Phillips Group The Protein Choreography Group In the Protein Choreography Group we identify and engineer mechanisms of dynamic functional control in protein molecules. We aim to understand the principles of allosteric regulation in biology and dysfunction in disease and to engineer protein dynamics for novel medicines and biotechnology tools. To understand how molecular sensors function, we develop interdisciplinary experimental and computational approaches, novel prototype instrumentation, software and mathematical models. Our group has an international reputation for advancing millisecond time-resolved hydrogen/deuterium-exchange mass spectrometry (HDX-MS) methods to study large, dynamic molecular systems. Our new non-equilibrium instrumentation and methods allow us to see, for the first time, precisely how proteins reconfigure to (in)activate and to perform enzyme catalysis. Applied to natural systems, this yields insight into fundamental biology, including Parkinson’s disease pathogenesis, diabetes and cancers. Applied to medicine, this drives the design of switchable antibodies that activate inside the body and new screening technologies to discover safer and more effective classes of drugs. Resolving the process of protein computation: Non-equilibrium protein structural dynamics Whilst it is becoming routinely possible to determine accurate structural models of proteins with high resolution, it is still challenging to ascertain the specific structurally dynamic changes that underpin protein functional switching. The archetypal allosteric enzyme, glycogen phosphorylase (GlyP) is one of the most studied and has a substantial therapeutic potential in treating metabolic diseases and cancers. However, a lack of understanding of its complex regulation, mediated by dynamic structural changes, hinder its exploitation as a drug target. Here, we precisely locate dynamic structural changes upon allosteric activation of GlyP, by developing a time-resolved non-equilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach. We resolved obligate transient changes in localized structure that are absent when directly comparing active/inactive states of the enzyme, thus rationalizing the mechanism of action of an allosteric activator. This approach has broad application to determine the structural kinetic mechanisms by which proteins are regulated. We are actively developing this approach to understand fundamental metabolic regulation, signal transduction and in quantum biology to understand the molecular basis for magnetosensation in migratory birds. Moreover, we now have the exciting possibility to develop scalable mathematical models to train AI tools that will enable the design of allosteric protein computation. Parkinson’s disease In Parkinson’s disease and other synucleinopathies, the intrinsically disordered, presynaptic protein alpha-synuclein misfolds and aggregates. We hypothesise that the exposure of alpha-synuclein to different cellular environments, with different chemical compositions, pH and binding partners, together with post-translational modifications alter its biological and pathological function by inducing changes in molecular conformation. Our custom instrumentation and software enable measurement of the amide hydrogen exchange rates of wild-type alpha-synuclein at amino acid resolution under physiological conditions, mimicking those in the extracellular, intracellular, and lysosomal compartments of cells. This correlates local structural dynamics at near amino acid resolution with pathophysiological function. We now have the exciting possibility to experimentally measure sub-populations of conformers of intrinsically disordered proteins under physiological conditions, use this to build data-driven atomistic models and correlate these with biological and pathological function. Biotechnology From our new understanding of how proteins move in response to – and to direct – their environment, we are interested to control them ourselves in order to create medicines, biosensors and other biotechnologies. We revealed the specific structural dynamic pathway for activation of a designed biosensor that bioluminesces in response to binding a drug. Engineering and exploiting synthetic allostery of NanoLuc luciferase – data-driven structural kinetics from HDX-MS We can now design bespoke protein biosensors to detect any molecular target of interest. Video (C) Will Rogers Biomedicine We have exploited these principles of equilibrium and non-equilibrium protein structural dynamics to uncover the rules for successful design and engineering of switchable antibody drugs, which are dosed as an inactive pro-drug and then activate passively at the site of a tumour. Mechanistic insights into the rational design of masked antibodies Cutting edge experimental and theoretical approaches We are active in developing new instrumentation for millisecond time-resolved hydrogen/deuterium-exchange mass spectrometry, new mass spectrometry methods, new analysis software and new mathematical and statistical models. This agile interdisciplinary approach enables us to ask – and answer – the most challenging and exciting questions. We have developed HDfleX software to empower you to flexibly generate the highest possible resolution HDX-MS data and analyse it with user-friendly robust hybrid significance testing. By automated fitting of the kinetic data, you will have more robust detection of significant changes in protein structure, dynamics and stability. Download it here. Join The Protein Choreography Group: contact jj.phillips@exeter.ac.uk PhD Studentship Opportunities Fully funded PhD studentship “Understanding the structural dynamics of genome editing enzymes“ Fully funded PhD studentship “Designer proteins to rewire living systems“ Fully funded PhD studentship “Control of chromatin remodeller activity to direct cell fate decisions“ Fully funded PhD studentship “Cryptochrome: Life’s quantum sensor“ Fully funded PhD studentship “Personalised biosensing for emergent targets” Post Doctoral Research Associate Opportunities No positions currently open. I am happy to discuss hosting of potential fellowship candidates.