Synthetic Components Network (SCN)

SSCCNN LLooggoo

The first annual conference of the

SSyynntthheettiicc CCoommppoonneennttss NNeettwwoorrkk SSyynntthheettiicc BBiioollooggyy ffrroomm tthhee bboottttoomm uupp

23 – 24 September 2009 St Anne’s College Oxford

SCN Annual Conference, 23rd – 24th September 2009 Welcome

Welcome message

Dear all,

Welcome to St Anne’s College, and the first Annual Conference of the Synthetic Components Network (SCN).

First of all thank you to everyone who has contributed to the exciting conference programme, which represents the breadth and depth of research and expertise across the Network. We hope that the programme, together with the poster sessions, will provide a real insight into some of the work already going on in the Network, and highlight some of the areas that are ripe for collaboration. Indeed, our overall objective is to foster communication and collaborations across the Network, but, of course, whether this happens is ultimately up to you.

We are also very pleased to welcome the PIs of three other BBSRC/EPSRC-funded Networks in Synthetic Biology. They will be taking part in the panel Q&A session on Wednesday evening. The aim here is not to define what synthetic biology is, but to explore what people understand by it more broadly. We hope you will use this session to find out about how the other Networks view Synthetic Biology, learn something of the projects that are underway in them, and to explore opportunities for wider collaborations.

Because new interactions and exploring potential collaborations are key, we have left plenty of time for networking and discussion over lunches, dinner, poster sessions, and in the bar!

Finally, your feedback on how this meeting goes, and how it might be improved in future will be very welcome. Please give this to us, to Kathleen Sedgley directly, or use the tear-out form at the end of this programme.

We hope you enjoy this first Annual Conference and the scientific and social interactions that it fosters.

Best wishes,

Dek Woolfson and Jonathan Rossiter

SCN Annual Conference, 23rd – 24th September 2009 Contents

Table of Contents

Welcome from Dek 2

Programme 4

Session 1: Components and self-assembly 6

Session 2: Encapsulation 11

Session 3: ELSI 15

Session 4: Responsive materials and movement 16

Session 5: Public engagement 19

Session 6: Towards systems 20

Panel Q&A session: What is Synthetic Biology and who cares? 25

Poster session PIs 29 PhDs and PDRAs 34

Delegate list 44

Thank you 46

Researcher exchange form 47

Feedback form 49

Maps 51

SCN Annual Conference, 23rd – 24th September 2009 Programme

Programme

------WEDNESDAY 23RD ------

09-30 – 10-20 Arrivals and coffee 10-20 – 10-30 Welcome Dek Woolfson, Bristol Session 1: Components and self-assembly Chair: Louise Serpell, Sussex 10-30 – 11-00 William Taylor, NIMR Stick models of proteins 11-00 – 11-30 Andrew Turberfield, Oxford DNA nanostructures and molecular machinery 11-30 – 11-50 Karen Marshall, Sussex Structures of amyloid-like fibres and crystals formed from a self-assembling peptide 11-50 – 12-10 James Arpino, Cardiff Engineering allosteric control over GFP fluorescence 12-10 – 12-30 Craig Armstrong, Bristol Peptide components for Synthetic Biology 12-30 – 14-00 Lunch Session 2: Encapsulation Chair: Andrew Turberfield, Oxford 14-00 – 14-30 Steve Evans, Leeds Encapsulation: lipid membranes 14-30 – 15-00 Hagan Bayley, Oxford Engineered protein pores as components of soft micromachines 15-00 – 15-20 Nikolaos Daskalakis, Leeds Generating proton-motive force in probe-loaded vesicles 15-20 – 15-40 Jon Howse, Sheffield Vesicles by design 15-40 – 17-00 Posters Tea Session 3: ELSI ELSI research in SynBio: What’s being done? What should be done? 17-00 – 18-00 Lead: Ainsley Newson, Bristol 18-00 – 18-30 Drinks 18-30 – 20-00 Dinner

~ Wednesday’s programme continues over leaf ~

SCN Annual Conference, 23rd – 24th September 2009 Programme

Panel What is Synthetic Biology, and who cares? Discussion Short talks form PIs of Networks in Synthetic Biology followed by a panel Q&A session

Chair: Kathy Sykes, Bristol 20-00 – 21-30 Rob Edwards, Durham SPPI-NET: a network for synthetic plant products for industry Alistair Elfick, Edinburgh SynBio Standards: Standards for the design and engineering of modular biological devices John Ward, UCL Synbion: the UCP Network in Synthetic Biology Dek Woolfson, Bristol Synthetic Components Network 21-30 - late Bar

------THURSDAY 24TH ------

Session 4: Responsive materials and movement Chair: Mark Dillingham, Bristol 09-00 – 09-30 Neil Cameron, Durham Responsive materials from sugars and peptides 09-30 – 10-00 Richard Berry, Oxford Protein motors 10-00 – 10-20 Joe Yeeles, Bristol Activation of a helicase motor protein upon encounter with a specific sequence in the DNA track 10-20 – 11-30 Discussion session Coffee Session 5: Public engagement Public engagement with Synthetic Biology 11-30 – 12-30 Lead: Philippa Bayley 12-30 – 14-00 Lunch and discussion (Management Committee Meeting) Session 6: Towards systems Chair: Beth Bromley, Bristol & Durham 14-00 – 14-30 Caroline Colijn, Bristol Mathematical modelling in Synthetic Biology 14-30 – 15-00 Nigel Savery, Bristol Gene regulation by natural and synthetic components 15-00 – 15-20 Mike Sternberg, Imperial Tools for protein modelling 15-20 – 15-40 Paul Gardner, Oxford Sugar synthesis in a protocellular model leads to a cell signalling response in bacteria 15-40 – 16-00 Eric Tippmann, Cardiff Application of physical organic chemistry to an expanded genetic code 16-00 – 16-10 Summary and departures

SCN Annual Conference, 23rd – 24th September 2009 Session 1: Components and self-assembly Taylor, William Institution: National Institute for Medical Research

Oral presentation

Title: Stick models of proteins

Key words: Protein structure / topology / fold space

Abstract

The specification of a protein fold is typically viewed as poorly defined, being sensitive to secondary structure elements that may be based on marginal or unconserved hydrogen

bonds. We use of a secondary structure lattice based on regular layers of secondary structure to overcome this problem. or decoy models, the structure is built directly from the lattice and so their fold is predefined. For known structures, the ideal lattice must be matched to the structure and although this step might appear susceptible to marginal effects, we do not rely on a single best fit but retain all good fits to different lattice cores.

This does not provide a unique definition of a protein fold but a match to any of the variations counts as a hit, giving a ``fail-safe'' position towards matching known folds. These predefined fold definitions can be encoded as simple string of text (called a topology string), and there is no ambiguity in whether a pair of folds are the same as they will either have identical strings or strings that contain mismatches. This approach avoids the

problems encountered using RMSD-based measures associated with length differences and statistical significance. We used the more familiar RMSD measures as an extensive cross-check on our topological measure and it was clear that it could not distinguish many distinct topological changes against the background 'noise' associated with secondary structure shifts and loop variation.

This level of protein structure analysis has been used in the prediction of protein structure as well as the classification of structure. Most recently these two studies have been combined in an analysis of the folds generated during structure prediction. Of the many thousands of distinct folds constructed, only one-in-ten were found to exist among the known structure. The remainder have been likened to cosmological dark matter.

Taylor, W.R ., Chelliah, V., Hollup, S.H., MacDonald, J.T., Jonassen, I. (2009) “Probing the 'dark matter' of protein fold-space”. Structure 17:1244-1252

SCN Annual Conference, 23rd – 24th September 2009 Session 1: Components and self-assembly

Turberfield, Andrew Institution: University of Oxford

Oral presentation

Title:0B DNA nanostructures and molecular machinery

Key words: Nanostructure / self-assembly / molecular motor / Brownian ratchet

Abstract

DNA is a wonderful material for nanoscale construction: it is a structural material whose self-assembly can be programmed by making use of its information-carrying capability, and its hybridization or hydrolysis can be used as to provide energy for molecular devices. I shall describe our recent work on self-assembled molecular structures and on molecular machinery, including the free-running bipedal molecular motor shown above, which is a chemically fuelled Brownian ratchet inspired by kinesin. [1] Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C. & Neumann, J.L. A DNA- fuelled molecular machine made of DNA. Nature 406, 605-608. (2000) [2] Turberfield, A.J. et al. DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 4 (2003) [3] Goodman, R.P. et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661-1665 (2005) [4] Erben, C.M., Goodman, R.P. & Turberfield, A.J. Single-Molecule Protein Encapsulation in a Rigid DNA Cage. Angew. Chem. Int. Ed. 45, 7414-7417 (2006) [5] Bath, J. & Turberfield, A.J. DNA nanomachines. Nature Nanotech. 2, 275-284 (2007) [6] Green, S.J., Bath, J. & Turberfield, A.J. Coordinated Chemomechanical Cycles: a Mechanism for Autonomous Molecular Motion. Phys. Rev. Lett. 101, 238101 [7] Bath, J., Green, S.J., Allen, K.E. & Turberfield, A.J., Mechanism for a Directional, Processive, and Reversible DNA Motor. Small 5, 1513-1516 (2009)

SCN Annual Conference, 23rd – 24th September 2009 Session 1: Components and self-assembly Marshall, Karen E Institution: University of Sussex

Oral presentation

Title: Structures of amyloid-like fibres and crystals formed from a self-assembling peptide

Key words: Amyloid structure / Electron Microscopy / X-ray fibre diffraction / self- assembly / biomaterials

Abstract

Many proteins and peptides share the ability to self-assemble to form long (μm), unbranching fibres known as amyloid. Despite the differing sequences of the precursors, the resulting amyloid fibres have a similar cross-β architecture in which the protein backbone is aligned perpendicular to the fibre axis and hydrogen bonded to form a ladder-like arrangement. Amyloid is associated with diseases such as Alzheimer’s Disease, Diabetes type 2 and the systemic amyloidoses, but is also known to play a functional role in a number of organisms including E. coli (curli fibres), spiders (silk) and, more recently, in mammals (Pmel17). This illustrates how nature has exploited the

properties of amyloid in an advantageous way. Understanding the rules that govern

amyloid-like self-assembly can therefore provide insight into amyloid accumulation in

disease and also into how it can be exploited as a biomaterial. Short peptide sequences provide excellent model systems with which to investigate the structural intricacies of amyloid. Mutating particular residues gives information on the roles of individual amino

acids in driving amyloid formation and their contribution to the stability of the final

structure. Electron microscopy, X-ray fibre diffraction and biophysical techniques have

been combined to investigate the structure and assembly of variants of an amyloid forming peptide. Our results show that even apparently subtle changes in sequence can result in significant structural differences and highlight the importance of electrostatic

charges in amyloid formation. These results contribute to the emerging knowledge on the

design of amyloid-based biomaterials.

SCN Annual Conference, 23rd – 24th September 2009 Session 1: Components and self-assembly

James, Arpino Institution: Cardiff University

Oral presentation

Title: Engineering allosteric control over GFP fluorescence

Key words: GFP / Cyt b562 / Redox / Biosensor / Domain insertion.

Abstract

Domain insertion or integral fusion protein construction provides a strategy for generating novel proteins with the potential to act as molecular switches for use as, for example, biosensors. It is postulated that the integral fusion architecture will intimately link the structures so allowing communication between two normally unrelated proteins. Predicting sites within a target protein that will tolerate the insertion of another domain while maintaining the structure and functions of both domains and allowing communication of functions between the domains is difficult. Using a transposon-based directed evolution approach, DNA cassettes encoding a desirable insert protein can be randomly inserted throughout a target gene [1,2]. This technology allows insertion positions throughout a host protein to be sampled for viability and selection of variants with switching properties. Here, we describe the construction of novel integral domain fusions in which the redox active, haem-binding protein, cytochrome b (Cyt b ), is inserted within the enhanced 562 562 green fluorescent protein (eGFP) reporter. Cyt b562 binds haem in a redox-dependent manner and has been shown to quench fluorescence when in close proximity to the fluorophore within GFP. Cyt b562 also shows a change in structural stability upon haem binding thereby making it an attractive candidate for allosteric control of eGFP fluorescence. Such a protein has the potential to act as a genetically encoded cellular sensor of redox state and haem co-factor binding.

Library analysis has identified 12 positions within eGFP tolerant to Cyt b562 insertion. Tolerated insertion positions within eGFP include those into loop regions and organised secondary structure. All 12 variants exhibit fluorescence quenching with haem-binding and all show a difference in fluorescence quenching when under either reducing or oxidising conditions. Comparison of the variants identified one (CG6) that showed a marked difference in fluorescence quenching with haem binding, resulting in essentially no fluorescence with excess haem. CG6 also exhibited the largest difference between reducing and oxidising conditions and has been used to sense changes in redox conditions.

1. D. Dafydd Jones. Nucleic Acids Research, 2005, Vol. 33, No. 9 e80 2. Wayne R. Edwards et al. Nucleic Acids Research, 2008, doi:10.1093/nar/gkn363

SCN Annual Conference, 23rd – 24th September 2009 Session 1: Components and self-assembly

Armstrong, Craig Institution: University of Bristol

Oral presentation

Title: Peptide components for Synthetic Biology

Key words: protein design / domains / Synthetic Biology

Abstract

A reasonable starting point for the bottom-up approach to synthetic biology is at the protein domain level (1). Nature apparently utilizes a finite number of folding domains in many combinations, to give numerous proteins with emergent functions (2, 3). A select few of these domains, including coiled coils and zinc fingers, have been the subject of detailed characterization and engineering, yielding rules that can be incorporated into the

design of assemblies containing such domains. Many other domains, however, are relatively unchartered from a design perspective.

This talk will describe how we have used our current knowledge of well characterized

domains to create building blocks for synthetic biology, and peptide switches (single polypeptide sequences with structural duality (4)). It will also cover how we plan to broaden the range of folds we can reliably design, with the aim of creating novel domain assemblies with predictable function.

1. E. H. C. Bromley, K. Channon, E. Moutevelis, D. N. Woolfson, A.C.S. Chem. Biol.

3, 38 (2008). 2. C. Chothia, Nature 357, 543 (1992).

3. R. D. Finn et al., Nucleic Acids Res. 36, D281 (2008).

4. E. Cerasoli, B. K. Sharpe, D. N. Woolfson, J. Am. Chem. Soc 127, 15008 (2005).

SCN Annual Conference, 23rd – 24th September 2009 Session 2: Encapsulation

Evans, Steve Institution: University of Leeds

Oral presentation

Title: Encapsulation: lipid membranes

Key words: Lipid bilayers/ vesicles / protocell / cytoskeleton /actin

Abstract

The presentation will discuss the importance of the often-overlooked “container” within with biologic systems function. The constituents and properties of the lipid bilayers from which the cell wall, sub-cellular organelles and vesicles are constructed will be outlined. A number of examples will be described that demonstrate advances in our ability to create synthetic biomimetic containers- that could find use to create minimal functional units as part of the development of more complex protocell. Such examples include the ability to create asymmetric giant unilamellar vesicles, hybrid vesicle formation, targeting

and tethering of vesicles, and vesicle self-replication. Additionally we will also consider

the production of a facsimile of a simple cytoskeletal cortex within /on GUV’s and planar membranes. Finally, we demonstrate that the complexity of such membrane mimics can be increased to include multiple membrane proteins, which work together to produce an external peptidoglycan scaffold. This opens the way to investigate and modify the

individual steps involved in bacterial cell wall formation.

SCN Annual Conference, 23rd – 24th September 2009 Session 2: Encapsulation

Bayley, Hagan Institution: University of Oxford

Oral presentation

Title: Engineered protein pores as components of soft micromachines

Key words: micromachine / nanopore / network / prototissue

Abstract

One goal of synthetic biology is the manufacture of micromachines from simple parts. Such machines would be motile, able to generate, store and use energy, capable of sensing and carrying out computation, and able to take up substrates and convert them to products. We have found that aqueous droplets can be connected by lipid bilayers to form networks in a hydrocarbon environment. We propose that these networks can be

used as the basis for the construction of "soft micromachines", in contrast to nano- and microdevices made from relatively rigid parts such as DNA and protein rods.

Proteins can be incorporated in to the bilayers of the networks, which we have termed "droplet interface bilayers". Therefore, we propose that membrane proteins will play a

major role in the functioning of droplet-based micromachines. Towards this end, we have

engineered the staphylococcal α-hemolysin pore by genetic manipulation and chemical modification to endow it with a variety of properties. For example, we have been able to alter the pore size, and its ion selectivity and rectification properties. We have also altered the pore so that it can be regulated by chemicals, light and temperature. With

these components, we have shown that droplet networks can behave like simple

electrical circuits, be used to form tiny batteries and respond to light. With these subsystems in place, the manufacture of the proposed micromachines may be in the offing.

SCN Annual Conference, 23rd – 24th September 2009 Session 2: Encapsulation

Daskalakis, Nikolaos N Institution: University of Leeds

Oral presentation

Title: Generating proton-motive force in probe-loaded vesicles

Key words: proton gradient / ubiquionol oxidase / vesicles / pH-sensitive probe / functionalised electrodes

Abstract

An important component of bottom-up designed biomimicking or bionanotechnological systems is the encapsulation in membrane vesicles and the regulation of transport across this membrane. Also in living cells, transport of ions across membranes is a vital process for signal transduction and energetics that is regulated by membrane proteins acting as ion-channels or pumps. In cell respiration membrane-bound redox enzymes

utilise the free energy generated by electron transfer reactions to translocate protons across membranes, generating a proton-motive force used in living cells for ATP synthesis. Here, experiments in which proton gradients are generated in lipid vesicles will be discussed. Vesicles are loaded with a pH-sensitive fluorescent probe and

intravesicular pH is monitored in real time. A simple method to generate a proton

gradient is by changing the pH of the extravesicular solution. A more elaborate method is also explored in which transmembrane transport is generated by proton-pumping

enzymes. Vesicles containing an ubiquinol oxidase, cytochrome bo3, from Escherichia Coli are adsorbed on gold electrodes, functionalised specifically to retain the integrity of

the vesicles. A proton-motive force is then formed and controlled by electrochemical

tuning of the lipophilic ubiquinone redox state.

SCN Annual Conference, 23rd – 24th September 2009 Session 2: Encapsulation

Howse, Jonathan Institution: Sheffield University

Oral presentation

Title: Vesicles by design

Key words: Vesicles / self-assembly / wetting / photolithography / SAMs

Abstract

Unilamellar polymer vesicles are formed when a block-copolymer self-assembles to form a single bilayer structure, with a hydrophobic core and hydrophilic surfaces, and the resulting membrane folds over and rearranges by connecting its edges to enclose a space. The physics of self-assembly tightly specifies the wall thickness of the resulting vesicle, but, both for polymer vesicles and phospholipids, no mechanism strongly selects for the overall size, so the size distribution of vesicles tends to be very polydisperse. This presentation will report on a method for the production of controlled size distributions of micrometer-sized (i.e. giant) vesicles combining the 'top-down' control of micron sized features (vesicle diameter) by photolithography and dewetting with the 'bottom-up' control of nanometer sized features (membrane thickness) by molecular self- assembly. It allows the spontaneous creation of unilamellar vesicles with a narrow size distribution that could find applications in drug and gene delivery, nano and micro reactors, substrates for macromolecular crystallography and model systems for studies of membrane function.

SCN Annual Conference, 23rd – 24th September 2009 Session 3: ELSI

Newson, Ainsley Institution: University of Bristol

Discussion session

Title: ELSI research in SynBio: What’s being done? What should be done?

Key words: Synthetic Biology / Ethical aspects / Social aspects / Legal aspects / Research Agenda

Abstract

In this session, the ethical research landscape in synthetic biology to date will be explored. The ELSI (Ethical, Legal and Social Issues) agenda in SynBio is quickly gaining momentum and is attracting both research funding and attention from policy- makers in the UK and abroad.

Part of the session will involve a brief overview of what it means to do ELSI research and

how researchers in synthetic biology can consider the ethical aspects of their work. The terrain of ELSI research will then be mapped through a quick review of what is happening and where.

Some of the substantive ethical questions that have already arisen (or which will arise) in

SynBio will then be raised for discussion. The possible development of ELSI activity in

SynBio – and any limits or challenges to this – will then be explored. Participation from the audience is encouraged and there will be plenty of time for discussion and debate.

SCN Annual Conference, 23rd – 24th September 2009 Session 4: Responsive materials and movement

Cameron, Neil Institution: Durham University

Oral presentation

Title: Responsive materials from sugars and peptides

Key words: polymers / sugars / peptides / controlled polymerisation / self-assembly

Abstract

As a result of advances in synthetic polymer chemistry in the last 10-15 years, an enormous range of synthetic macromolecules that are both highly functional AND well- defined in terms of chain length and architecture is now available. There are several methodologies used to prepare such polymers, one of which will be discussed in this lecture: Reversible Addition Fragmentation chain Transfer (RAFT) polymerisation. RAFT

utilises highly efficient free radical chain transfer agents, such as dithioesters and trithiocarbonates, to prepare polymers with excellent control over chain length, narrow polydispersity indices and many different chain architectures and topologies (di-, tri- and multi-block copolymers; star polymers; hyperbranched polymers). In this lecture, the

ability of RAFT to prepare polymers with pendant biologically-relevant functionalities,

such as sugars and peptides, is presented. By controlling macromolecular architecture, these polymers can be made to assemble in aqueous solution into a range of nanoscale species, including spherical and wormlike micelles as well as vesicles (polymersomes). Bio-related functionality is expressed on the external surface of the resulting nanoscale

species, which can therefore be considered as very crude models of biological entities

such as viruses and cells.

SCN Annual Conference, 23rd – 24th September 2009 Session 4: Responsive materials and movement Berry, Richard Institution: University of Oxford

Oral presentation

Title: Protein motors

Key words: Molecular motors / single-molecules

Abstract

Biological molecular motors show us how directed motion can be generated by nanometer-scale devices that work at the energy scale of the thermal bath. Observations of functioning single molecular motors allow us to see fundamental processes of statistical physics unfolding in microscopic detail at room temperature, something that was unimaginable only a few decades ago. I will introduce molecular motors and the

physics relevant to their mechanisms before focusing on our recent experiments on the bacterial flagellar motor, the rotary device responsible for bacterial locomotion.

SCN Annual Conference, 23rd – 24th September 2009 Session 4: Responsive materials and movement

Yeeles, Joseph Institution: University of Bristol

Oral presentation

Title: Activation of a helicase motor protein upon encounter with a specific sequence in the DNA track

Key words: DNA motor protein / DNA helicase / DNA repair / energy transduction

Abstract

Helicases are ATP driven motor proteins that are essential for many aspects of DNA metabolism including replication and repair. They catalyse the unwinding of the DNA double helix into its component single-strands. The AddAB helicase-nuclease is a bacterial enzyme that is responsible for recognising and processing broken double- stranded DNA molecules. The enzyme unwinds and resects broken DNA ends, forming

structures that facilitate the faithful repair of breaks by promoting DNA replication. AddAB is a heterodimeric enzyme constructed of multiple modular domains, each of

which is responsible for conferring a specific function on the complex. Such functions

include DNA end-binding, DNA unwinding, DNA cleavage and DNA sequence recognition. The enzyme is powered by a single Superfamily 1A helicase motor domain, which facilitates rapid and highly processive DNA unwinding. Uniquely, the helicase activity of AddAB is stimulated in cis when the enzyme encounters a specific regulatory

sequence that is embedded in the DNA track along which it translocates. The molecular

basis of helicase stimulation has been investigated using both in silico modelling and in vitro DNA unwinding assays, which reveal a novel mechanism for the activation of a DNA helicase.

SCN Annual Conference, 23rd – 24th September 2009 Session 5: Public engagement

Bayley, Philippa Institution: University of Bristol, Centre for Public Engagement

Discussion session

Title: Public engagement with Synthetic Biology

Key words: Public engagement / tools / dialogue

Abstract

Engaging the public with the emerging science of Synthetic Biology, as well as with the ethical, legal and social issues that surround it, is an integral part of the Synthetic Components Network. Public engagement might involve anything from festivals, science cafes, or school visits, through to working with policy makers or the media. The Network wants to support its members to share their work with a range of audiences by creating

and sharing resources and tools for public engagement, as well as organising events in which all network members can participate.

At this practical session we will share resources that have already been developed by

Network members and by other networks and organisations, both to support researchers and to use with public audiences. We’ll talk about training, funding and public engagement opportunities that are coming up, and identify any needs in this area for Network members. This session will be informal and conversational, but you will leave

with clear ideas for engaging with the public.

SCN Annual Conference, 23rd – 24th September 2009 Session 6: Towards systems

Colijn, Caroline Institution: University of Bristol

Oral presentation

Title: Mathematical modelling in Synthetic Biology

Key words: mathematical models / gene regulatory networks / metabolism

Abstract

In this talk I will outline the broad potential for mathematical modelling and simulation in the field of synthetic biology. Models can play a range of useful roles, including requiring assumptions to be clearly elucidated, examining the quantitative impact of different system structures or assumptions, or integrating diverse data to explore complex interactions. All of these and more will have considerable relevance to synthetic biology,

particularly in “bottom-up” approaches where novel elements are to be combined and will have numerous, complex interactions. I will describe how models can assist in understanding the dynamics and function of gene regulatory networks. For example, so- called network motifs are small networks that are found far more often in real biological

systems than one would expect; understanding their origin and function means that the

useful functional properties of these motifs can be integrated into synthetic systems. Small sets of interacting genes can be modelled with ordinary differential equations, allowing the simulation and analysis of prospective cellular functions to guide experimental work. Finally I will discuss the integration of models of cellular metabolism

with gene regulation.

SCN Annual Conference, 23rd – 24th September 2009 Session 6: Towards systems

Savery, Nigel Institution: University of Bristol

Oral presentation

Title: Gene regulation by natural and synthetic components

Key words: Gene regulation / DNA-binding proteins / transcription factors / RNA polymerase

Abstract

Timely and accurate expression of genetic information is essential for life. In this talk I shall review the mechanisms by which bacteria control the expression of their genes in response to multiple signals, discuss some examples of synthetic gene regulatory networks, and consider the challenges invo lved in creating artificial systems for controlling gene expression.

SCN Annual Conference, 23rd – 24th September 2009 Session 6: Towards systems

Sternberg, Mike Institution: Imperial College London

Oral presentation

Title: Tools and resources for protein modelling

Key words: Protein / modelling / prediction / structure / function

Abstract

The Structural Bioinformatics Group at Imperial College London has developed several

resources for protein modelling which will be presented (see www.sbg.bio.ic.ac.ukHU ).UH

The most powerful method for protein structure prediction is to build a model based on homologues (templates) of known structure. A major challenge is developing powerful methods to recognise such homologues when the relationships are remote and standard sequence approaches fail. Our fold recognition program Phyre (Lawrence Kelley, Ben Jefferys , Ricardo Bennett-Lovsey & MJES) is available as a public web server and performed very well at the latest blind trial of structure prediction CASP8. In the absence of a known template, alternate methods are required and we (Ben Jefferys, Lawrence Kelley & MJES) are developing poing, which uses a simplified model of two centres per residue and simulates the pathway of folding using Langevin dynamics. Results of testing poing for structure prediction will be reported.

Another challenge is assigning function to a protein sequence or structure. We (Mark Wass & MJES) have developed Confunc which generates enhanced sequence signatures from homologues of known function to suggest function for a sequence. Two strategies have been developed to provide additional functional information given a protein structure. Mark Wass & MJES have developed an approach to predict which residues will be involved in ligand binding given a protein structure and this approach performed well at CASP8. We (Lawrence Kelley, Huma Lodhi, Stephen Muggleton and MJES) have developed a method using support vector inductive logic programming to predict whether a protein will bind NAD or FAD.

SCN Annual Conference, 23rd – 24th September 2009 Session 6: Towards systems

Gardner, Paul Institution: University of Oxford

Oral presentation

Title: Sugar synthesis in a protocellular model leads to a cell signalling response in bacteria

Key words: Artificial cells / Quorum sensing

Abstract:

The design of systems with life-like properties from simple chemical components may offer insights into biological processes, with the ultimate goal of creating an artificial chemical cell that would be considered to be alive. Most efforts to create artificial cells have concentrated on systems based on complex natural molecules such as DNA and RNA. Here we have constructed a lipid-bounded proto-metabolism that synthesizes

complex carbohydrates from simple feedstocks that is capable of engaging the natural quorum sensing mechanism of the marine bacterium Vibrio harveyi and stimulating a proportional bioluminescent response. This encapsulated system may represent a first step towards the realisation of a cellular ‘mimic’. and astarting point for bottom-up

designs of other chemical cells, perhaps that display complex behaviours such as

communication with natural cells.

SCN Annual Conference, 23rd – 24th September 2009 Session 6: Towards systems

Tippmann, Eric Institution: Cardiff University

Oral presentation

Title: Application of physical organic chemistry to an expanded genetic code

Key words: nonnatural amino acids

Abstract

New approaches for the translational and post-translational modification of proteins are presented. Using the fundamentals of physical organic chemistry, nonnatural amino acids may be chemically tailored to possess specific properties for highly specialised applications, for example, in the charting of biological pathways. In this scenario, a novel amino acid handle, with chemistry modulated with pH or ultraviolet light, could allow the

spatiotemporal control of an enzyme’s activity. Such amino acids are genetically

encoded in vivo, using a suitable host organism, in response to a recoded amber stop codon. The overall goals of our research are to develop novel amino acids, but also to advance the understanding of the mechanism and function of bioorthogonal translation elements.

SCN Annual Conference, 23rd – 24th September 2009 NSB Panel Q&A Session

Edwards, Rob Institution: University of Durham

Panel Discussion: What is Synthetic Biology and who cares?

PI: SPPI- NET: a network for synthetic plant products for industry

Key words: Biorenewables / plant biofactories/ rational metabolic engineering

Abstract

SPPI-NET has been created as a response to our increasing use of biologically renewable materials as feedstocks for industry as replacements for fossil fuel sources. Current activities in biorefining such as the Integrated Biorefining Tecnologies Initiative (IBTI) have identified existing plant and microbial biomass as sources of polymers, platform and speciality chemicals. However, most plant sources are not optimised for the efficient delivery of an extended range of useful chemical inputs for industry. In addition, many natural products do not perform as well as synthetic alternatives with respect to chemical and/or physical characteristics. If we are to move fully to a bio- based economy we must therefore consider radically improving plants and microbes as future biochemical factories. While some of these improvements can be incremental and take advantage of existing technologies such as marker-assisted breeding and genetic engineering of key metabolic traits to improve the chemical productivity of crops, such

approaches are effectively limited to improving what is already in nature.

Using synthetic biology approaches SPPI-NET has the goal of radically re-engineering the metabolism and physiology of plants for non-food industrial applications in the chemical and materials industries. Taking a lead from the physical sciences it should be possible to custom produce biologically derived chemicals/materials with properties which match or exceed those derived from synthetic chemistry. Such an ambitious long term objective requires integrated working between plant scientists, chemists, process engineers and modellers. Clearly an early challenge for the network is to identify and

assemble such cartels of interdisciplinary workers. In another important strand of

activity, the social and societal issues surrounding such radical biological engineering needs to be carefully considered. The risks and benefits of large scale synthetic biology programmes need to be understood and disseminated to the public.

SCN Annual Conference, 23rd – 24th September 2009 NSB Panel Q&A Session

Elfick, Alistair Institution: University of Edinburgh

Panel Discussion: What is Synthetic Biology and who cares?

PI: SynBio Standards: Standards for the design and engineering of modular biological devices

Key words: Standardisation / Characterisation / Measurement

Abstract

The SynBioStandards Network is an innovative and interdisciplinary network for UK academics working in Synthetic Biology. Pulling together researchers from the worlds of engineering, biological sciences, computer science and the social sciences, the Network aims to create a space for them to share ideas, and to develop a common language and set of tools for Synthetic Biology research.

Activities of the Network are primarily concerned with issues relating to standards and characterisation in Synthetic Biology. This is one of the main challenges faced by synthetic biology researchers, and one that will require ongoing dialogue. The SynBioStandards Network is not a standard-setting body, but we hope to develop approaches and protocols that are accepted as de facto gold standards and, as such, adopted by Synthetic Biology researchers worldwide. To achieve this we are contributing to the BioBricks Foundation, Request for Comment process.

The SynBioStandards Network is funded for three years from June 2008. The members

initially represented in this Network are from Imperial College London, University of Cambridge, The University of Edinburgh, University of Glasgow, and University of Newcastle. We hope that membership of the Network will expand over time, and we aim to build bridges with groups worldwide who are grappling with similar questions.

SCN Annual Conference, 23rd – 24th September 2009 NSB Panel Q&A Session

Ward, John Institution: University College London

Panel Discussion: What is Synthetic Biology and who cares?

PI: Synbion: the UCL Network in Synthetic Biology

Key words: Filamentous phages / biological electronics / opto-electronics / designed biomolecular devices

Abstract

The aim of the SynBion Network is to explor e what biologically designed elements could achieve in the fields of electronics, optics, opto-electroincs, magnetics and combinations of these fields. We aim to make Designed Biomolecular Devices based on structures that already have properties of self-assembly. Biological systems such as bacteriophage (i ncluding spherical and filamentous phages) assemble into stable, robust structures with regular placements of surface proteins. They are able to be designed to have altered surfaces by established gene fusion technology. We can thus design ordered structures using the properties of phages as a scaffold with the added property that phages can replicate their structure due to their normal infection and growth cycles. Taken together these points now allow us to look at an array of exciting possibilities. Could we use the inherent self-assembly and robust properties of such phages to design biological entities that are useful electronic devices? Can we design hybrid entities with several properties such as light harvesting, electron transfer, magnetic orientation and enzyme activity? Could the attached enzyme(s) be activated by electron transfer or light or could they lead to activation by energy transfer? Preliminary work and expertise across several different fields has shown that it is possible to design, build and test examples of these devices. A new area of work within the Synbion network is on metabolic pathway engineering. Novel enzymes can be grafted onto existing pathways or segments of these pathways. Pathways for the synthesis of useful chiral chemicals can be made this way or designed de novo. SynBion is led by Professor John Ward of the Institute for Structural and Molecular Biology at UCL with Dr Irilenia Nobeli from the Department of Crystallogrophy at Birkbeck. The Synbion Network also includes 5 other universities in the UK.

SCN Annual Conference, 23rd – 24th September 2009 NSB Panel Q&A Session

Woolfson, Dek Institution: University of Bristol

Panel Discussion: What is Synthetic Biology and who cares?

PI: The Synthetic Components Network: towards Synthetic Biology from the bottom up

Key words:

Abstract

What is Synthetic Biology? Firstly, I’m not sure I know what “Synthetic Biol ogy” is exactly; I can’t define it precisely. However, I don’t think that this necessarily a bad thing. After all, as virtually everyone who writes about it is at pains to point out: it’s a new, emerging and exciting area ….. and it’s going to change the world. Hype aside, why stifle or overburden such an embryonic and exciting field with a precise definition? Of course, some framework or working definition would useful, so I’ll get off the fence, and there are plenty of definitions of the field around. The one that I favour, probably because it’s broad, is: “Synthetic Biology is (A) the design and construction of new biological parts, devices, and systems, and (B) the re-design of existing, natural biological systems for useful purposes”. But is this too broad to be useful?

An alternative, is to define the area by example. I’ll attempt to do this with reference to what my group call “Synthetic-Biology Space” (Bromley et al., (2008) ACS Chem Biol 3 38), and I’ll describe possible paths that are being taken through this space by researchers such as Venter, Keasling, Rasmussen and ourselves.

One of the most useful things that we’ve found in my group is that the “Synthetic-Biology

approach” encourages ambitious and imaginative projects, which can be very rewarding. I’ll highlight this with two examples from my own research effort; namely, the design and applications of mimics for the extracellular matrix, and the design of a protein-based motor from scratch. I think these fit the spirit of Synthetic Biology, even if they aren’t iGEM, or genome/metabolic engineering. In my view, we should not over-define Synthetic Biology, but we should encourage ambitious projects that fit the above broad definition and see what emerges.

Who cares?

With the hype noted above—which, after all, gets researchers fired up, brings it to the public attention, and, hopefully, gets funders to dig into their pockets—we should all care what Synthetic Biology is, how it’s done and who does it. We should also be aware of public concerns, and how we might respond if challenged on them.

SCN Annual Conference, 23rd – 24th September 2009 Poster session : PIs

Elfick, Alistair Institution: University of Edinburgh

Poster session

Title: Does Synthetic Biology measure up?

When we engineer new functionality into a biological organism we need robust and accurate ways to interrogate our system to ensure correct operation. For full characterisation we may be looking at an extensive range of single cell and population based measures, utilising some sort of reporting machinery – often fluorescent protein expression. It is the case that the reporting machinery used may place significant

energetic or metabolic load on the cell. In this poster we review current reporting strategies and consider alternatives which are being developed as measurement systems for Synthetic Biology.

SCN Annual Conference, 23rd – 24th September 2009 Poster session : PIs

Rossiter, Jonathan Institution: University of Bristol

Poster session

Title: Artificial organisms: Soft robotics and Synthetic Biology

Artificial organisms are soft robots that resemble natural biological organisms. They contain some of the same general components or ‘organs’ and exhibit similar behavioural and functional characteristics. An artificial organism has, for example, an artificial ‘stomach’, a ‘brain’ and a body which is moved using artificial muscles. The biomimetic features of soft artificial organisms set them apart from traditional, hard,

robotics. Working towards practical artificial organisms the Bristol Robotics Laboratory has been

researching the fundamental components of soft artificial organisms. These include a

microbial fuel cell which acts as an artificial stomach, electro-active artificial muscles, and an artificial cerebellum. The potential of synthetic biology is to compliment the top- down robotics approach with a bottom-up development of nano- and micro-materials and structures which will enable new capabilities in artificial organisms. These include

muscular contractile mechanisms which mimic the natural actin/myosin and

tubule/kinesin mechanisms, and electo- and chemo-active polymer materials which show the same scaleable characteristics as biological muscle. Other materials, structures and mechanisms which may enable new micro and soft robotics are also being sought.

SCN Annual Conference, 23rd – 24th September 2009 Poster session : PIs

Serpell, Lousie Institution: University of Sussex

Poster session

Title: Peptide and protein self-assembly

A large number of proteins and peptides are known to assemble to form highly ordered, stable fibres and some of these are associated with disease. In the Amyloidoses, proteins or peptides assemble to form amyloid fibrils that are deposited in the tissues and these assemblies are rich in beta-sheet structure. In an effort to understand the assembly process that occurs in diseases such as Alzheimer’s disease and to exploit the

stability of these beta-sheet assemblies, we have been exploring the structure of these highly organised fibrils using a number of disease-related and novel peptides. Techniques include X-ray fibre diffraction, electron microscopy, circular and linear dichroism with fluorescence and dynamic light scattering. Our work aims to better

understand the role of sequence and side chains for driving assembly and how this

translates to stability and strength in ordered fibrillar aggregates.

SCN Annual Conference, 23rd – 24th September 2009 Poster session : PIs

Wass, Mark Institution: Imperial College London

Poster session

Title: Ligand binding site prediction using homologous structures and conservation

Knowledge of ligand binding sites is important for identifying protein function. In the post genomics era with the accumulation of millions of sequences, functional characterisation has become an important task for bioinformatics. We present an approach for the prediction of binding sites, which was among the best performing methods at CASP8 (Critical Assessment of Structure Prediction). Given a target sequence, sequence based

methods can be used to predict binding sites. However, while the availability of protein structures is limited, structural data can result in more successful predictions. Our method uses protein structure prediction to identify a structure for the target, which is used to investigate potential binding sites. Two different techniques are combined.

Firstly, structures homologous to a query sequence are identified and those with bound

ligands are superimposed onto the predicted structure of the query. Agreement of ligand binding sites in multiple homologous structures is used to identify the binding site on the target. Secondly, sequence based conservation methods are used and conserved residues are mapped onto the predicted target structure. Final predictions combine these

two methods. At CASP8 our method obtained 82% coverage and 56% accuracy1 and

was classed as the joint best method with the LEE group.

Wass M N and Sternberg. Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins (2009) In Press.

SCN Annual Conference, 23rd – 24th September 2009 Poster session : PIs

Woolfson, Dek Institution: University of Bristol

Poster session

Title: The Woofson group: protein design

The primary basic research interest of the group is the informational aspect of the protein-folding problem; that is, how does the sequence of a protein determine its active, three-dimensional structure? Our approach is to test and advance understanding of protein folding by designing new proteins . We are also interested in developing the designs for potential applications in the areas of bionanotechnology and synthetic

biology; for example, we are currently engineering peptides that self-assemble into fibrous and gel materials for applications in 3D cell culture and tissue engineering.

We take a multi-disciplinary approach to this research, which involves: bioinformatics to

garner sequence-to-structure relationships from protein-sequence and structure databases; rational peptide and protein design to test the rules that we find; biophysical methods—such as spectroscopy (CD, FT-IR, NMR) and microscopy (EM, AFM and light microscopy)—to characterise the designed proteins experimentally; and

molecular and cell biology to produce the designs and test their bioactivity.

More specifically, we have a long-standing interest in exploring one particular and ubiquitous protein-folding motif known as the -helical coiled coil, and applying the

understanding gained in the design of new coiled coil-based protein assemblies and

materials. More recently, we have started applying our bioinformatics and experimental methods that we have developed to a broader spectrum of protein-folding motifs, including zinc fingers, EF hands, -structured proteins and small enzymes.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Bath, Jon Institution: University of Oxford

Poster session

Title: Molecular motors built from DNA

The Second Law of Thermodynamics requires that directed motion be accompanied by dissipation of energy. A molecular motor that uses a chemical fuel must be a catalyst that couples chemical change to a mechanical cycle. We demonstrate the working principles of an autonomous, linear motor constructed from DNA that is driven by the hydrolysis of a DNA fuel using a reaction cycle in which one of two identical feet is first

lifted from its track then reattached. We show how the catalytic activities of the feet can be coordinated to achieve directional movement.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Boyle, Aimee Institution: University of Bristol

Poster session

Title: The design of closed peptide-based nanostructures

The rational design of peptide-based assemblies is challenging for many reasons, not least because the rules that govern their sequence-to-structure relationship are not fully elucidated. However, attempting such assemblies can be highly rewarding as it could provide a route to new structures and functions with potential applications in biotechnology and synthetic biology. We have advocated a bottom-up approach to the

design problem, where building blocks (or ‘tectons’) are programmed with the necessary information for folding and assembly. We have used the α-helical coiled-coil as our building block as it has well defined rules that govern the oligomerisation state and partner specificity. Using such rules, we have developed sequences for new, mutually

exclusive pairs of heterodimers. Here we present new constructs, in which two such

sequences are joined by a disordered and flexible peptidic linker to render polypeptides intended to oligomerise, cyclise and so form discrete, closed nanostructures. The linker length was sequentially increased in order to allow the peptides to sample different oligomerisation states resulting in the formation of a range of nanostructures.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Conn, Andrew Institution: University of Bristol

Poster session

Title: Cilia-inspired IPMC micro-actuators

In nature, unidirectional fluid flows are often induced at micro-scales by cilia and related organelles. Controlling fluid flows is beneficial at these scales for a range of novel robotic and medical applications, whether the flow is used for propulsion (e.g. swimming robots) or mass transfer (e.g. prosthetic trachea). Ionic Polymer Metal Composites (IPMCs) are innovative smart materials that can be used directly as active propulsive

surfaces rather than a traditional motor and propeller. IPMCs also have the added benefit of having the capacity for built in force sensing.

The aim of this research is to develop IPMC actuators with segmented electrodes that

can mimic the motion of cilia-like organelles. The segmenting process improves the kinematical performance of the actuator, but also increases the control complexity. As with eukaryotic cilia and flagella found in mammals, a segmented IPMC actuator can generate both flexural (asymmetric) and undulatory (symmetric) motions from the same

physical structure. Modulating the driving frequency and phase difference of the

segmented electrodes controls the motion. The Focused Ion Beam (FIB) technique is being investigated as a fabrication process for

cutting, segmenting and electrically connecting micro-scale IPMC actuators. FIB

systems are capable of milling to sub-micron accuracy and creating precise electrical connections by sputtering Gallium. The results of feasibility studies on fabricating segmented IPMC actuators with a FIB system are presented here along with prototype micro-actuator designs.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Heron, Andrew et al Institution: University of Oxford

Poster session

Title: Communication in droplet interface bilayers networks

Droplet interface bilayers (DIBs) form between lipid monolayer-encased aqueous droplets submerged in oil. DIB are a versatile platform for membrane protein investigations. Both major structural classes of membrane protein, α-helix bundles and β barrels, represented by channels and pores, respectively, spontaneously insert into DIBs when freshly expressed by cell-free transcription and translation. Electrodes embedded

within the droplets allow the measurement of transmembrane ionic currents carried by individual channels and pores. On the basis of these findings, we have devised a chip- based approach for the rapid screening of blockers against ion channels.

Furthermore, networks of droplets can be used to build micro-scale biological devices that communicate internally through proteins inserted into the bilayer interfaces. Droplets networks have been used to make tiny batteries, to sense light, and to build devices that can process electrical information and function as a current limiter, a half-wave rectifier

and a full-wave rectifier. The engineering of micro-scale biological devices to process

electrical information is appealing not only from the standpoint of miniaturization, but also because interfacing with living tissue might be better tolerated than with traditional electronics.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Kelley, Laurence Institution: Imperial College London

Poster session

Title: Discovering rules for protein-ligand specificity using support vector inductive logic programming

The spatial arrangement of key amino acids in a folded protein, on the surface or buried in clefts, are often the determinants of its biological function. A central aim of molecular biology is to understand the relationship between such substructures or surfaces and biological function, leading both to function prediction and function design. We present a new general method for discovering the features of binding pockets that confer specificity

for particular ligands. Using a recently developed machine-learning technique which couples the rule-discovery approach of Inductive Logic Programming with the statistical learning power of Support Vector Machines, we are able to discriminate, with high precision (90%) and recall (86%) between pockets that bind FAD and those that bind

NAD on a large benchmark set given only the geometry and composition of the

backbone of the binding pocket without the use of docking. In addition we learn rules governing this specificity which can feed into protein functional design protocols. An analysis of the rules found suggest that key features of the binding pocket may be tied to conformational freedom in the ligand. The representation is sufficiently general to be

applicable to any discriminatory binding problem. All programs and datasets are freely

available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/HU .UH

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Kendall, James Institution: University of Leeds

Poster session

Title: Development of biosensors based on tethered biomimetic membranes

The cell membrane is capable of detecting a varied spectrum of compounds with high specificity via the use of ion channel receptor s, making this a valuable tool for biosensing applications. A simplified biomimetic membrane known as a bilayer lipid membrane can be tethered to an electrode and ionophores incorporated, allowing the formation of an electrochemical biosensor. Here we have utilised self-assembled monolayers (SAMs),

composed of EO3-cholesterol (EO3C) and 6-mercaptohexanol (6MH), to form tethered bilayer lipid membranes (tBLMs) from Escherichia coli lipids on gold surfaces. Surface concentrations of EO3C and 6MH on the electrodes have been varied to optimise membrane properties. These tBLMs have been functionalised with ionophores such as

valinomycin and gramicidin, which were then studied using electrochemical impedance

spectroscopy (EIS). This work paves the way for the incorporation of ion channels into tBLMs for more advanced biosensors.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

King, Patrick Institution: University of Bristol

Poster session

Title: Investigating and manipulating the assembly of a peptide-based self- assembling fibrous system

The rational design of peptide-based fibrous systems has become an important and growing field within materials research due to their potential use as tissue engineering scaffolds. In 2000 our research group reported the rational design of the self-assembling fibre (SAF) system1, which comprises two leucine-zipper peptides designed to form sticky ended dimers that propagate into long non-covalent α-helical coiled-coil fibrils. A

combination of biophysical techniques has revealed mature SAFs to be an average of ~40 microns in length and ~70 nm in width, with a high level of internal order2. Rational peptide redesign has led to SAF systems that demonstrate improved stability3, altered morphology2,4, and that have been shown to produce hydrogels for use in 3D tissue

culture5. Investigation into the pathway through which the SAF system assembles will

allow us to further our understanding of how the system can be manipulated to improve future designs.

To this end, we have used a combination of biophysical techniques to investigate the

SAF assembly pathway. Circular dichroism spectroscopy, NMR spectroscopy, transmission electron microscopy, and fluorescence microscopy have revealed that SAFs form via a nucleation and growth mechanism. Assembly initially occurs in three dimensions, until an hour into assembly, after which fibre growth is predominantly

epitaxial. The introduction of ‘terminator’ mutants that cannot assemble into fibres has

allowed us to isolate the initial folding of the system, which has been characterised using circular dichroism spectroscopy and analytical ultracentrifugation. Using our knowledge of the SAF assembly pathway and the use of ‘terminator’ peptide mutants, we have rationally manipulated the system to vary fibre length and morphology.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Krzeminski, Lukasz Institution: University of Leeds

Poster session

Title: Designing and engineering FluoRox electrodes: FRET principle implemented in an amperometric biosensor

Amperometric glucose biosensors are commercially successful and well-studied analytical devices that measure glucose levels directly in blood. Despite the advances made on glucose sensors, biosensors are still challenged by limited sensitivity. The FluoRox project aims to develop the next generation of biosensors that combine the success of amperometric biosensor with the extreme sensitivity of optical detection. The

principle of this new method is based on the Föster resonance energy transfer (FRET) between a fluorescent label linked to a redox enzyme and its redox site. It has been found that the fluorescence's intensity changes upon the redox reaction at the enzyme's active site. The challenge is to engineer functional biosensor electrodes that will

measure these fluorescence changes, while controlling the redox state of the surface-

immobilised enzymes using electrochemical methods. Electrochemical, surface analytical and fluorescence techniques indicate that nitrite reductase can be immobilised on a so-called tethered lipid bilayer membrane (tBLM) or polyaniline (PANi) modified electrodes. These findings enable us to build an electrode surface-confined enzyme-

label system that would give a fluorescence response upon the specific analyte turn-

over.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Mahmoud, Zahra Institution: University of Bristol

Poster session

Title: Functionalisation of designed self-assembled peptide fibres

The abililty to design and functionalise synthetic biomaterials to mimic cellular microenviroments has potential applications in the field of regenerative tissue engineering. Our work focuses on functionalisation of a model self-assembling fibre sytem (SAF), which can be altered to form hydrogels. We present two routes for the decoration of the SAFs – (1) a non-covalent decoration route using 11-mer proteinogenic

peptides; and (2) a covalent decoration route using click chemistry. We show that the structure and order of the self-assembling fibres can be exploited to recruit charged peptides; this decoration is persistent and stable at physiological pH. The small size of the peptides lends itself to recombinant technology and affords a straightforward route

for time-dependent doping of tissue culture gels with growth factors.

The second route involves modification of the primary peptide sequence to incorporate click functionality. We show that azide group can be incorporated into one of the SAF

peptides, and these peptides assemble to form fibres that are similar to the parent. This

allows us decorate fibres covalently with gold nanoparticles, and lends itself to the display of organic and inorganic molecules functionalised with alkynes.

Together we can exploit these routes to gain spatial and temporal control over

decoration of fibres, and subsequently hydrogels, with functional proteins.

SCN Annual Conference, 23rd – 24th September 2009 Poster session: PhD and PDRA

Muscat, Richard Institution: University of Oxford

Poster session

Title: A linear motor constructed from DNA

We present a mechanism for autonomous and unidirectional movement of a cargo along a DNA track, driven by the hybridization of a DNA fuel. The track is a series of stepping points, or stators, at 6nm intervals that a cargo strand can bind to. Initially, the cargo is restricted to one position on the track by a set of removal strands that occupy all other stators.

Movement of the cargo is achieved by the addition of a set of DNA fuel strands. Each

stator has a corresponding fuel; however, the fuel remains unreactive to a stator-removal duplex. The presence of the cargo allows the hybridization of the fuel to the stator, transferring the cargo an adjacent stator in place of the removal strand. The process can then start again with the next fuel in the sequence. The direction the cargo strand travels

in can be adjusted by altering the sequence of the fuel strands.

This mechanism has been demonstrated on two- and three-stator tracks.

SCN Annual Conference, 23rd – 24th September 2009 Delegate list

Delegate list

Craig Armstrong University of Bristol [email protected] UH

James Arpino Cardiff University [email protected] UH

George Banting University of Bristol [email protected] UH

Jonathan Bath University of Oxford [email protected] UH

Hagan Bayley University of Oxford [email protected] UH

Philippa Bayley University of Bristol [email protected] UH

Richard Berry University of Oxford [email protected] UH

Paula Booth University of Bristol [email protected] UH

Aimee Boyle University of Bristol [email protected] UH

Leo Brady University of Bristol [email protected] UH

Beth Bromley University of Bristol [email protected] UH

Neil Cameron Durham University [email protected] UH

Daniel Carew University of Bristol [email protected] UH

Hsi-cheng Chi University of Bristol [email protected] UH

Daniel Chubb Imperial College London [email protected] UH

Caroline Colijn University of Bristol [email protected] UH

Andrew Conn University of Bristol [email protected] UH

Nikolaos N. Daskalakis University of Leeds [email protected] UH

Mark Dillingham University of Bristol [email protected] UH

Robert Edwards Durham University [email protected] UH

Alistair Elfick University of Edinburgh [email protected] UH

Stephen Evans University of Leeds [email protected] UH

Jordan Fletcher University of Bristol [email protected] UH

Paul Gardner University of Oxford [email protected] UH

Anthony Genot University of Oxford [email protected] UH

Andrew Heron University of Oxford [email protected] UH

Jonathan Howse University of Sheffield [email protected] UH

Benjamin Jefferys Imperial College London [email protected] UH

Lars Jeuken University of Leeds [email protected] UH

Benjamin Johnson University of Leeds [email protected] UH

Dafydd Jones Cardiff University [email protected] UH

Lawrence Kelley Imperial College London [email protected] UH

James Kendall University of Leeds [email protected] UH

Julie Kent UWE [email protected] UH

Patrick King University of Bristol [email protected] UH

Lukasz Krzeminski University of Leeds [email protected] UH

Parminder Lally University of Oxford [email protected] UH

James MacDonald NIMR [email protected] UH

Giovanni Maglia University of Oxford [email protected] UH

Zahra Mahmoud University of Bristol [email protected] UH

SCN Annual Conference, 23rd – 24th September 2009 Delegate list

Ewan Main University of Sussex [email protected] UH

Karen Marshall University of Sussex [email protected] UH

Kyle Morris University of Sussex [email protected] UH

Rachel Murray At-Bristol [email protected] UH

Richard Muscat University of Oxford [email protected] UH

Ainsley Newson University of Bristol [email protected] UH

Jonathan Phillips University of Sussex [email protected] UH

Alyssa Rosenbloom University of California [email protected] UH

Jonathan Rossiter University of Bristol [email protected] UH

David Rusling University of Bristol [email protected] UH

Michael Sadowski NIMR [email protected] UH

Nigel Savery University of Bristol [email protected] UH

Kathleen Sedgley University of Bristol [email protected] UH

Louise Serpell University of Sussex [email protected] UH

Michael Sternberg Imperial College London [email protected] UH

Ruhma Syeda University of Oxford [email protected] UH

Kathy Sykes University of Bristol [email protected] UH

William Taylor NIMR [email protected] UH

Eric Tippmann Cardiff University [email protected] UH

Andrew Turberfield University of Oxford [email protected] UH

John Ward University College London ward@biochemistry.ucl.ac.ukHU UH

Mark Wass Imperial College London [email protected] UH

Sean Watson UWE [email protected] UH

Dek Woolfson University of Bristol [email protected] UH

Joseph Yeeles University of Bristol [email protected] UH

Nathan Zaccai University of Bristol [email protected] UH

SCN Annual Conference, 23rd – 24th September 2009 Thank you

Thank you

Thank you all for visiting the first Synthetic Components Network annual conference, I hope it has been an interesting and productive meeting.

We are always eager to hear your thoughts on the events we put on. Was there anything that you particularly liked, or anything you think we should have done differently?

Please let us know – we need your input to make sure the events we organise are

how you’d like them to be. Do speak to Kathleen at the conference, email scn-HU

[email protected],UH or use the tear-out feedback form at the back of this booklet.

Thanks again for coming,

SCN Management Committee

SCN Annual Conference, 23rd – 24th September 2009 Researcher exchange form

Researcher exchange form

Short title for the exchange Name of Exchange Applicant Position (PhD Student / post-doc) Group Lead Home Institution Host Group Lead Host Institution Is your exchange the result of an interaction via the SCN If yes please provide brief details e.g., from Inaugural Meeting Details of proposed dates, time frame, and travel & accommodation costs requested, up to a maximum of £400.00 Please also provide a brief description below of the exchange project/activity (using the space provided only). Please include any details of matching funds available to you.

Please tear out the completed form and hand to Kathleen, or to apply later visit

http://www.bris.ac.uk/scn/exchange/HU U

SCN Annual Conference, 23rd – 24th September 2009 Feedback form

Feedback form

SCN Annual Conference 23 – 24 September 2008

Good Average Excellent Below par Don’t care

Venue □ □ □ □ □

Quality of talks □ □ □ □ □

Opportunities □ for interaction □ □ □ □

Food □ □ □ □ □

Information and correspondance □ □ □ □ □

Any further Comments:

Please tear out the completed form and hand to Kathleen

SCN Annual Conference, 23rd – 24th September 2009 Maps

St Anne’s site map

Oxford city centre map

St Anne’s