Building a binding community - Capacity and capability for affinity and kinetic analysis of molecular interactions.

The cells of our bodies contain many thousands of different molecules. Like the parts making a machine, these have to work together correctly for us to be healthy. Some molecules work with each other, assembled into long-lasting machines to do their jobs. Other molecules work as short signals which are quickly switched off.

Sometimes these normal processes go wrong, through cancer or genetic mutation. The machine we want to buy will help us understand what has gone wrong with these molecules. It will also help us find molecules we might develop into drugs to get things working correctly again.

All other organisms including those causing disease such as bacteria and viruses also contain molecules making machines and sending signals. Understanding how these molecules work can help us target diseases. We can also use the machine to develop tests to detect diseases more quickly.

Like Lego versus Duplo - the shape, size and stickiness of those different molecules affects which ones are able to interact with each other. However, the comparison with children's toys is only useful as a starting point for thinking about how molecules stick to each other, or don't.
It turns out there's a whole set of words to describe Lego bricks. The bumps on each block are called "studs" which fit into holes in another brick. The shape and size of "studs" is important for the blocks sticking to each other. If molecules worked like Lego, then our job would be easy. It's child's play understanding how Lego works.

Biology though uses different kinds of studs to stick molecules together. Molecules are more like a mixture of Lego studs, Duplo and Velcro - different shapes of sticky bits. It becomes very difficult to predict which molecules will interact with each and how tightly, or which won't interact. Sometimes we just need to mix things and see what happens.

The machine we want to buy will do this mixing, telling us how strongly molecules will stick to each other and which molecules can't stick to each other. It will do this for hundreds of molecules, running overnight. With lots of information, we can better design more experiments to help us understand how molecules work and what happens when things go wrong, causing diseases.

Correct functioning of cells and organisms requires a complex set of interactions to work correctly. These interactions are described by properties such as affinity, kinetics and cooperativity. Mis-function perhaps through genetic disease changes molecular function with affinity and kinetics being part of the characterisation. Molecular interactions are key at multiple stages in the life-cycles of pathogenic organisms including viruses and bacteria. Development of drugs to target pathogens also requires assays to compare the affinity and kinetics of molecular interactions.

We are applying for funds to enable us to determine the affinity and kinetics of molecular interactions for a wide range of biomolecules including DNA & RNA; sugars, oligo- & polysaccharides and protein-protein interactions. Our preferred machine is a Biacore T200 surface plasmon resonance instrument.

Specificity is a key part of understanding molecular interactions as even small changes in sequence or structure can have large effects on affinity and kinetics. The proposed machine will enable us to determine specificity of interactions by testing analyte binding to three ligands in the same experiment. One way we use this feature is to determine how clinical sequence variants affect protein function.

The machine will be located in our existing biological sciences research facility where it will benefit from professional management to maximise usage across a diverse research community.