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Artificial synthesis of complex nanoscale biological machines

At the time of his death, Richard Feynman left an insightful comment on his blackboard:Ìý"What I cannot create, I do not understand". Here Feynman sets a challenging benchmark for scientific discovery, especially in biological systems whose properties depend on the interplay of many components. The reality is that although our understanding of biology has continued to grow exponentially since Feynmann’s death, his approach was simply not possible in biology. Instead, biologists adopt a ‘top-down’ approach; we let nature build things such as ecosystems, organisms, cells or large protein complexes, then we try to understand them. This provides assurance that we are studying correctly assembled systems, but restricts our ability to simplify or manipulate them to understand their various components. 30 years later, are things about to change?

We study complex and supramolecular biological machines by artificially constructing them form the bottom up. Two machines that we currently work on are the bacterial flagellar motor, a molecular motor that can rotate at over 100,000 rpm and ultrasensistive sensor that allows it to switch directions in milliseconds or the type III secretion system, bacteria’s molecular syringe that injects virulence factors directly into host cells. To build these machines we design and synthesise custom nanoscale structures made from DNA that we use to template the assembly of engineered protein components. This fundamentally new approach to biology allows us to explore fascinating questions about the molecular world, which are at the heart of how life exists. For example, how do many thousands of ‘brainless’ molecules self-organise into sophisticated functional machinery? Or once assembled, how do these ‘brainless’ molecules somehow talk with each other to coordinate their activities?

Bioinspired technologies

After 60 years of miniaturisation, man made devices have reached the scale of biological protein machines. But compared to nature’s machines, nanoscale man-made devices are rather crude and basic. After all, biology has had a 4 billion year head start. Hence, the concept of synthesising biological machines naturally takes the imagination to bio-nano hybrid technologies, which are so often the subject of science fiction. We are also exploring the possibility of turning fiction into reality by harnessing synthetic nanomachines for technological advance. One example shown below is a cooperative DNA origami structure where the same principles that drive the ultrasensitive switch in the bacterial flagellar motor are being applied to construct a biosensor for viral pathogens.

Structure and activity of membrane proteins with simultaneous single molecule fluorescence and electrophysiologal measurements

Integral membrane proteins, such as ion channels and G-protein coupled receptors are important players in cellular signalling processes and constitute some of the most important protein targets for drug delivery. However, their hydrophobic surfaces, flexibility and lack of stability outside their native membrane environment, present technical challenges for investigating their structure and activity by conventional methods (e.g. NMR and X-ray crystallography). To overcome this challenge we are currently establishing a setup (developed in Oxford) for investigating membrane proteins within their natural membrane surroundings. The setup consists of a supported lipid membrane formed between a hydrogel surface and a water droplet and is designed to facilitate parallel current and fluorescence measurements of single reconstituted membrane proteins. We envision thisÌýmultidisciplinaryÌýstrategy will provide unprecedented insights into the molecular mechanism governing the activation and function of integral membrane proteins, which will be imperative for the development of novel drug-design strategies.

Adapting Bacterial Motility in the Laboratory using Experimental Evolution

The bacterial flagellar motor is one of the pinnacles of evolution, and one of the oldest sources of motility in existence. We use biophysics, microbiology and genetic engineering techniques to examine exactly which small changes result in the emergence of the complex outboard motor that powers the ‘salmonella speedboat’. We apply selection pressure to evolve changes in the motor, such as changing its energy source, and then characterize the genetic and phenotypic changes the motor undergoes throughout this process. This project involves microscopy, single molecule fluorescence, microbiology and bacterial genetics, and provides a platform for work at the interdisciplinary intersection of physics, evolutionary biology, and biochemistry, to explore the complex origins of nature’s fastest rotary motor.