Dr D. Dafydd Jones

Dr D. Dafydd Jones

Reader, School of Biosciences

School of Biosciences

Email:
jonesdd@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4290
Location:
Main Building, Park Place, Cardiff, CF10 3AT
Media commentator

Research overview

The main focus of my research group is exploring the structural and functional plasticity of proteins. Our research involves the study and engineering of specific protein systems, construction of artificial protein scaffolds and utilisation of expanded genetic code for non-natural amino acid incorporation. Much of the group's work has a basis in synthetic biology whereby we construct new protein components or modify existing proteins for new applications, including single molecule electron transfer. Both rational protein engineering and directed evolution are used to create new proteins and structural biology, single molecule analysis, molecular dynamics, biophysics and biochemistry are used to investigate the properties of these novel proteins. We have also recently developed several transposon-based methods for the directed evolution of proteins using non-homologous recombination.

After gaining my BSc in Biochemistry from the University of Wales, I studied for my PhD in protein structure and engineering at Cambridge University under the supervision of Prof Richard Perham, being awarded my doctorate degree in 1999.

My further research has centered on protein structure and engineering, having held research positions in both the academic (MRC Centre for Protein Engineering in Cambridge and the Department of Chemistry, Cambridge University) and industrial (Marie Curie Industrial Fellowship at Novozymes A/S Copenhagen, Denmark) sectors. I moved to Cardiff in September 2003.

Amongst my various teaching duties, I am coordinator for the Professional Training Year (sandwich) program for the Biomolecular degree schemes.

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 and folding

The structure, function and folding of a range of proteins are investigated using biochemical, biophysical, structural biology and molecular dynamics. The group focuses on serine proteases, notably the subtilisin class, fluorescent proteins, luciferase and lipoyl domains. Our achievements the first crystal structure of an intracellular subtilisin that revealed an original combined mechanism for protease regulation inside the cell; high resolution structure of one of the most important variants of GFP (EGFP) that reveals alternate conformations of critical functional residues; structural basis of novel protein misfolding events.

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 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. Both rational protein engineering and a recently developed transposon-based non-homologous directed evolution method are used to construct artificial protein scaffolds. We use various metal/porphyrin binding proteins (e.g. cyt b 562), DNA binding proteins (e.g. leucine zippers), enzymes (e.g. TEM-1) and fluorescent proteins as the templates for our novel protein switches.

Single molecule studies of electron transfer proteins

Electron 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 transfer system at the single molecule, there is potential for the adaptation for use as nanodevices, including molecular transistors. The Jones groups has been involved in a interdisciplinary research collaboration aimed at investigating the single molecule behaviour of electron transfer proteins. Electron transfer (ET) proteins are engineered for defined and controlled interactions with metal surfaces. 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.

Engineering proteins using an expanded genetic code

We are exploring the an expanded of the genetic code to engineer proteins that sample 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 to proteins. 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.

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

Collaborations

Internal

External

  • Prof Jens Ulstrup and Dr Qijin Chi (Single protein molecule ET - DTU, Denmark)
  • Dr Paul Barker (Protein engineering - University of Cambridge)
  • Dr Mark Howard (Protein NMR – University of Kent)
  • Prof Keith Wilson (Structural biology – York University)