The Cinderella Molecule

Steven Shapin

  • Gene Machine: The Race to Decipher the Secrets of the Ribosome by Venki Ramakrishnan
    Oneworld, 272 pp, £20.00, September 2018, ISBN 978 1 78607 436 2

RNA gets no respect. It is similar in make-up to its charismatic chemical cousin, with small structural variations. DNA is a very long double-stranded helix while many forms of RNA are shorter and single-stranded; one of the four nitrogenous bases in DNA is different from its equivalent in RNA; and the base-bearing backbone in RNA contains the five-carbon sugar ribose, while its equivalent in DNA has one less oxygen atom – hence deoxyribose (so RNA is ‘ribonucleic acid’ while DNA is ‘deoxyribonucleic acid’). It’s the physiological role of these small differences that accounts for RNA’s status as the Cinderella of the nucleic acid family. You don’t see corporate mission statements declaring that ‘innovation is in our RNA’ (CommBank), or car advertisements claiming that ‘adventure is in our RNA’ (Land Rover). When the much missed Arsène Wenger said that Arsenal were ‘an attacking team’, he didn’t add that forward play was ‘in our RNA’. And you won’t find an encyclopedia entry explaining that ‘Your RNA is what makes you uniquely you.’ The schematised DNA double-helix is one of the instantly recognisable graphic icons of modern bioscience, indeed of modernity itself, but if you aren’t a biochemist or geneticist, you’ll have no idea what RNA looks like and little notion of its role in the scheme of life.

When Watson and Crick discovered the structure of DNA in 1953 (Crick bounding into a Cambridge pub and bragging that they had solved ‘the secret of life’), the molecular basis of heredity was immediately apparent. The sequence of bases in one strand of DNA was shown to be complementary to the sequence in the other, meaning that each strand, once separated, could act as a template for reproducing its sister strand, yielding chemically identical double-helical progeny. This is the molecular mechanism by which like produces like. It was also apparent – though the biochemical pathways were not then understood – that the sequence of bases along the DNA strands might constitute a functional code: a blueprint detailed enough to instruct cellular mechanisms how to go about building the structures and conducting the processes of life. But the structures themselves either contained proteins or required those proteins called enzymes to be constructed, ordered and regulated. There are a lot of proteins in living organisms, maybe ten million different forms, each made up from a palette of twenty amino acids and each assuming specific three-dimensional configurations that allow it to perform its vital functions. The emerging research agenda of molecular biology was, therefore, a problem of translation. What were the processes and structures through which DNA code became protein reality? How did sequences of four DNA bases specify each of the twenty amino acids, and how were these amino acids then assembled into proteins? One task for post-Watson-Crick molecular biology was to crack the code; another was to discover the molecular mechanisms of code-translation.

Some years after the discovery in 1953, Crick and Watson announced the so-called Central Dogma of Molecular Biology, a widely circulated version of which stated that DNA makes RNA and that RNA makes protein. The DNA code, they said, was read by forms of ‘messenger RNA’ (mRNA) which then carried those coded instructions from the cell nucleus to extra-nuclear sites where proteins were constructed. The amino acid building blocks were transported there by particular types of ‘transfer RNA’ (tRNA). The role of DNA in both heredity and in coding for proteins was in principle solved, and all that remained for molecular biology was the problem of how all this worked in practice. For some scientists, the theoretical solution was the great prize and the work that remained to be done was a series of mopping-up operations or puzzle-solving, what the historian Thomas Kuhn called ‘normal science’.

By the 1950s it had become clear that the cellular organelle where proteins were manufactured was the ribosome – given its name by an American microbiologist. The ribosome was known to be an extremely complex structure. But what was its atomic architecture? How did its molecular bits and pieces fit together? How did it work in protein manufacture? You couldn’t tell very much about ribosomal structure by seeing it directly, for example by electron microscopy: the resolution then wasn’t nearly good enough. The question for scientists was whether there were available techniques – or whether new techniques could be developed – that would make it possible to infer and represent the detailed three-dimensional structure of the ribosome, each atom in its proper place.

This is where Venkatraman Ramakrishnan comes into the story. Born in Tamil Nadu, he took a degree in physics at university in Gujarat in the year he turned 19, then left India to do his doctoral work at an unexceptional university in the American Midwest. Ramakrishnan didn’t set out to discover the ‘secret of life’ or even to work on biological subjects. His early story, as he modestly tells it in Gene Machine, is not one of vision and vocation but of drift and accident. Molecular biology was founded in the mid-20th century largely by physicists who had wandered into biology, and Ramakrishnan strayed in too, drawn by the excitement following on the Watson-Crick discovery. In 1976 – physics doctorate in hand, newly married and with two young children – he decided to take up biological research, the precise nature of which remained to be determined. What he knew about ribosomes at the time didn’t make them an appealing subject. The distinguished South African molecular biologist Sydney Brenner had said, as Ramakrishnan tells it, that discovering the structure of the ribosome was a ‘trivial problem’, while Watson reckoned that the structure was so dauntingly complicated – experimentally the opposite of ‘trivial’ – that it might never be worked out. But as a post-doc at Yale, Ramakrishnan came into the orbit of researchers who believed that various forms of radiation, including those produced by new types of particle accelerators, might help to establish how atoms were arrayed in the ribosome.

A few things were already known about its structure and about the functions of its parts. Unlike nuclear DNA, the ribosome consists not of one molecule but many, comprising about a million atoms. It is made up of around two-thirds ribosomal RNA (rRNA) and one-third proteins, of more than fifty different types. The ribosome has two physically separable sub-units: the ‘small sub-unit’, which ‘reads’ the mRNA, and the ‘large sub-unit’, where the amino acids are assembled into the polypeptide chains of proteins. In the 1980s, ribosome research was significantly defined by the search for its structure, driven by the conviction that discovering a complete three-dimensional structure for the ribosome was a condition of coming to understand how it read the DNA code and made proteins. There were reasons for wanting to know this beyond disinterested biological curiosity. It was already known, for instance, that antibiotics act on the microbial ribosome, disrupting protein synthesis. Ramakrishnan doesn’t seem to have been consumed by practical problems of drug-action, but pharmaceutical concerns ultimately affected the availability of funding for research into ribosome structure.

At the time Ramakrishnan entered the field, however, ribosome research was unfashionable: tough science, messy science, dealing with intractable materials, with no guarantee that any then existing or imagined future techniques could solve such a complex structure. In 1981, having finished his post-doc, Ramakrishnan sent out nearly fifty applications for academic jobs, all of which failed. Some universities apparently doubted whether his English was good enough for teaching purposes; some were sceptical about his qualifications for doing serious biological research; others seemed to share the view that ribosome work just wasn’t going anywhere. He was rescued by the high-energy physics institutions established during the Cold War, where he used their radiation beams to investigate ribosome structure. Several years later, having spent some time at the Oak Ridge National Laboratory in Tennessee, Ramakrishnan was offered a position as staff scientist at the Brookhaven National Laboratory on Long Island, where he remained for 12 years until 1995; in 1999 he took up his current position at the Laboratory of Molecular Biology in Cambridge. The following year, Ramakrishnan’s team at Cambridge solved the structure of the small sub-unit. Shortly after that, scientists at Yale worked out the large sub-unit; then, in 2007, a structure for the whole ribosome was established. What followed were the rewards expected for an achievement of that scope and significance: a share of the 2009 Nobel Prize in chemistry, a knighthood, India’s highest civilian honour, and in 2015 the presidency of the Royal Society.

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There were several approaches to solving the ribosome, but the young Ramakrishnan banked on crystallography. The technique was simple in principle, but very hard to execute in practice. You make a crystal – that is, a purified regular latticed structure of the molecule or molecular aggregate in question – and then subject it to various forms of radiation, notably X-rays. The diffraction patterns obtained reveal where the constituent atoms are arrayed in space. Rosalind Franklin’s ‘Photo 51’ of crystallised DNA – which Watson and Crick famously obtained without her knowledge or permission – was used as crucial evidence of its double-helical structure. But it was an entirely different matter to obtain X-ray crystallographic images at a high enough level of resolution to discover the atom-by-atom three-dimensional structure of complex biological molecules such as proteins.

Proteins are very large, irregularly shaped, floppy molecules. Arranging the physical conditions in which they might adopt the ordered structure of crystals is extremely tricky. The first crystallographic structural solutions of proteins were achieved in the late 1950s and early 1960s by Cambridge scientists working on myoglobin and haemoglobin. Early on, Ramakrishnan joined other structural biologists in solving some of the ribosomal proteins, but the ribosome itself, or even its component sub-units, were orders of magnitude more difficult.

First, you needed to find ribosomes stable enough even to attempt crystallisation: these were discovered by researchers in Israel, Germany and Russia working on micro-organisms living in extremely hot or salty water. Then you had to get these organisms to grow in lab conditions; to extract and purify the ribosomes; to get the sub-units – and eventually entire ribosomes – to form crystals good enough to work with; to ensure that crystal-making procedures found effective in one lab also worked in other labs and in other researchers’ hands; to devise techniques ensuring that the ribosomes weren’t damaged by the same X-rays used to produce diffraction patterns; to write software programmes to interpret those patterns; and finally to achieve the extraordinarily high resolutions that would make possible the determination of atom-by-atom structure. Ribosome crystal-growing, crystal-image-interpreting, the writing of appropriate software and devising conventions for the graphic representation of molecular structure are as messy, delicate, time-consuming and complex as anything in modern science. Watson and Crick modelled the structure of DNA; solving the structure of the ribosome would mean seeing it.

To Ramakrishnan, the ribosome is a machine, but you can also think of it as a factory – an organised system of machines – and ribosome discovery, like so much present-day science, was itself done through factory-like divisions of technical labour. No one scientist, or any one type of scientist, could solve the problem on their own. Some researchers could engineer the right sort of ribosome crystals; some could produce the diffraction patterns; others could write the computer programmes to make sense of the patterns; and a few others – especially Ramakrishnan himself – had the networking skills to bring together the findings of dispersed research groups, and the drive and imagination to attempt things that others thought impossible. Samples circulated around the world and researchers moved from lab to lab, learning the unique skills on offer at each establishment. Ramakrishnan’s account of the discovery of the ribosome has aspects of the picaresque. Almost every step towards the solution involved the movement of people between scientific establishments around the world, from one lab, international conference or coffee-table talk to the next.

Gene Machine comes advertised as ‘a personal story’, perhaps gesturing to James Watson’s The Double Helix: A Personal Account of the Discovery of the Structure of DNA (1968). But it is personal in a different way. There are eccentric ‘personalities’: one of Ramakrishnan’s assistants keeps himself motivated in the achingly cold conditions needed to grow ribosome crystals by playing Johnny Cash CDs; a Ferrari-owning Californian RNA scientist names his computers after Italian grand prix drivers. Ramakrishnan himself is a vegetarian, ‘near teetotaller’ family man: there is no Jim Watson-style chasing after ‘popsies’. The young Ramakrishnan admits to being ambitious, but also despairs that his contributions will ever be properly recognised and chides himself for caring about what he calls the ‘politics’ of professional recognition and scientific prizes. There are a few passages in Gene Machine that have a tint of the ‘red in tooth and claw’ picture of science in The Double Helix: secrets are shielded from rivals, and requests are made that the distribution of information be restricted. But on the whole information and ideas flow freely. There’s intense competition but there is also co-operation and collegiality, both formal and informal. A few of the ribosome researchers get on each other’s nerves; but there are only a few thoroughgoing jerks, and no hint of the physical violence that Watson reported he feared from Rosalind Franklin. Ramakrishnan says he doesn’t ‘subscribe to the heroic narrative of science’ or to the conception of scientific discovery as a flash of insight. The timescale for ribosome research wasn’t day-by-day but year-by-year, even decade-by-decade. There is drama in the telling of the story, but the excitement doesn’t reside in the vivid personal narrative that made The Double Helix a bestseller; it is in Ramakrishnan’s descriptions of the often frustrating extended labour of ribosome research and the dogged persistence of ribosome researchers.