Anthony Russell Clarke, 1959-2016

‌Tony - or as many knew him, Clarke - was a brilliantly flamboyant scientist, wit and raconteur. To his friends, students and colleagues Clarke was chaos incarnate. Anyone who worked with him can testify to the apparent disarray of his lab and life. The humdrum cycle of the working week didn’t impinge on Tony’s habits. For Tony there was no such thing as ‘work/life balance’, there was just Life. Sometimes the most appropriate thing to do with life was to head out to sea on his beloved boat, at other times the lab was the place to be. His wayward lifestyle made Tony a challenging person to work with; society doesn’t care for chaos, it prefers tidy plans, filed reports and scheduled meetings. Tony never attended staff meetings (he was very proud of that).

And so to many it was incredibly difficult to pinpoint how or why his group and indeed his mind worked so productively. It appeared to the outsider that disorder reigned. In fact true chaos ruled; chaos from which, as in nature itself, beauty and order emerge. Of course something is needed to trigger the emergence of order from a chaotic system. And in Tony’s case the attractor around which order condensed was his unwavering insistence on experimental rigour and reproducibility.

Inspiration, creativity, curiosity: Tony had these in spades. Everyone who ever worked with him couldn’t help but admire his intellect, wit, charm and passion. And so they overlooked, as best they could, his social transgressions. Most of his exasperated superiors let him get on with his research, content with his prolific outputs; the wise garnered his genius. Meanwhile his PhDs and postdocs rallied around trying to keep his admin on track by digging out the most important forms and documents hidden in his office’s archaeological filing system (the deeper in a stack, the older the documents). This remained a workable system threatened only by the occasional tectonic movements that disrupted the order.

Tony literally had an encyclopaedic knowledge - gained when very young by devouring the family Encyclopaedia Brittanica. He was an avid twitcher, brilliant sailor and cook, with an immense passion for English and American literature. And a sun worshipper extraordinaire. Above all, Tony was an outstanding and intuitive scientist and superb teacher. He received a SERC Personal Fellowship at 26, a Lister Fellowship at 36 and a personal chair at 41, churning out seminal work in enzymology, protein engineering, protein folding and prion disease throughout his career. His lectures were legendary, inspiring hundreds of undergraduates into the research arena, many of them to his own lab. Amazingly, he mentored over 30 postgraduate students through their PhDs, many of whom went onto illustrious careers in the UK and around the world.

Tony was one of a dying breed of scientists, uninterested in prestige, accolades or politics, driven solely by discovery, communication and education. His research career was cut short following an accident and brain injury; before that, in the years between 1980 and retirement, his contributions to biochemistry and molecular biology are renowned.

The first major impact that Tony made was in the field of protein engineering while he was a postgraduate associate with John Holbrook. Even though still a postgraduate, Tony was undoubtedly the driving force behind this project. Starting in the early 80s, Tony was amongst the very first to apply the then new methods in molecular biology to the analysis of protein structure and function. One signal achievement of his at that time was to change the specificity of Bacillus lactate dehydrogenase from one substrate to another by site-directed mutagenesis. Tony, with help from Bill Chia, Dale Wigley and others, created mutants of lactate dehydrogenase that could no longer metabolise lactate but instead were highly active against malate, a different compound that the native enzyme ignored completely. This was perhaps the first case in which a radical change in enzyme specificity had been obtained by rational design, a breakthrough that has since become the pathfinder for much of modern biotechnology. Many years ahead of the times, today this would be coined Synthetic Biology.

A second major achievement came in the way in which Tony used site-directed mutagenesis and other techniques from molecular biology to dissect protein dynamics. Again using lactate dehydrogenase as a test bed, he and his colleagues first removed all of the tryptophans from the protein so as to give a protein with no natural fluorescence, tryptophan being the sole amino acid with significant fluorescence. They then made a series of derivatives of the protein each carrying an individual tryptophan at a pre-selected position. They could thus use fluorescence to monitor the dynamics of the section of the protein carrying that single tryptophan.

In the early 1990’s Tony turned his talents to the conundrum of protein folding - in other words, addressing the question of how nature has solved the problem of producing a functional, uniquely folded protein from a polymer chain with almost infinite flexibility, comprising tens to hundreds of amino acids. Living organisms have also evolved to do this such that the folding free energy is modest, typically 5 to 20 kcal/mol; presumably this facilitates recycling. To explore the kinetics of protein folding Tony applied tryptophan fluorescence and his considerable skills as both a practical and theoretical practitioner of kinetics (in Sir Alan Fersht’s words, ‘He was a very fine exponent of kinetics’). Tony was always a brilliant recruiter of exceptional students and a fantastic motivator. His team were at the pioneering forefront of using chemical denaturants to unfold and refold proteins to measure and develop kinetic theory to understand the mechanism of this fascinating process. He used proteins with different secondary structures, and used site-directed mutagenesis and double mutant cycles to probe and extract thermodynamic information from the folding process. In a set of NMR experiments with his lifelong friend and collaborator, Jon Waltho, the team were able to study hydrogen-bonding patterns in the folding intermediate of a protein. When this tour de force was combined with thermodynamic data from many kinetics experiments, a model of protein folding emerged that persists to this day. For a typical protein domain, folding proceeds via a rapid collapse to an intermediate state that possesses native-like internal hydrogen bonding. This is followed by a slow step whereby the final rearrangements of amino acids and dehydration of the hydrophobic core reveals the exquisite three-dimensional jigsaw that is the native state.

In addition to Tony’s work on the spontaneous refolding of proteins, a serendipitous moment led Tony and his group to work on the mechanism of a protein folding machine, known as a chaperonin. One afternoon Peter Lund, a Bristol alumnus returning from San Francisco to take up a lectureship at the University of Birmingham, called into the Bristol Biochemistry department to visit old friends and seek expertise in protein folding to develop an assay in a new research area. He had begun working on the GroEL-GroES chaperonin system that had just been shown to use energy from ATP to massively enhance the folding efficiency of proteins that otherwise had a propensity to misfold and form insoluble aggregates. A collaboration between Tony and Peter quickly materialised and they showed that the chaperonin binds unfolded protein tightly, preventing aggregation, and the binding of ATP reverses this interaction. Tony then applied his experience of using kinetics and spectroscopic techniques gained in his studies on lactate dehydrogenase to dissect the mechanism of the chaperonin-assisted folding reaction. Specifically, his group showed that each ring of the GroEL complex bound ATP cooperatively, inducing a large conformational change that opened up a large cavity, which was capped on one end by the GroES co-protein. A collaboration with Helen Saibil (Birkbeck, London) led to the visualisation of these large protein complexes using the recently developed technique of cryo-electron microscopy and a publication in Nature. Tony also made the controversial proposal that the chaperonin worked by using the energy derived from ATP to unfold proteins that have folded incorrectly before releasing them again to attempt to refold correctly. Over time this idea has gained increasing experimental support from groups in Germany and the USA, and is now accepted as being one of the principal features of the mechanism. Further painstaking work by Tony’s group made major contributions to our current understanding of the mechanism of this complex protein folding machine. This work propelled Tony onto the international stage, where he was regularly invited to speak at conferences across the world, his keen intellect, quick wit, good company and sometimes outrageous behaviour making him a respected and popular member of the international scientific community. During the decade before his retirement he also turned his attention to the poorly-understood thermosome, a homologous chaperonin from archaea, revealing both similarities and important major differences with the better understood GroEL-ES system.

Following a seminar at the Biochemistry Department in Bristol in 1991 and intense scientific discussions at the pub afterwards, a long-term collaboration was established between Tony and John Collinge in London to study the structural biology of prions, then highly controversial, apparently ‘protein-only’ infectious agents that cause fatal brain diseases such as Creutzfeldt-Jakob disease (CJD) in humans, scrapie in sheep and bovine spongiform encephalopathy (BSE or “mad cow disease”) in cattle. The collaboration was extremely productive, leading to a succession of high-profile publications on prion protein folding, prion structure and the kinetics of prion propagation, and to a very close friendship between Tony and John. When the MRC Prion Unit was formed in 1998, Tony took up a half-time position at the Unit, not only leading its structural biology programme but contributing with characteristic intellectual generosity, brilliance and willingness to challenge any dogma, to nearly all the research groups at the Unit for many years. His contribution to prion research has been immense. He provided insightful input into many projects, always insisting on the highest quality of data and its most rigorous statistical analysis, yet invariably working with great humour and informality that charmed co-workers. In addition to his seminal insights into understanding the basic molecular biology and the development of a ‘General Model’ of prion propagation, his insights were fundamental to applied and translational developments. These led to the development of methods to prion-decontaminate surgical instruments and both monoclonal antibody and small molecule therapeutics now in development for human trial in the treatment of CJD.

He retired through ill health at 55 with 183 papers, including four in Nature and two in Science, and an H-index of 49 (still counting) under his belt - not that he would care! But the numbers don’t do his achievements justice: his real legacy lies in the results of his infectious passion for science. He showed us that curiosity was key, that it was the exploratory process that was the interesting bit. Those that had the honour to work alongside him (for he always treated his charges as equals) are left with a lifelong love of discovery. After a day's work anyone still around would be compelled to adjourn across the road to the Robin Hood for beers and to discuss science, experiments, results - amongst other things! A tradition he claims to have initiated - it is almost certainly true. These would often end up in late-night Clarkian monologues at his Clifton flat. Clarke could be wild and reckless; he burnt out early, but those of us whom he took along for the ride will benefit from his energy, charm, generosity and criticism throughout our lives and careers. His loyalty to his friends was unwavering and always reciprocated.

It is perhaps worth noting that within hours of his death the hundreds of people whose lives he touched, spread as they were over decades of scientific discovery and thousands of miles, had all learned of his passing. The ‘Clarke-collective’ had begun to grieve. The world is a far less interesting place without Tony Clarke. His family, friends, students and colleagues will miss him greatly. Unique is an overused word, but Tony was indeed a very rare and alas now extinct breed, of whom we will never see the like again.

Tony will be hugely missed by all his colleagues and friends in Bristol, London and around the world. There will be an opportunity for all of us to celebrate his life in a symposium in Bristol in his honour (date and venue to be announced).

Cheers Clarkey.

Tony is survived by two daughters Charlotte ‘Binks’ and Louise ‘LuLu’.

Written by Steve Burston, John Collinge (MRC Prion Unit), Ian Collinson, Steve Halford, Mark Lorch (University of Hull) and Richard Sessions

Professor Tony Clarke Image credit: Photograph taken by Emma Cordwell
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