A biomolecular-design approach in synthetic biology: towards synthetic cytoskeletons

Lead Research Organisation: University of Bristol
Department Name: Chemistry

Abstract

Biology provides a wealth of information, materials and inspiration for engineering new biomaterials and functional systems. In turn, these new entities may find applications in areas from electronics through to medicine. It is early in the development of our understanding of the principles upon which biological components--proteins, cells, tissues etc--are built; and we are only just beginning to tap the potential of this knowledge. Endeavours to reduce biological complexity to principles and manageable building blocks, and then piece these together to form new materials and systems are known as 'synthetic biology'. This is a very new and exciting science. There's a catch, however: we're not very good at it at the moment. Natural biological systems largely comprise six types of molecule: carbohydrates, lipids, nucleic acids, proteins, a wide variety of 'small molecules' and water. Each of these have their own niche functions: water is the solvent; amongst other things, small molecules provide the common currency of energy and rapid means of signalling throughout biology; carbohydrates provide structure and accessible sources of energy; lipids form the membranes that wrap up cells and functional compartments within cells; and nucleic acids store and pass on the information to make proteins, cells and so on. We have left proteins until last as they are somewhat unique in that they perform a myriad of functions: some are structural, others signal, many act on small molecules, more still provide the basis of our defence and immune systems, and so on. A key feature of Nature is that it uses 'self-assembly' to piece its components together--i.e., the above biomolecules are somehow programmed to interact and cooperate in precise ways--which is very different from how our everyday technologies are currently built. This proposal has two broad aims: first, we aim to reduce the complexity of Nature and create a toolkit of bioinspired building blocks, which will allow the programmed and reliable self-assembly of new biomaterials and functional systems. Second, we will make a start at piecing the building blocks together to form biomimetic systems that capture the key features of biological assemblies such as networks of proteins and cells, albeit crudely in the first instance. One of the targets of our study are small proteins called peptides, which can be made in the lab relatively easily. We wish to learn from Nature how the different chemistries of certain peptides instructs them to form the well-defined 3D structures upon which much of biology is built. This will require examining natural peptides, finding 'rules' that drive their folding and self-assembly. Our second targets are the lipid membranes. We need these to help encapsulate the protein assemblies that we plan to make, and we need encapsulation so that we can gain some control over the systems that we aim to generate. This is precisely why biology uses encapsulation. Why do all of this? The famous physicist, Richard Feynman once remarked that what he could not build, he did not understand. This is the principle that we have adopted for our research: we plan to look at natural biological systems, learn from them, and then test our understanding by designing and attempting to construct new simplified systems. This will not be easy and there is a risk of failure. However, the potential rewards are high: we stand to learn how some of biology's components assemble at the very least; and this understanding can then be applied by us and by others to create new biomaterials, devices and systems that might eventually find applications in medicine, electronics and analytical science.

Technical Summary

This is a multi-disciplinary proposal involving bioinformatics analysis of peptide- and protein-folding motifs; peptide chemistry to create the target peptide tectons and self-assembling units; and a range of biophysical techniques to characterise molecules in solution, with micelles and in lipid-based membrane systems. Towards objectives 1 and 2-i.e., the creation toolkit of peptide and lipid-based tectons and self-assembling units, and the Pcomp Database-we will combine bioinformatics with peptide design, synthesis and characterisation. In particular, we will glean sequence-to-structure relationships for defined protein structures, such as antiparallel helix-turn-helix motifs. The resulting protein-folding rules will be tested experimentally through de novo peptide design. Along with more-basic building blocks, these designs will be synthesised and then characterised by solution-phase biophysics (CD, FT-IR and fluorescence spectroscopy, ITC and AUC) and advanced microscopy (light, confocal, electron and atomic force). Towards objective 3-the generation of new biomaterials and encapsulated multi-component systems-we will test and develop principles and methods for combining the above tectons and self-assembling units to create new materials and self-organising systems. Similar biophysical and microscopic techniques will be used to characterise these new materials and systems. To help achieve our ambitious goals, we propose a team comprising: group leaders expert in peptide design, synthesis and characterisation (Woolfson), and membrane-protein folding, assembly and characterisation (Booth); and post-doctoral scientists experienced in bioinformatics (Bartlett), peptide chemistry (Thomson), peptide biophysics (TBA) and lipid biophysics (TBA). In addition, we have a number of collaborations-in protein crystallography, physical chemistry, vesicle fusion, advanced microscopy and optical tweezers-which will be called upon as the programme progresses.

Publications

10 25 50
 
Description We have made a series of peptide modules for applications in synthetic biology. We have applied this in an entirely new mode for constructing self-assembling nanoparticles and peptide cages that could find applications in drug delivery, vaccine development and biotechnology.
Exploitation Route See above - drug delivery, vaccine development and biotechnology. We have patent protected this technology.
Sectors Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Title Self-assembling peptide cages from coiled-coil peptide modules 
Description Invention based on our 2013 Science paper. 
IP Reference WO2014167350 
Protection Patent granted
Year Protection Granted 2014
Licensed No
Impact Led to new BBSRC awards for cell delivery and vaccine development. Is part of the BBSRC-funded BrisSynBio SBRC portfolio.
 
Description BBSRC PR: Designer barrel proteins 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Science publication, Computational design of water-soluble a-helical barrels [Science 24 October 2014: Vol. 346 no. 6208 pp. 485-488 DOI: 10.1126/science.1257452] was publicised on the BBSRC news page.

Unknown.
Year(s) Of Engagement Activity 2014
URL http://www.bbsrc.ac.uk/news/industrial-biotechnology/2014/141024-pr-bristol-team-creates-barrel-prot...
 
Description Parliamentary Science Committee presentation 2014 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Approximately 200 people attended the Parliamentary and Scientific Committee meeting on the 17th June 2014. The audience included Parliamentarians, members of scientific bodies, science-based industry and academics.
http://www.scienceinparliament.org.uk/sample-page/programme/
This meeting has subsequently been written up and included in the Autumn 2014 Science in Parliament (Vol 71 No 4: pgs 20 - 26) publication.

Unknown
Year(s) Of Engagement Activity 2014
URL http://www.scienceinparliament.org.uk/wp-content/uploads/2013/09/Autumn-Contents-page.pdf
 
Description Pint of Science Festival: Dark side of protein science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact As part of the Pint of Science Festival, researchers from BrisSynBio participated in the 'Dark Matters' event. The event was held in Friska café, Bristol, and involved scientific crafts and discussions between researchers and the public.
Director of BrisSynBio, Professor Dek Woolfson, along with Gail Bartlett, Jack Heal, Drew Thomson and Chris Wood organised the event 'Dark Matters'. Analogous to the idea of dark matter, protein science focuses on the protein structures that could theoretically exist but are not present in natural biology.
Year(s) Of Engagement Activity 2015
URL http://www.bristol.ac.uk/publicengagementstories/stories/2015/dark-side-protein-science.html
 
Description Pint of Science, Bristol, UK, May 2015, "From galaxies of stars to a new universe of proteins" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Part of the Pint of Science 2015 Programme in Bristol. About 60 people attended.
Year(s) Of Engagement Activity 2015
URL https://pintofscience.co.uk/event/dark-matters/
 
Description RSC: Synthetic Biology: The Free Edinburgh Festival Fringe Show (Heal) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Supported by an award from the Royal Society of Chemistry,the Edinburgh Fringe Festival hosted its first science stand-up on the subject of synthetic biology. Jack Heal's 'Do Scientists Dream of Synthetic Sheep?' show took a comedic approach to genome engineering, de-extinction and more - with the crowd helping to shape its direction with questions and discussion. The show considered questions from artificial life to Jurassic Park, and ran for 21 days.
Purpose: To interest the public in science.
Outcome: The comic felt freshly enthused about doing [synthetic biology] research.
Reflection: Free shows encourage people to take risks in their choices of which shows to see. This spirit is perfect for science outreach events which have to try hard to avoid becoming 'by scientists, for scientists'.

None yet.
Year(s) Of Engagement Activity 2014,2015
URL http://www.bristol.ac.uk/publicengagementstories/stories/2016/jack-heal.html?platform=hootsuite
 
Description Synthetic proteins for a synthetic biology: faster, fitter, stronger 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Better Humans Science Café, Bristol, UK, October 5 2016, "Synthetic proteins for a synthetic biology: faster, fitter, stronger"
Year(s) Of Engagement Activity 2016
 
Description The rise and rise of synthetic biology in the UK: science, policy and public perception 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Invited to Houses of Parliament, London, UK, June 2014, to speak to the Parliamentary and Scientific Committee.
Year(s) Of Engagement Activity 2014
URL http://www.scienceinparliament.org.uk/wp-content/uploads/2014/05/17-June-AGM-agenda.pdf