Protein Choreography

Protein molecules are nanoscale machines that support almost all life processes. My research aims to understand how proteins change their structure in order to sense their environment and to catalyse chemical reactions. Knowledge of these biophysical rules will enable us to engineer proteins as biotechnology tools and medicines and will underpin the discovery of important new classes of drugs that are safer and less toxic than current chemotherapy.

The processes of life are dynamic - it is change on a molecular level that enables us to grow and move, but also to become ill and treat disease. Just as the shape and posture of our body can determine our readiness to perform a task, the structure and conformation of a protein molecule can determine its function or activity. Humans make over 20,000 unique proteins and each of these needs to move in order to function - often undergoing dramatic changes in shape with no clear mechanism to link these to the environmental triggers.

Crucially, it is the ability for proteins to reconfigure dynamically and rapidly that underpins many critical activities in biology, disease and medicine. However, we are currently limited to study proteins, including many important enzymes, at high resolution in space or time - but not both. Static structural models have contributed to major advances, such as in gene editing technology.

This structural information is also critically important for drug discovery, accurately guiding design and optimisation efforts. These are major new applications that rely on precisely controlling dynamic changes in protein structure. These aims - and our understanding of fundamental biology - will be greatly advanced by bridging high resolution information in both time and space.

We now have a unique opportunity to make measurements of the structural perturbations in large enzymes both with high structural resolution (per amino acid building block) and high temporal resolution (per millisecond). A vast number of naturally occurring proteins across all of life employ allostery to regulate biological processes in response to their changing environment, notably the archetypal allosteric enzyme, glycogen phosphorylase.

With our prototype instrumentation, we have provided a quantitative description of the intra-molecular regulation in the archetypal allosteric enzyme, glycogen phosphorylase.

To observe changes in structure during the processes of enzyme regulation, we then created a novel method: non-equilibrium hydrogen/deuterium-exchange mass spectrometry (neHDX-MS). This resolved unexpected transient structural changes at near-amino acid resolution that occur during allosteric activation of glycogen phosphorylase, revealing that a short section - just 1% of the protein - dynamically reconfigures to facilitate activation of the enzyme.

Excitingly, these changes are absent when the protein is measured in the inactive or active states, hence they went unnoticed for decades in this extensively studied enzyme.

Our new method represents a straightforward way to identify transient protein dynamics that occur during almost any allosteric process. Therefore, we are now focused on its application to gene editing enzymes to identify currently hidden features that critically enable their regulation and catalytic function. We will then screen changes made to these highly focused locations in an effort to optimise properties critical to their use as biotechnology tools, such as specificity and efficiency.

This research programme brings together expertise in building novel experimental methods, cutting edge data science approaches, development of new software tools and a direct relevance to fundamental biology and applications in biotechnology and drug discovery.