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Dafydd Jones

Yr Athro Dafydd Jones

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Ysgol y Biowyddorau

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Prif ffocws y grŵp Jones yw plastigrwydd strwythurol a swyddogaethol proteinau. Mae ein hymchwil yn cynnwys astudio a pheirianneg amrywiaeth o systemau protein, gan ganolbwyntio ar broteinau fflwroleuol a systemau ymwrthedd gwrthfiotig. Mae llawer o waith y grŵp yn gorwedd ar y rhyngwyneb rhwng bioleg, cemeg a ffiseg ac mae ganddo sail yn ochr brotein bioleg synthetig lle rydym yn adeiladu cydrannau proteinau newydd, sgaffaldiau newydd a systemau bionanohybrid. Mae gennym ddiddordeb cyfranogol mewn cyflwyno cemeg newydd i broteinau trwy ddefnyddio dulliau cod genetig estynedig a phroteinau sy'n rhyngwynebu mewn modd wedi'i ddylunio gyda nano-ddeunyddiau i gynhyrchu ar gyfer nanoddyfeisiau protein-giât ac electroneg biomoleciwlaidd. Rydym hefyd wedi datblygu nifer o ddulliau sy'n seiliedig ar drosposon ar gyfer esblygiad dan gyfarwyddyd proteinau gan ddefnyddio ailgyfuniad nad yw'n homologous. Mae'r grwpiau'n defnyddio amrywiaeth o ddulliau gan gynnwys dylunio cyfrifiadurol, peirianneg protein rhesymegol ac esblygiad wedi'i gyfarwyddo â bioleg strwythurol, dadansoddi moleciwlau sengl, deinameg molecwlaidd, bioffiseg a thechnegau biocemegol a ddefnyddir i ymchwilio i briodweddau'r proteinau newydd hyn.

Adnoddau

Dyma ddolen i fy Tutoria PyMOLl <<<<<

Newyddion

Cydgynllwynio gwych rhwng Sébastien Côté (U o Montreal, Canada), Chang-Seuk Lee (Prifysgol Merched Seoul, S Korea) ac eto gyda Matteo Palma (QMUL) ar sut y gwnaethom ddefnyddio efelychiadau cyfrifiadurol a modelu i ragweld sut y bydd proteinau yn giât electrostatically transistorau effaith maes nanodiwb carbon. Cyhoeddwyd y gwaith ymchwil yn Nature Communications

Mae gennym grant TRT BBSRC newydd i weithio ar ddatblygu offer protein fflwroleuol newydd i fonitro ffurfio protein cymhleth. Cydweithrediad gwych gyda'i gydweithwyr 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'i gydweithwyr Georgina Menzies , Stephen Wells, a Chris Pudney yn dangos bod gylcans wedi gwneud y radish ceffylau ensym commerical pwysig peroxidase yn fwy anhyblyg - ie'n fwy anhyblyg - a'i wneud yn llawer mwy egnïol a sefydlog o'i gymharu â'i ffurf nad yw'n glycosylated. Defnyddiwyd cyfuniad da o arbrofi ac efelychu i ddangos sut y cafodd yr effeithiau strwythurol a'r ddeinameg eu manfestio. 

Roedd gennym lawer o ddiddordeb yn ein papur diweddar mewn Deunyddiau Swyddogaethol Uwch ynghylch defnyddio proteinau blawd i gategori dargludiad nanotiwbiau carbon yn optegol, gan gynnwys erthyglau a amlygwyd yn Phys.org, AAS EurekAlert, Rhwydweithiau Technoleg ymhlith eraill. Yn y bôn, rydym yn dangos y gall GFP alluogi naill ai transistor optegol neu swyddogaeth cof yn seiliedig ar sut rydym yn atodi'r protein i'r CNT yn ffotocemegol. Mae hyn i gyd wedi'i alluogi gan gemeg phenyl azide wedi'i amgodio yn enetig. 

Papur newydd a gyhoeddwyd yn Open Biology gan ddefnyddio biocemeg, bioleg strwythurol a dynameg moleciwlaidd i ddeall addasiad oer o esterase IV teulu. Gwelwn nad dynameg byd-eang a lleol yw'r prif ysgogwyr ar gyfer gweithgarwch oer ond yn fwyaf tebygol o ryngweithio toddyddion a mynediad i'r safle gweithredol. Cydweithrediad rhyngwladol rhagorol â Nehad Noby ym Mhrifysgol Alexandria yn yr Aifft ynghyd â Stephen Wells a Chris Pudney yng Nghaerfaddon.

Papur newydd a gyhoeddwyd yn Angewandte Chemie Int Ed yn cyfuno bioleg synthetig â nanowyddoniaeth ynghylch sut mae dargludedd yn newid trwy nanodiwb carbon trwy newid yr arwyneb electrostatig protein lleol o fewn hyd Debyd. Yn hanfodol oedd diffinio'r rhyngweithio protein-CNT fel y gallwn reoli pa arwyneb electrostatig sy'n dod yn agos at y CNT. Rydym wedi dod at  ein gilydd i  Rydym yn defnyddio hyn i ganfod proteinau sy'n gysylltiedig ag achosi ymwrthedd i wrthfiotigau cyffredin. Cydweithrediad gwych arall gyda Matteo Palma yn QMUL.

Grant Gorwelion Newydd EPSRC hynod gystadleuol a ddyfarnwyd am ddatblygu chwiliedydd coch / IR wedi'i amgodio yn enetig ar gyfer dulliau bioddelweddu newydd. Cydweithrediad ardderchog gyda Paola Borri, Wolfgang Langbein a Pete Watson.

Ymchwil

The Jones group focus on understanding the molecular basis of protein plasticity in terms of structure, function and folding, and its application to the construction of new protein components and systems. The ultimate aim is to address one of the fundamental questions in biology: how amino acid sequence encodes the information for a protein to fold to its functional 3D structure. Our group collaborates chemists, structural biologists, computer modellers and physicists. Constructing new protein components means our work is closely aligned with the areas of synthetic biology and nanoscience/nanotechnology.

Protein structure, function, dynamics and engineering

The structure, function and folding of a range of proteins are investigated using biochemical, biophysical, structural biology and molecular dynamics. One of the main focuses of the group currently are fluorescent proteins, haem binding proteins and ß-lactam antimicrobial resistance systems. We also have an interest in various enzymes including the subtilisin serine proteases and cold-active esterases.

A full list of the structure determined by the group can be found here.

Construction of artificial protein scaffolds

The ability to design new proteins with activities not part of the natural repertoire is essential as part of the development of synthetic biology and bionanotechnology. As a general approach for creating tailored protein components with unique but useful properties, we couple the structures and hence functions of normally unrelated proteins or even non-protein materials so as to link the function. To achieve this, existing proteins will require radical redesign or even the creation of new scaffolds. However, natural proteins provide the inspiration and guidance during construction. One key aspect we aim for is synergy between different components so that one component “talks” to the other.

The group uses a variety of approaches to construct these new scaffold including: (1) domain insertion by directed evolution; (2) rational domain grafting; (3) linking proteins via click chemistry; (4) constructing bionanohybrids in which proteins are linked to secondary molecular systems such as DNA origami and nano-carbon.

We have recently successfully demonstrated designed interfacing of proteins to both the side-wall and end wall of nano-carbon systems using both light and click chemistry approaches. The two systems are functionally coupled due to the designed and intimate interface between the two molecular systems.

Single molecule studies of electron and energy transfer proteins

Electron and energy transfer plays a vital role in biology being pivotal to processes such as photosynthesis, respiration and enzyme catalysis. Such proteins essentially work at the single molecule but most approaches at analyse at the bulk level so all the important detail becomes averaged out. Furthermore, given that proteins self assemble, organise and modulate electron/energy transfer system at the single molecule, there is potential for the adaptation for use as nanodevices, including molecular transistors and biomolecular electronics. The Jones groups has been involved in interdisciplinary research collaborations aimed at investigating the single molecule behaviour these systems. Proteins are engineered for specific residues to allowed defined and precise interactions with conducting surface and materials. This has led to several important developments in the area of molecular electronics and single protein molecule studies. Notably, we have demonstrated for the first time direct coupling of a protein to both electrodes allowing ET to be monitored at the single molecule level.

Our studies revealed that cytochrome b562 was remarkably conductive and exhibited transistor-like behaviour with current modulated electrochemically. We have also shown that protein surfaces can electrostatically gate conductance through nano-carbon materials so paving the way for next-generation biosensors.

Engineering proteins using an expanded genetic code

We use an expanded genetic code to engineer proteins to contain new chemical diversity. The shared genetic code restricts most organisms to the incorporation of the same 20 amino acids into proteins, thus limiting the chemical functionality available. Expansion of the genetic code to allow the incorporation of potentially useful non-natural amino acids into a growing polypeptide chain in vivo will generate proteins with novel and enhanced physicochemical and biological properties not accessible in Nature. This in turn will provide new approaches for studying both the molecular and cellular aspect of protein function and for adapting proteins for biotechnological applications. The group are developing computational approaches to predict the effect of non-natural amino acid incorporation on protein function, and to use the new chemistry to adapt proteins for use in areas ranging from novel bioimaging approaches to bottom-up bionanohybrid assembly.

Transposon-based methods for directed evolution

We have also developed a range of transposon-based technologies to sample various different mutational events not normally sampled during directed evolution. The method can be used to insert or delete multiples of three nucleotides resulting in the in-frame deletion or insertion of amino acids at random positions in a protein. Indel mutations alter the structure and hence function of protein in ways not accessible to substitution mutations alone thus expanding the sequence, structure and functional space sampled by directed evolution. We have also extended these methods to allow the replacement of one trinucleotide sequence with another either predetermined (e.g. TAG) or random (e.g. NNN) sequence. This allows directed evolution to perform a "scanning mutagenesis" function and overcome the "codon bias" problems inherent with existing directed evolution methods. The transposon-based method has also been used to create new protein scaffolds by recombining two normally disparate, non-homologous proteins, so creating novel chimeric proteins.

Funding

  • BBSRC
  • EPSRC
  • KESS
  • MRC
  • Wellcome Trust
  • Commonwealth SC

Postgraduate research students

  • Ms Rebecca Gwyther
  • Ms Rochelle Ahmed
  • Ms Athena Zitti
  • Mr Ozan Aksakal
  • Ms Lainey Williamson (2nd-supervisor).

Collaborations

Internal

External

  • Dr Matteo Palma (QMUL). Bionanohybirds for conductance
  • Dr Eugen Stulz (Southampton). Nanoscale assemblies
  • Dr Chris Pudney (Bath). Protein dynamics and fluoresence.
  • Dr Nehad Noby (Alexandria University, Egypt). Esterase structure and engineering
  • Prof Alexander Nemukhin (Lomonosov Moscow State University, Russian Federation). QM/MM of fluorescent proteins.

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

Ozan Aksakal

Ozan Aksakal

Arddangoswr Graddedig

Athena Zitti

Athena Zitti

Arddangoswr Graddedig

Contact Details

Email JonesDD@caerdydd.ac.uk
Telephone +44 29208 74290
Campuses 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