, A. H. et al. 2023. A proofreading mutation with an allosteric effect allows a cluster of SARS-CoV-2 viruses to rapidly evolve. Molecular Biology and Evolution 40 (10) msad209. (10.1093/molbev/msad209)
- Evans, O. et al. 2023. Low-temperature plasmonically enhanced single-molecule spectroscopy of fluorescent proteins. Presented at: The European Conference on Lasers and Electro-Optics 2023 26-30 June 2023. 2023 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC). IEEE. (10.1109/cleo/europe-eqec57999.2023.10231465)
- Ramakrishnan, K. et al. 2023. Glycosylation increases active site rigidity leading to improved enzyme stability and turnover. The FEBS Journal 290 (15), pp.3812-3827. (10.1111/febs.16783)
- Stano, P. et al., 2023. Editorial: Fiat lux! Light-driven and light-controlled synthetic biological parts, devices, systems and processes. Frontiers in Bioengineering and Biotechnology 11 1201962. (10.3389/fbioe.2023.1201962)
- Zitti, A. and Jones, D. 2023. Expanding the genetic code: a non-natural amino acid story. Biochemist 45 (1), pp.2-6. (10.1042/bio_2023_102)
- Ahmed, R. D. et al. 2023. Fluorescent proteins: Crystallization, structural determination, and nonnatural amino acid incorporation. In: Sharma, M. ed. Fluorescent Proteins: Methods and Protocols. Vol. 2564, Methods in Molecular Biology Springer. , pp.99-119. (10.1007/978-1-0716-2667-2_5)
2022
- Lee, C. et al., 2022. Fabrication and functionalisation of nanocarbon-based field-effect transistor biosensors. ChemBioChem 23 (23) e202200282. (10.1002/cbic.202200282)
- Cervantes-Salguero, K. et al., 2022. Single molecule DNA origami nanoarrays with controlled protein orientation. Biophysics Reviews 3 (3)(10.1063/5.0099294)
- Gwyther, R. E. A. et al. 2022. Differential bio-optoelectronic gating of semiconducting carbon nanotubes by varying the covalent attachment residue of a green fluorescent protein. Advanced Functional Materials 32 (22) 2112374. (10.1002/adfm.202112374)
- Noby, N. et al., 2022. Structure-guided engineering of a family IV cold-adapted esterase expands its substrate range. International Journal of Molecular Sciences 23 (9) 4703. (10.3390/ijms23094703)
2021
- Noby, N. et al., 2021. Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism. Open Biology 11 (12) 210182. (10.1098/rsob.210182)
- Xu, X. et al., 2021. Tuning electrostatic gating of semiconducting carbon nanotubes by controlling protein orientation in biosensing devices. Angewandte Chemie International Edition 60 (37), pp.20184-20189. (10.1002/anie.202104044)
- Johnson, R. L. et al. 2021. Designed artificial protein heterodimers with coupled functions constructed using bio-orthogonal chemistry. Frontiers in Chemistry 9 733550. (10.3389/fchem.2021.733550)
- Freeley, M. et al., 2021. DNA-directed assembly of carbon nanotube-protein hybrids. Biomolecules 11 (7) 955. (10.3390/biom11070955)
- Sabah Auhim, H. et al., 2021. Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step. Chemical Science 12 (22), pp.7735-7745. (10.1039/D0SC06693A)
- Worthy, H. L. et al. 2021. The crystal sructure of Bacillus cereus HblL1. Toxins 13 (4) 253. (10.3390/toxins13040253)
- Pope, J. R. et al. 2021. Association of fluorescent protein pairs and it's significant impact on fluorescence and energy transfer. Advanced Science 8 (1) 2003167. (10.1002/advs.202003167)
2020
- Karuna, A. et al. 2020. Quantitative imaging of B1 cyclin expression across the cell cycle using green fluorescent protein tagging and epi-fluorescence. Cytometry Part A 97 (10), pp.1066-1072. (10.1002/cyto.a.24038)
- Bowen, B. J. et al. 2020. Switching protein metalloporphyrin binding specificity by design from iron to fluorogenic zinc. Chemical Communications 56 (31), pp.4308-4311. (10.1039/D0CC00596G)
- Thomas, S. K. et al. 2020. Site-specific protein photochemical covalent attachment to carbon nanotube side walls and its electronic impact on single molecule function. Bioconjugate Chemistry 31 (3), pp.584-594. (10.1021/acs.bioconjchem.9b00719)
2019
- Gwyther, R. E. , Jones, D. D. and Worthy, H. L. 2019. Better together: building protein oligomers naturally and by design. Biochemical Society Transactions 47 (6), pp.1773-1780. (10.1042/BST20190283)
- Worthy, H. L. et al. 2019. Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry. Communications Chemistry 2 83. (10.1038/s42004-019-0185-5)
- Gulácsy, C. E. et al., 2019. Excitation-energy-dependent molecular beacon detects early stage neurotoxic Aβ aggregates in the presence of cortical neurons. ACS Chemical Neuroscience 10 (3), pp.1240-1250. (10.1021/acschemneuro.8b00322)
2018
- Zaki, A. et al., 2018. Defined covalent assembly of protein molecules on graphene using a genetically encoded photochemical reaction handle. RSC Advances 8 , pp.5768-5775. (10.1039/c7ra11166e)
- Elliott, M. and Jones, D. D. 2018. Approaches to single molecule studies of metalloprotein electron transfer using scanning probe-based techniques. Biochemical Society Transactions 46 (1), pp.1-9. (10.1042/BST20170229)
- Halliwell, L. M. et al. 2018. ΔFlucs: brighter photinus pyralis firefly luciferases identified by surveying consecutive single amino acid deletion mutations in a thermostable variant. Biotechnology and Bioengineering 115 (1), pp.50-59. (10.1002/bit.26451)
2017
- Freeley, M. et al., 2017. Site-specific one-to-one click coupling of single proteins to individual carbon nanotubes: a single-molecule approach. Journal of the American Chemical Society 139 (49), pp.17834-17840. (10.1021/jacs.7b07362)
- Marth, G. et al., 2017. Precision templated bottom-up multiprotein nanoassembly through defined click chemistry linkage to DNA. ACS Nano 11 (5), pp.5003-5010. (10.1021/acsnano.7b01711)
2016
- Hartley, A. M. et al., 2016. Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle. Chemical Science 7 (10), pp.6484-6491. (10.1039/C6SC00944A)
2015
- Hartley, A. M. et al. 2015. Functional modulation and directed assembly of an enzyme through designed non-natural post-translation modification. Chemical Science 6 (7), pp.3712-3717. (10.1039/C4SC03900A)
- Arpino, J. A. J. et al., 2015. In-frame amber stop codon replacement mutagenesis for the directed evolution of proteins containing non-canonical amino acids: identification of residues open to bio-orthogonal modification. PLoS ONE 10 (5) e0127504. (10.1371/journal.pone.0127504)
- Rohamare, S. et al., 2015. Cloning, expression and in silico studies of a serine protease from a marine actinomycete (Nocardiopsis sp. NCIM 5124). Process Biochemistry 50 (3), pp.378-387. (10.1016/j.procbio.2014.12.025)
- Reddington, S. C. et al., 2015. Directed evolution of GFP with non-natural amino acids identifies residues for augmenting and photoswitching fluorescence. Chemical Science 6 (2), pp.1159-1166. (10.1039/C4SC02827A)
- Reddington, S. C. et al., 2015. Genetically encoded phenyl azide photochemistry drives positive and negative functional modulation of a red fluorescent protein. RSC Advances 5 (95), pp.77734-77738. (10.1039/C5RA13552D)
2014
- Jones, D. D. et al. 2014. Transposon-based approaches for generating novel molecular diversity during directed evolution. In: Gillam, E. M. J. , Copp, J. M. and Ackerley, D. eds. Directed Evolution Library Creation: Methods and Protocols. Vol. 1179, Methods in Molecular Biology Springer. , pp.159-172. (10.1007/978-1-4939-1053-3_11)
- Arpino, J. J. et al. 2014. Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure. Structure 22 (6), pp.889-898. (10.1016/j.str.2014.03.014)
- Arpino, J. A. J. , Rizkallah, P. and Jones, D. D. 2014. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein. Acta Crystallographica Section D Biological Crystallography 70 (8), pp.2152-2162. (10.1107/S139900471401267X)
2013
- Morris, J. L. et al. 2013. Aryl azide photochemistry in defined protein environments. Organic Letters 15 (4), pp.728-731. (10.1021/ol3028779)
- Reddington, S. C. et al. 2013. Different photochemical events of a genetically encoded phenyl azide define and modulate GFP fluorescence. Angewandte Chemie - International Edition 52 (23), pp.5974-5977. (10.1002/anie.201301490)
- Reddington, S. C. et al. 2013. Genetically encoding phenyl azide chemistry: new uses and ideas for classical biochemistry. Biochemical Society Transactions 41 (5), pp.1177-1182. (10.1042/BST20130094)
2012
- Arpino, J. et al. 2012. Structural basis for efficient chromophore communication and energy transfer in a constructed didomain protein scaffold. Journal of the American Chemical Society 134 (33), pp.13632-13640. (10.1021/ja301987h)
- Della Pia, E. A. et al., 2012. Orientation-dependent electron transport in a single redox protein [RETRACTED]. ACS Nano 6 (1), pp.355-361. (10.1021/nn2036818)
- Arpino, J. , Rizkallah, P. and Jones, D. D. 2012. Crystal structure of enhanced green fluorescent protein to 1.35 Å resolution reveals alternative conformations for Glu222. PLoS ONE 7 (10) e47132. (10.1371/journal.pone.0047132)
- Della Pia, E. A. et al. 2012. Redox tuning of cytochrome b562 through facile metal porphyrin substitution. Chemical Communications 48 (86), pp.10624-10626. (10.1039/c2cc34302a)
- Della Pia, E. A. et al. 2012. Fast electron transfer through a single molecule natively structured redox protein. Nanoscale 4 (22), pp.7106-7113. (10.1039/c2nr32131a)
- Della Pia, E. A. et al., 2012. Direct binding of a redox protein for single-molecule electron transfer measurements. Small 8 (15), pp.2341-2344. (10.1002/smll.201102416)
- Gamble, M. D. et al. 2012. The role of substrate specificity and metal binding in defining the activity and structure of an intracellular subtilisin. FEBS Open Bio 2 , pp.209-215. (10.1016/j.fob.2012.07.001)
- Reddington, S. C. , Tippmann, E. M. and Jones, D. D. 2012. Residue choice defines efficiency and influence of bioorthogonal protein modification via genetically encoded strain promoted Click chemistry. Chemical Communications 48 (67), pp.8419-8421. (10.1039/c2cc31887c)
2011
- Della Pia, E. A. et al. 2011. Single-molecule mapping of long-range electron transport for a cytochrome b562 variant. Nano Letters 11 (1), pp.176-182. (10.1021/nl103334q)
- Gamble, M. D. et al. 2011. Regulation of an intracellular subtilisin protease activity by a short propeptide sequence through an original combined dual mechanism. Proceedings of the National Academy of Sciences 108 (9), pp.3536-3541. (10.1073/pnas.1014229108)
- Jones, D. D. 2011. Recombining low homology, functionally rich regions of bacterial subtilisins by combinatorial fragment exchange. PLoS ONE 6 (9) e24319. (10.1371/journal.pone.0024319)
2010
- Edwards, W. R. et al. 2010. Regulation of β-Lactamase activity by remote binding of Heme: functional coupling of unrelated proteins through domain insertion. Biochemistry 49 (31), pp.6541-6549. (10.1021/bi100793y)
- Vevodova, J. et al., 2010. Crystal structure of an intracellular subtilisin reveals novel structural features unique to this subtilisin family. Structure 18 (6), pp.744-755. (10.1016/j.str.2010.03.008)
2009
- Baldwin, A. J. et al. 2009. Expanded chemical diversity sampling through whole protein evolution. Molecular Biosystems 5 (7), pp.764-766. (10.1039/B904031E)
- Stott, K. M. et al., 2009. A Surface Loop Directs Conformational Switching of a Lipoyl Domain Between a Folded and a Novel Misfolded Structure. Structure 17 (8), pp.1117-1127. (10.1016/j.str.2009.07.001)
2008
- Baldwin, A. J. et al. 2008. Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Research 36 (13) e77. (10.1093/nar/gkn358)
- Edwards, W. R. et al., 2008. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Research 36 (13)(10.1093/nar/gkn363)
- Jones, D. D. and Perham, R. N. 2008. The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex. Biochemical Journal 409 , pp.357-366. (10.1042/BJ20071119)
- Meltzer, M. et al., 2008. Allosteric activation of HtrA protease DegP by stress signals during bacterial protein quality control. Angewandte Chemie - International Edition 47 (7), pp.1332-1334. (10.1002/anie.200703273)
2007
- Jones, D. D. and Perham, R. N. 2007. The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex. Biochemical Journal 409 , pp.357-366. (10.1042/BJ20071119)
- Simm, A. M. et al., 2007. Investigating protein structural plasticity by surveying the consequence of an amino acid deletion from TEM-1 β-lactamase. FEBS Letters 581 (21), pp.3904-3908. (10.1016/j.febslet.2007.07.018)
2005
- Jones, D. D. and Barker, P. 2005. Controlling self-assembly by linking protein folding, DNA binding and the redox chemistry of heme. Angewandte Chemie International Edition , pp.6337-6341. (10.1002/anie.200463035)
- Jones, D. D. 2005. Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 β-lactamase to an amino acid deletion. Nucleic Acids Research 33 (9)(10.1093/nar/gni077)
2004
- Jones, D. D. and Barker, P. D. 2004. Design and characterisation of an artificial DNA-binding cytochrome. ChemBioChem 5 (7), pp.964-971. (10.1002/cbic.200300569)
2002
- Perham, R. N. et al., 2002. Substrate channelling in 2-oxo acid dehydrogenase multienzyme complexes. Biochemical Society Transactions 30 (2), pp.47–51. (10.1042/0300-5127:0300047)
2001
- Jones, D. D. et al. 2001. Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex. Journal of Molecular Biology , pp.49-60. (10.1006/jmbi.2000.4257)
2000
- Jones, D. D. et al. 2000. Restricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli†,‡. Biochemistry 39 (29), pp.8448–8459. (10.1021/bi992978i)
- Jones, D. et al. 2000. Structural determinants of post-translational modification and catalytic specificity for the lipoyl domains of the pyruvate dehydrogenase multienzyme complex of Escherichia coli. Journal of Molecular Biology 295 (2), pp.289-306. (10.1006/jmbi.1999.3335)
Articles
- Regan, D. et al. 2026. Genetically encoding stimulated raman-scattering probes for cell imaging using infrared fluorescent proteins. The Journal of Physical Chemistry Letters 17 (34), pp.9862-9868. (10.1021/acs.jpclett.6c02085)
- Stevenson, C. J. et al., 2026. Genetic encoding of 3-cyano-tyrosine and its use in controlling the chromophore isomeric state of the fluorescent protein mKate. International Journal of Molecular Sciences 27 (16) 7184. (10.3390/ijms27167184)
- Wirawan, R. et al., 2026. Structural basis for independent pore function of Vpb4 from Bacillus thuringiensis. Nature Communications 17 8198. (10.1038/s41467-026-74567-y)
- Kurttila, M. et al., 2026. Environmental dipolar relaxation during excited-state proton transfer in green fluorescent protein. Journal of the American Chemical Society 148 (7), pp.7544-7551. (10.1021/jacs.5c21097)
- Zitti, A. et al. 2025. Structure, function and dynamics of mCoral, a pH-responsive engineered variant of the mCherry fluorescent protein with improved hydrogen peroxide tolerance. International Journal of Molecular Sciences 27 (1) 154. (10.3390/ijms27010154)
- Ahmed, R. D. et al. 2025. Chromophore charge-state switching through copper-dependent homodimerisation of an engineered green fluorescent protein. Chemical Science 16 (46), pp.22136-22146. (10.1039/D5SC06589E)
- Regan, D. et al. 2025. Genetically encoding stimulated Raman-scattering probes for cell imaging using infrared fluorescent proteins. null (10.48550/arXiv.2511.08564)
- Ahmed, R. D. et al. 2025. Molecular dynamics guided identification of a brighter variant of superfolder Green Fluorescent Protein with increased photobleaching resistance. Communications Chemistry 8 174. (10.1038/s42004-025-01573-4)
- Gwyther, R. E. A. et al. 2024. Optimising CNT-FET biosensor design through modelling of biomolecular electrostatic gating and its application to β-lactamase detection. Nature Communications 15 7482. (10.1038/s41467-024-51325-6)
- Grigorenko, B. L. et al., 2024. Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in the GFP-like fluorescent proteins. Organic and Biomolecular Chemistry 22 , pp.337-347. (10.1039/D3OB01450A)
- Mack, A. H. et al. 2023. A proofreading mutation with an allosteric effect allows a cluster of SARS-CoV-2 viruses to rapidly evolve. Molecular Biology and Evolution 40 (10) msad209. (10.1093/molbev/msad209)
- Ramakrishnan, K. et al. 2023. Glycosylation increases active site rigidity leading to improved enzyme stability and turnover. The FEBS Journal 290 (15), pp.3812-3827. (10.1111/febs.16783)
- Stano, P. et al., 2023. Editorial: Fiat lux! Light-driven and light-controlled synthetic biological parts, devices, systems and processes. Frontiers in Bioengineering and Biotechnology 11 1201962. (10.3389/fbioe.2023.1201962)
- Zitti, A. and Jones, D. 2023. Expanding the genetic code: a non-natural amino acid story. Biochemist 45 (1), pp.2-6. (10.1042/bio_2023_102)
- Lee, C. et al., 2022. Fabrication and functionalisation of nanocarbon-based field-effect transistor biosensors. ChemBioChem 23 (23) e202200282. (10.1002/cbic.202200282)
- Cervantes-Salguero, K. et al., 2022. Single molecule DNA origami nanoarrays with controlled protein orientation. Biophysics Reviews 3 (3)(10.1063/5.0099294)
- Gwyther, R. E. A. et al. 2022. Differential bio-optoelectronic gating of semiconducting carbon nanotubes by varying the covalent attachment residue of a green fluorescent protein. Advanced Functional Materials 32 (22) 2112374. (10.1002/adfm.202112374)
- Noby, N. et al., 2022. Structure-guided engineering of a family IV cold-adapted esterase expands its substrate range. International Journal of Molecular Sciences 23 (9) 4703. (10.3390/ijms23094703)
- Noby, N. et al., 2021. Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism. Open Biology 11 (12) 210182. (10.1098/rsob.210182)
- Xu, X. et al., 2021. Tuning electrostatic gating of semiconducting carbon nanotubes by controlling protein orientation in biosensing devices. Angewandte Chemie International Edition 60 (37), pp.20184-20189. (10.1002/anie.202104044)
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- Worthy, H. L. et al. 2019. Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry. Communications Chemistry 2 83. (10.1038/s42004-019-0185-5)
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- Elliott, M. and Jones, D. D. 2018. Approaches to single molecule studies of metalloprotein electron transfer using scanning probe-based techniques. Biochemical Society Transactions 46 (1), pp.1-9. (10.1042/BST20170229)
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- Reddington, S. C. et al., 2015. Directed evolution of GFP with non-natural amino acids identifies residues for augmenting and photoswitching fluorescence. Chemical Science 6 (2), pp.1159-1166. (10.1039/C4SC02827A)
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- Arpino, J. A. J. , Rizkallah, P. and Jones, D. D. 2014. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein. Acta Crystallographica Section D Biological Crystallography 70 (8), pp.2152-2162. (10.1107/S139900471401267X)
- Morris, J. L. et al. 2013. Aryl azide photochemistry in defined protein environments. Organic Letters 15 (4), pp.728-731. (10.1021/ol3028779)
- Reddington, S. C. et al. 2013. Different photochemical events of a genetically encoded phenyl azide define and modulate GFP fluorescence. Angewandte Chemie - International Edition 52 (23), pp.5974-5977. (10.1002/anie.201301490)
- Reddington, S. C. et al. 2013. Genetically encoding phenyl azide chemistry: new uses and ideas for classical biochemistry. Biochemical Society Transactions 41 (5), pp.1177-1182. (10.1042/BST20130094)
- Arpino, J. et al. 2012. Structural basis for efficient chromophore communication and energy transfer in a constructed didomain protein scaffold. Journal of the American Chemical Society 134 (33), pp.13632-13640. (10.1021/ja301987h)
- Della Pia, E. A. et al., 2012. Orientation-dependent electron transport in a single redox protein [RETRACTED]. ACS Nano 6 (1), pp.355-361. (10.1021/nn2036818)
- Arpino, J. , Rizkallah, P. and Jones, D. D. 2012. Crystal structure of enhanced green fluorescent protein to 1.35 Å resolution reveals alternative conformations for Glu222. PLoS ONE 7 (10) e47132. (10.1371/journal.pone.0047132)
- Della Pia, E. A. et al. 2012. Redox tuning of cytochrome b562 through facile metal porphyrin substitution. Chemical Communications 48 (86), pp.10624-10626. (10.1039/c2cc34302a)
- Della Pia, E. A. et al. 2012. Fast electron transfer through a single molecule natively structured redox protein. Nanoscale 4 (22), pp.7106-7113. (10.1039/c2nr32131a)
- Della Pia, E. A. et al., 2012. Direct binding of a redox protein for single-molecule electron transfer measurements. Small 8 (15), pp.2341-2344. (10.1002/smll.201102416)
- Gamble, M. D. et al. 2012. The role of substrate specificity and metal binding in defining the activity and structure of an intracellular subtilisin. FEBS Open Bio 2 , pp.209-215. (10.1016/j.fob.2012.07.001)
- Reddington, S. C. , Tippmann, E. M. and Jones, D. D. 2012. Residue choice defines efficiency and influence of bioorthogonal protein modification via genetically encoded strain promoted Click chemistry. Chemical Communications 48 (67), pp.8419-8421. (10.1039/c2cc31887c)
- Della Pia, E. A. et al. 2011. Single-molecule mapping of long-range electron transport for a cytochrome b562 variant. Nano Letters 11 (1), pp.176-182. (10.1021/nl103334q)
- Gamble, M. D. et al. 2011. Regulation of an intracellular subtilisin protease activity by a short propeptide sequence through an original combined dual mechanism. Proceedings of the National Academy of Sciences 108 (9), pp.3536-3541. (10.1073/pnas.1014229108)
- Jones, D. D. 2011. Recombining low homology, functionally rich regions of bacterial subtilisins by combinatorial fragment exchange. PLoS ONE 6 (9) e24319. (10.1371/journal.pone.0024319)
- Edwards, W. R. et al. 2010. Regulation of β-Lactamase activity by remote binding of Heme: functional coupling of unrelated proteins through domain insertion. Biochemistry 49 (31), pp.6541-6549. (10.1021/bi100793y)
- Vevodova, J. et al., 2010. Crystal structure of an intracellular subtilisin reveals novel structural features unique to this subtilisin family. Structure 18 (6), pp.744-755. (10.1016/j.str.2010.03.008)
- Baldwin, A. J. et al. 2009. Expanded chemical diversity sampling through whole protein evolution. Molecular Biosystems 5 (7), pp.764-766. (10.1039/B904031E)
- Stott, K. M. et al., 2009. A Surface Loop Directs Conformational Switching of a Lipoyl Domain Between a Folded and a Novel Misfolded Structure. Structure 17 (8), pp.1117-1127. (10.1016/j.str.2009.07.001)
- Baldwin, A. J. et al. 2008. Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Research 36 (13) e77. (10.1093/nar/gkn358)
- Edwards, W. R. et al., 2008. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Research 36 (13)(10.1093/nar/gkn363)
- Jones, D. D. and Perham, R. N. 2008. The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex. Biochemical Journal 409 , pp.357-366. (10.1042/BJ20071119)
- Meltzer, M. et al., 2008. Allosteric activation of HtrA protease DegP by stress signals during bacterial protein quality control. Angewandte Chemie - International Edition 47 (7), pp.1332-1334. (10.1002/anie.200703273)
- Jones, D. D. and Perham, R. N. 2007. The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex. Biochemical Journal 409 , pp.357-366. (10.1042/BJ20071119)
- Simm, A. M. et al., 2007. Investigating protein structural plasticity by surveying the consequence of an amino acid deletion from TEM-1 β-lactamase. FEBS Letters 581 (21), pp.3904-3908. (10.1016/j.febslet.2007.07.018)
- Jones, D. D. and Barker, P. 2005. Controlling self-assembly by linking protein folding, DNA binding and the redox chemistry of heme. Angewandte Chemie International Edition , pp.6337-6341. (10.1002/anie.200463035)
- Jones, D. D. 2005. Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 β-lactamase to an amino acid deletion. Nucleic Acids Research 33 (9)(10.1093/nar/gni077)
- Jones, D. D. and Barker, P. D. 2004. Design and characterisation of an artificial DNA-binding cytochrome. ChemBioChem 5 (7), pp.964-971. (10.1002/cbic.200300569)
- Perham, R. N. et al., 2002. Substrate channelling in 2-oxo acid dehydrogenase multienzyme complexes. Biochemical Society Transactions 30 (2), pp.47–51. (10.1042/0300-5127:0300047)
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Book sections
- Ahmed, R. D. et al. 2023. Fluorescent proteins: Crystallization, structural determination, and nonnatural amino acid incorporation. In: Sharma, M. ed. Fluorescent Proteins: Methods and Protocols. Vol. 2564, Methods in Molecular Biology Springer. , pp.99-119. (10.1007/978-1-0716-2667-2_5)
- Jones, D. D. et al. 2014. Transposon-based approaches for generating novel molecular diversity during directed evolution. In: Gillam, E. M. J. , Copp, J. M. and Ackerley, D. eds. Directed Evolution Library Creation: Methods and Protocols. Vol. 1179, Methods in Molecular Biology Springer. , pp.159-172. (10.1007/978-1-4939-1053-3_11)
Conferences
- Evans, O. et al. 2023. Low-temperature plasmonically enhanced single-molecule spectroscopy of fluorescent proteins. Presented at: The European Conference on Lasers and Electro-Optics 2023 26-30 June 2023. 2023 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC). IEEE. (10.1109/cleo/europe-eqec57999.2023.10231465)
Ymchwil
Mae'r grŵp Jones yn canolbwyntio ar ddeall sail foleciwlaidd plastigrwydd protein o ran strwythur, swyddogaeth a phlygu, a'i gymhwyso i adeiladu cydrannau a systemau protein newydd. Y nod yn y pen draw yw mynd i'r afael ag un o'r cwestiynau sylfaenol mewn bioleg: sut mae dilyniant asid amino yn amgodio'r wybodaeth ar gyfer protein i blygu i'w strwythur 3D swyddogaethol. Mae ein grŵp yn cydweithio â chemegwyr, biolegwyr strwythurol, modelwyr cyfrifiadurol a ffisegwyr. Mae adeiladu cydrannau protein newydd yn golygu bod ein gwaith wedi'i alinio'n agos â meysydd bioleg synthetig a nanowyddoniaeth/nanotechnoleg.
Strwythur protein, swyddogaeth, deinameg a pheirianneg
Ymchwilir i strwythur, swyddogaeth a phlygu ystod o broteinau gan ddefnyddio biocemegol, bioffisegol, bioleg strwythurol a dynameg moleciwlaidd. Un o brif ffocws y grŵp ar hyn o bryd yw proteinau fflwroleuol, proteinau rhwymo haem a systemau ymwrthedd gwrthficrobaidd ß-lactam . Mae gennym hefyd ddiddordeb mewn ensymau amrywiol gan gynnwys y subtilisin serine proteases ac esterases oer-weithredol.
Gellir dod o hyd i restr lawn o'r strwythur a bennir gan y grŵp yma.
Adeiladu sgaffaldiau protein artiffisial
Mae'r gallu i ddylunio proteinau newydd gyda gweithgareddau nad ydynt yn rhan o'r repertoire naturiol yn hanfodol fel rhan o ddatblygiad bioleg synthetig a bionanotechnoleg. Fel dull cyffredinol ar gyfer creu cydrannau protein wedi'u teilwra gyda phriodweddau unigryw ond defnyddiol, rydym yn cyplu strwythurau ac felly swyddogaethau proteinau nad ydynt yn gysylltiedig fel arfer neu hyd yn oed deunyddiau nad ydynt yn brotein er mwyn cysylltu'r swyddogaeth. Er mwyn cyflawni hyn, bydd angen ailgynllunio radical neu hyd yn oed creu sgaffaldiau newydd ar broteinau presennol. Fodd bynnag, mae proteinau naturiol yn darparu'r ysbrydoliaeth a'r arweiniad yn ystod y gwaith adeiladu. Un agwedd allweddol yr ydym yn anelu ato yw synergedd rhwng gwahanol gydrannau fel bod un elfen yn "siarad" â'r llall.
Mae'r grŵp yn defnyddio amrywiaeth o ddulliau i adeiladu'r sgaffaldiau newydd hyn gan gynnwys: (1) mewnosod parth trwy esblygiad wedi'i gyfeirio; (2) impio parth rhesymegol; (3) cysylltu proteinau trwy gemeg clic; (4) adeiladu bionanohybridau lle mae proteinau yn gysylltiedig â systemau moleciwlaidd eilaidd fel origami DNA a nano-carbon.
Yn ddiweddar, rydym wedi dangos yn llwyddiannus rhyngwynebu wedi'i gynllunio o broteinau i wal ochr a wal ben systemau nano-carbon gan ddefnyddio dulliau cemeg golau a chlic. Mae'r ddwy system wedi'u cysylltu'n swyddogaethol oherwydd y rhyngwyneb wedi'i gynllunio ac agos rhwng y ddwy system foleciwlaidd.
Astudiaethau moleciwl sengl o broteinau trosglwyddo electronau ac ynni
Mae trosglwyddo electronau ac ynni yn chwarae rhan hanfodol mewn bioleg gan fod yn ganolog i brosesau fel ffotosynthesis, resbiradaeth a catalysis ensymau. Yn y bôn, mae proteinau o'r fath yn gweithio ar y moleciwl sengl ond mae'r rhan fwyaf o ddulliau yn dadansoddi ar y lefel swmp felly mae'r holl fanylion pwysig yn cael eu cyfartalu. Ar ben hynny, o ystyried bod proteinau yn hunan-ymgynnull, trefnu a modiwleiddio system trosglwyddo electronau/ynni yn y moleciwl sengl, mae potensial i'w haddasu i'w defnyddio fel nanoddyfeisiau, gan gynnwys transistorau moleciwlaidd ac electroneg biomoleciwlaidd. Mae'r grwpiau Jones wedi bod yn rhan o gydweithrediadau ymchwil rhyngddisgyblaethol gyda'r nod o ymchwilio i ymddygiad moleciwl unigol y systemau hyn. Mae proteinau yn cael eu peiriannu ar gyfer gweddillion penodol i ganiatáu rhyngweithiadau diffiniedig a manwl gywir ag arwyneb a deunyddiau dargludol. Mae hyn wedi arwain at sawl datblygiad pwysig ym maes electroneg foleciwlaidd ac astudiaethau moleciwlau protein sengl. Yn nodedig, rydym wedi dangos am y tro cyntaf cyplu uniongyrchol o brotein i'r ddau electrod sy'n caniatáu i ET gael ei fonitro ar lefel y moleciwl sengl.
Datgelodd ein hastudiaethau fod cytochrome b562 yn hynod ddargludol ac yn arddangos ymddygiad tebyg i transistor gyda cherrynt wedi'i fodiwleiddio yn electrocemegol. Rydym hefyd wedi dangos bod arwynebau protein yn gallu dargludedd electrostatig trwy ddeunyddiau nano-carbon felly paratoi'r ffordd ar gyfer biosynwyryddion y genhedlaeth nesaf.
Peirianneg proteinau gan ddefnyddio cod genetig estynedig
Rydym yn defnyddio cod genetig estynedig i beiriannu proteinau i gynnwys amrywiaeth cemegol newydd. Mae'r cod genetig a rennir yn cyfyngu'r rhan fwyaf o organebau i ymgorffori'r un 20 asidau amino mewn proteinau, gan gyfyngu ar yr ymarferoldeb cemegol sydd ar gael. Bydd ehangu'r cod genetig i ganiatáu ymgorffori asidau amino nad ydynt yn naturiol a allai fod yn ddefnyddiol mewn cadwyn polypeptid sy'n tyfu in vivo yn cynhyrchu proteinau gyda phriodweddau ffisiocemegol a biolegol newydd a gwell nad ydynt yn hygyrch yn Nature. Bydd hyn yn ei dro yn darparu dulliau newydd ar gyfer astudio agwedd foleciwlaidd a chellog swyddogaeth protein ac ar gyfer addasu proteinau ar gyfer cymwysiadau biotechnolegol. Mae'r grŵp yn datblygu dulliau cyfrifiadurol i ragweld effaith ymgorffori asid amino annaturiol ar swyddogaeth protein, ac i ddefnyddio'r cemeg newydd i addasu proteinau i'w defnyddio mewn meysydd sy'n amrywio o ddulliau bioddelweddu newydd i gydosod bionanohybrid o'r gwaelod i fyny.
Dulliau sy'n seiliedig ar drawsposon ar gyfer esblygiad wedi'i gyfeirio
Rydym hefyd wedi datblygu ystod o dechnolegau sy'n seiliedig ar transposon i samplu amrywiol ddigwyddiadau treiglad gwahanol nad ydynt fel arfer yn cael eu samplu yn ystod esblygiad cyfeiriedig. Gellir defnyddio'r dull i fewnosod neu ddileu lluosrifau o dri niwcleotid sy'n arwain at ddileu neu fewnosod asidau amino yn y ffrâm mewn safleoedd ar hap mewn protein. Mae treigladau indel yn newid strwythur ac felly swyddogaeth protein mewn ffyrdd nad ydynt yn hygyrch i fwtaniadau amnewid yn unig gan ehangu'r dilyniant, y strwythur a'r gofod swyddogaethol a samplwyd gan esblygiad cyfeiriedig. Rydym hefyd wedi ymestyn y dulliau hyn i ganiatáu disodli un dilyniant trinucleotid gydag un arall naill ai wedi'i bennu ymlaen llaw (e.e. TAG) neu ar hap (e.e. NNN). Mae hyn yn caniatáu i esblygiad cyfeiriedig gyflawni swyddogaeth "sganio mutagenesis" a goresgyn y problemau "rhagfarn codon" sy'n gynhenid gyda dulliau esblygiad cyfeiriedig presennol. Mae'r dull sy'n seiliedig ar drawsposon hefyd wedi cael ei ddefnyddio i greu sgaffaldiau protein newydd trwy ailgyfuno dau brotein gwahanol fel arfer, nad ydynt yn homolog, gan greu proteinau chimerig newydd.
Cyllid
- Cartref
- Swyddi
- KESS
- Swyddi
- Ymddiriedolaeth Wellcome
- Y Gymanwlad SC
Myfyrwyr ymchwil ôl-raddedig
- Ameilia Francis
- John Mclarnon
- Danoo Vitsupakorn
- Athena Zitti
Cydweithio
Mewnol
- Yr Athro Paola Borri (Biowyddorau) a Wolfgang Langbein (Ffiseg) (dulliau bioddelweddu newydd)
- Yr Athro Colin Berry (peirianneg protein pryfleiddiol a bioleg strwythurol)
- Yr Athro Emyr Macdonald (Moleciwl protein sengl ET - Ffiseg)
- Dr Pierre Rizkallah (Pennu strwythur protein – Meddygaeth)
- Dr Oliver Castell (Fflworoleuedd un moleciwl – Fferylliaeth)
- Dr Georgina Menzies (dynameg foleciwlaidd - Biowyddorau)
Allanol
- Dr Matteo Palma (QMUL). Bionanohybirds ar gyfer dargludedd
- Dr Eugen Stulz (Southampton). Cynulliadau ar raddfa nano
- Dr Chris Pudney (Caerfaddon). Dynameg protein a fflworoleu.
- Dr Nehad Noby (Prifysgol Alexandria, yr Aifft). Strwythur a pheirianneg esterase
- Dr Will Kelton (Prifysgol Waikato, Seland Newydd)
- Dr Sebastian Cote (Prifysgol Montreal, Canada).
- Dr Ivan Bobrinetskiy (Sefydliad BioSense)
-
Addysgu
Main teaching duties
1st Year. BI1001. Research Techniques
2nd Year. BI2232. Biochemistry.
3rd Year. BI3255. Synthetic Biology and Protein Engineering (Module lead). BI3001 - Final Year Project.
4th Year. BI4001. Advanced Reseach Project.
Bywgraffiad
Ar ôl ennill fy BSc mewn Biocemeg o Brifysgol Cymru, astudiais ar gyfer fy PhD mewn strwythur protein a pheirianneg ym Mhrifysgol Caergrawnt dan oruchwyliaeth yr Athro Richard Perham, gan dderbyn fy ngradd doethuriaeth ym 1999.
Mae fy ymchwil bellach wedi canolbwyntio ar strwythur protein a pheirianneg, ar ôl dal swyddi ymchwil yn y sectorau academaidd (Canolfan Peirianneg Protein MRC yng Nghaergrawnt a'r Adran Cemeg, Prifysgol Caergrawnt) a Chymrodoriaeth Ddiwydiannol Marie Curie yn Novozymes A / S Copenhagen, Denmarc). Symudais i Gaerdydd ym mis Medi 2003.
Rwyf wedi gwasanaethu ar banel thema Strwythur a Swyddogaeth Moleciwlaidd y Gymdeithas Biocemegol, gan drefnu dwy gynhadledd peirianneg protein lwyddiannus gan ddenu rhai o'r ymchwilwyr gorau o bob cwr o'r byd. Rwyf hefyd yn represenatives y DU o INPEC (International Network of Protein Engineering Centres).
Ymhlith fy ndyletswyddau addysgu amrywiol, rwy'n gydlynydd modiwl BI3255 (Bioleg synthetig a Pheirianneg Protein).
Meysydd goruchwyliaeth
Peirianneg protein, yn enwedig protein fflwroleuol
Adeiladu BioNanoHybrids defnyddiol lle mae protein yn gweithredu fel y lefel moleciwl sengl yn cael ei ddefnyddio i fodiwleiddio deunyddiau cynnal fel nano-carbon.
ymwrthedd gwrthficrobaidd.
Bioleg strwythurol ensym a dynameg.
Goruchwyliaeth gyfredol
Athena Zitti
News articles
Contact Details
+44 29208 74290
Adeilad Syr Martin Evans, Ystafell Cardiff School of Biosciences, Main Building, Museum Avenue, Cardiff, CF10 3AT, Rhodfa'r Amgueddfa, Caerdydd, CF10 3AX
Themâu ymchwil
Arbenigeddau
- Proteinau a peptidau
- Peirianneg foleciwlaidd feddygol asidau a phroteinau niwcleig
- Nanobiotechnoleg
- Biocemeg
- Dylunio a pheirianneg protein
