The Protein-Imaging Technique Taking Over Structural
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manipulating peer review to boost their From 2014 to 2018, Chou was named as a microscopes and more sophisticated soft- citations. Chou’s case is the first to be highly cited researcher in a list produced by ware for transforming the images they cap- revealed since that announcement. “While Clarivate Analytics, an information-services tured into sharper molecular structures. thankfully rare, such practices are an abuse firm in Philadelphia, Pennsylvania, that owns That paved the way for the current growth of the peer-review system and undermine the the citation database Web of Science. But his of cryo-EM, says Sjors Scheres, a structural hard work and commitment that editors and name does not appear on the 2019 list; last biologist and specialist in the technique at the reviewers devote to ensuring the integrity of year, Clarivate decided to remove scientists MRC Laboratory of Molecular Biology (LMB) the scholarly record,” a spokesperson says. whose papers showed “unusually high levels in Cambridge, UK. “Elsevier has developed analytical tools to of self-citation”. Richard Henderson, an LMB structural help detect such practices and is committed Elsevier hasn’t yet decided what to do about biologist who shared the 2017 Nobel Prize in to implementing technology to flag citation papers that Chou handled that liberally cite his Chemistry for his work developing the tech- manipulation before publication.” work, the spokesperson says. nique, says that even after these advances, growth was slow at first, because only a small number of labs had access to the equipment. But when they started using cryo-EM to pro- duce detailed maps of molecules such as the ribosome — cells’ protein-making machines THE PROTEIN-IMAGING — other scientists, as well as their institutions and funders, quickly took notice. “All the TECHNIQUE TAKING OVER people who had invested in other things and made the wrong decisions, it took them a year STRUCTURAL BIOLOGY to catch up,” says Henderson. He estimates that, by 2024, more protein The number of structures being determined by structures will be determined by cryo-EM than by X-ray crystallography. Cryo-EM has cryo-electron microscopy is growing explosively. already supplanted X-ray crystallography for one category of proteins that scientists are By Ewen Callaway crystals, but the technique languished because especially interested in — those embedded in it tended to produce low-resolution structures cell membranes. Many such membrane-bound revolutionary technique for — some scientists called it blobology. proteins are implicated in disease and serve as determining the 3D shape of Breakthroughs in hardware and software targets for drugs. proteins is booming. Last week, a in 2012–13 produced more sensitive electron database that collects protein and Advanced imaging other molecular structures obtained STRUCTURE SLEUTHS The structures of molecules determined by Ausing cryo-electron microscopy, or cryo-EM, Most structures of proteins and other biological cryo-EM are also getting more detailed, thanks acquired its 10,000th entry. molecules are still solved with X-ray crystallography. to continuing improvements in hardware and But a revolutionary technique called cryo-electron Submissions to the Electron Microscopy microscopy (cryo-EM) is catching up. software, says Scheres. Data Bank (EMDB) — a popular repository for Initially, the sharpest cryo-EM structures 12,000 structures solved using electron microscopy were of highly stable proteins that were used — have increased exponentially in recent years, 10,000 to test the limits of the technology. But Scheres largely because of the explosive growth in the X-ray crystallography has noticed that researchers are increasingly number of cryo-electron microscopes in lab- 8,000 obtaining very high-resolution structures oratories worldwide (see ‘Structure sleuths’). of medically important molecules, such as 6,000 The EMDB curates structures solved with other cell-membrane proteins, even though they microscopy methods, but the vast majority 4,000 tend to flop around. use cryo-EM. “We’re now coming to the point where the 2,000 The technique involves flash-freezing per year released Structures easy samples have been done and people are Electron microscopy solutions of proteins or other biomolecules, 0 looking at more complex problems,” says and then bombarding them with electrons 2003 2007 2011 2015 2019 Ardan Patwardhan, a structural biologist at to produce microscope images of individual The electron microscopy line shows structures submitted to the the European Molecular Biology Laboratory– Electron Microscopy Data Bank. Nearly all use cryo-EM. molecules. These are used to reconstruct the European Bioinformatics Institute in Hinxton, Fine detail 3D shape, or structure, of the molecule. Such UK, who leads the team that runs the EMDB. Cryo-EM can now resolve features that structures are useful for uncovering how pro- are less than 2 ångströms across. Henderson expects the boom in cryo-EM teins work, how they malfunction in disease structures to slow at some point. One factor 25 and how to target them with drugs. that could sap growth, he says, is the high cost For decades, structural biologists preferred 20 Average of the most powerful microscopes, which can to use X-ray crystallography, a technique that exceed £5 million (US$7 million). They also involves crystallizing proteins, pummelling 15 cost thousands of pounds each day to run, them with X-rays and reconstructing their and require specialized labs that minimize shape from the resulting tell-tale patterns of 10 Highest vibrations. Henderson is campaigning to diffracted light. X-ray crystallography pro- (Å) Resolution convince firms to develop cheaper, but still duces high-quality structures, but it’s not easy 5 useful, microscopes that could spread the to use with all proteins — some can take months technique even further. “At the moment, you or years to crystallize, and others never crys- 0 cannot go wrong by putting more investment SOURCE: EMDB SOURCE: tallize at all. Cryo-EM doesn’t require protein 2003 2007 2011 2015 2019 into cryo-EM,” he says. Nature | Vol 578 | 13 February 2020 | 201 ©2020 Spri nger Nature Li mited. All ri ghts reserved. ©2020 Spri nger Nature Li mited. All ri ghts reserved. .