A low velocity molecular collider for computer-controlled biochemical reactions.

There are diverse techniques for studying biomolecular interactions e.g. proteins-ligand, proteins-nucleic acid
and protein-protein interactions. On-rates, off-rates and equilibrium constants are of wide interest in industrial
and fundamental research. Drug development needs to quickly isolate, identify and characterise "strong
binder" small molecules or biologics, especially in screening. Cryo-EM has energised the study of multicomponent
protein machines and the disciplines of mechanistic biochemistry are being revived. However,
proteins are expensive to produce and purify but for biological realism must be used at high concentration
but most analytical approaches create large dilutions. This creates demand for miniaturised reaction systems
that concentrate samples, allow precise manipulation of reactions conditions and give molecular
characterisation. Beyond determination of physical constants there is also the need to establish if one protein
modifies another during interaction e.g. some components of complexes are enzymes and assembled (or
partly assembled) complexes may be enzymes e.g. signalling scaffold assemblies, ribosomes, coatomers,
GroEL/ES chaperones etc.
We will use radically new electrophoretic methods to create a platform for computer manipulation of
biochemical interactions. With their prototype QbQ ("cubic") system GMD, the industry partner, has built a
platform that allows the generation and manipulation of the motions of ultra-sharp molecular bands in a
microfluidic channel (See Figure 1 below). By developing QbQ for protein work we will discover how to control
protein concentrations, band composition, band width and direction of motion of bands inside a fluid channel.
We will then "collide" bands with each other in the sense of crossing motion paths while characteristics of
speed, concentration, encounter time/duration and temperature are controlled by software.
QbQ has potential to complement and then surpass the most well-established analytical approaches. It
avoids steric hindrance from absorption of one binding partner to a surface (SPR) and negates mass transport
limitations (SPR and NMR). QbQ preserves the advantages of microscale thermophoresis (MST) over
dynamic light scattering (DLS) and similar techniques e.g. mm long light paths and mg/ml concentrations yet
surpasses MST because dilute proteins are concentrated on the chip and the motions and interactions of
proteins can be controlled simultaneously.
Ultimately this creates the possibility for logical operations and loops to control the progression of chemical
processes. For example, "if (sample A x sample B == Characteristic C) then react C with D Else react C with
E". Having software controlled chemical reactions can create possibilities of mimicking complex, sequential
biochemical processes in a small chip. The system can lend itself to quantitative (screening) and qualitative
(analytical) investigations. We will specifically investigate protein-protein interactions in signal transduction
but also create "value branch points" at which the research progress can be captured as design principles for
new devices useful in other applications (drug screening).
This project fits the BBSRC definitions used in the DTP3 application for allocation of LIDo research
studentships, specifically "Technology Development". Signalling is a general BBSRC interest and specifically
encompassed in (i) Regenerative Biology (ii) Immunology and (iii) Stem cells aims.