{"id":32459,"date":"2016-02-19T07:42:42","date_gmt":"2016-02-19T06:42:42","guid":{"rendered":"https:\/\/renewable-carbon.eu\/news\/?p=32459"},"modified":"2016-02-12T16:24:20","modified_gmt":"2016-02-12T15:24:20","slug":"new-method-opens-crystal-clear-views-of-biomolecules","status":"publish","type":"post","link":"https:\/\/renewable-carbon.eu\/news\/new-method-opens-crystal-clear-views-of-biomolecules\/","title":{"rendered":"New method opens crystal clear views of biomolecules"},"content":{"rendered":"

A scientific breakthrough gives researchers access to the blueprint of thousands of molecules of great relevance to medicine and biology. The novel technique, pioneered by a team led by DESY scientist Professor Henry Chapman from the Center for Free-Electron Laser Science CFEL and reported this week in the scientific journal Nature, opens up an easy way to determine the spatial structures of proteins and other molecules, many of which are practically inaccessible by existing methods. The structures of biomolecules reveal their modes of action and give insights into the workings of the machinery of life. Obtaining the molecular structure of particular proteins, for example, can provide the basis for the development of tailor-made drugs against many diseases. \u201cOur discovery will allow us to directly view large protein complexes in atomic detail,\u201d says Chapman, who is also a professor at the University of Hamburg and a member of the Hamburg Centre for Ultrafast Imaging CUI.<\/strong><\/p>\n

\"Slightly
Slightly disordered crystals of complex biomolecules like that of the photosystem II molecule shown here produce a complex continous diffraction pattern (right, the disorder is greatly exaggerated) under X-ray light that contains far more information than the so-called Bragg peaks of a strongly ordered crystal alone (left). Credit: DESY, Eberhard Reimann<\/figcaption><\/figure>\n

To determine the spatial structure of a biomolecule, scientists mainly rely on a technique called crystallography. The new work offers a direct route to \u201cread\u201d the atomic structure of complex biomolecules by crystallography without the usual need for prior knowledge and chemical insight. \u201cThis discovery has the potential to become a true revolution for the crystallography of complex matter,\u201d says the chairman of DESY’s board of directors, Professor Helmut Dosch.<\/p>\n

In crystallography, the structure of a crystal and of its constituents can be investigated by shining X-rays on it. The X-rays scatter from the crystal in many different directions, producing an intricate and characteristic pattern of numerous bright spots, called Bragg peaks (named after the British crystallography pioneers William Henry and William Lawrence Bragg). The positions and strengths of these spots contain information about the structure of the crystal and of its constituents. Using this approach, researchers have already determined the atomic structures of tens of thousands of proteins and other biomolecules.<\/p>\n

But the method suffers from two significant barriers, which make structure determination extremely difficult or sometimes impossible. The first is that the molecules must be formed into very high quality crystals. Most biomolecules do not naturally form crystals. However, without the necessary perfect, regular arrangement of the molecules in the crystal, only a limited number of Bragg peaks are visible. This means the structure cannot be determined, or at best only a fuzzy \u201clow resolution\u201d facsimile of the molecule can be found. This barrier is most severe for large protein complexes such as membrane proteins. These systems participate in a range of biological processes and many are the targets of today’s drugs. Great skill and quite some luck are needed to obtain high-quality crystals of them.<\/p>\n

\u201cExtreme Sudoku in three dimensions\u201d<\/h3>\n
\"The
The analysis of the Bragg peaks alone (top) reveals far less details than the analysis of the continuous diffraction pattern (bottom). Magnifying glasses show real data. Credit: DESY, Eberhard Reimann<\/figcaption><\/figure>\n

The second barrier is that the structure of a complex molecule is still extremely difficult to determine, even when good diffraction is available. \u201cThis task is like extreme Sudoku in three dimensions and a million boxes, but with only half the necessary clues,\u201d explains Chapman. In crystallography, this puzzle is referred to as the phase problem. Without knowing the phase \u2013 the lag of the crests of one diffracted wave to another \u2013 it is not possible to compute an image of the molecule from the measured diffraction pattern. But phases can\u2019t be measured. To solve the tricky phase puzzle, more information must be known than just the measured Bragg peaks. This additional information can sometimes be obtained by X-raying crystals of chemically modified molecules, or by already knowing the structure of a closely-related molecule.<\/p>\n

When thinking about why protein crystals do not always \u201cdiffract\u201d, Chapman realised that imperfect crystals and the phase problem are linked. The key lies in a weak \u201ccontinuous\u201d scattering that arises when crystals become disordered. Usually, this non-Bragg, continuous diffraction is thought of as a nuisance, although it can be useful for providing insights into vibrations and dynamics of molecules. But when the disorder consists only of displacements of the individual molecules from their ideal positions in the crystal then the \u201cbackground\u201d takes on a much more complex character \u2013 and its rich structure is anything but diffuse. It then offers a much bigger prize than the analysis of the Bragg peaks: the continuously-modulated \u201cbackground\u201d fully encodes the diffracted waves from individual \u201csingle\u201d molecules.<\/p>\n

\u201cIf you would shoot X-rays on a single molecule, it would produce a continuous diffraction pattern free of any Bragg spots,\u201d explains lead author Dr. Kartik Ayyer from Chapman’s CFEL group at DESY. \u201cThe pattern would be extremely weak, however, and very difficult to measure. But the \u2018background\u2019 in our crystal analysis is like accumulating many shots from individually-aligned single molecules. We essentially just use the crystal as a way to get a lot of single molecules, aligned in common orientations, into the beam.\u201d With imperfect, disordered crystals, the continuous diffraction fills in the gaps and beyond the Bragg peaks, giving vastly more information than in normal crystallography. With this additional gain in information, the phase problem can be uniquely solved without having to resort to other measurements or assumptions. In the analogy of the Sudoku puzzle, the measurements provide enough clues to always arrive at the right answer.<\/p>\n

The best crystals are imperfect crystals<\/h3>\n

This novel concept leads to a paradigm shift in crystallography \u2014 the most ordered crystals are no longer the best to analyse with the novel method. Instead, the best crystals are imperfect crystals. \u201cFor the first time we have access to single molecule diffraction \u2013 we have never had this in crystallography before,\u201d he explains. \u201cBut we have long known how to solve single-molecule diffraction if we could measure it.\u201d The field of coherent diffractive imaging, spurred by the availability of laser-like beams from X-ray free-electron lasers, has developed powerful algorithms to directly solve the phase problem in this case, without having to know anything at all about the molecule. \u201cYou don\u2019t even have to know chemistry,\u201d says Chapman, \u201cbut you can learn it by looking at the three-dimensional image you get.\u201d<\/p>\n

To demonstrate their novel analysis method, the Chapman group teamed up with the group of Professor Petra Fromme from the Arizona State University (ASU), and other colleagues from ASU, University of Wisconsin, the Greek Foundation for Research and Technology – Hellas FORTH, and SLAC National Accelerator Laboratory in the U.S. They used the world’s most powerful X-ray laser LCLS at SLAC to X-ray imperfect microcrystals of a membrane protein complex called Photosystem II that is part of the photosynthesis machinery in plants.<\/p>\n

Including the continuous diffraction pattern into the analysis immediately improved the spatial resolution around a quarter from 4.5 \u00c5ngstr\u00f6m to 3.5 \u00c5ngstr\u00f6m (an \u00c5ngstr\u00f6m is 0.1 nanometres). The obtained image gave fine definition of molecular features that usually require fitting a chemical model to see. \u201cThat is a pretty big deal for biomolecules,\u201d explains co-author Dr. Anton Barty from DESY. \u201cAnd we can further improve the resolution if we take more patterns.\u201d The team had only a few hours of measuring time for these experiments, while full-scale measuring campaigns usually last a couple of days.<\/p>\n

The scientists hope to obtain even clearer and higher resolution images of photosystem II and many other macromolecules with their new technique. \u201cThis kind of continuous diffraction has actually been seen for a long time from many different poorly-diffracting crystals,\u201d says Chapman. \u201cIt wasn\u2019t understood that you can get structural information from it and so analysis techniques suppressed it. We\u2019re going to be busy to see if we can solve structures of molecules from old discarded data.\u201d<\/p>\n

Reference:
\nMacromolecular diffractive imaging using imperfect crystals; Kartik Ayyer et al.; Nature (2016); DOI: 10.1038\/nature16949<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

A scientific breakthrough gives researchers access to the blueprint of thousands of molecules of great relevance to medicine and biology. The novel technique, pioneered by a team led by DESY scientist Professor Henry Chapman from the Center for Free-Electron Laser Science CFEL and reported this week in the scientific journal Nature, opens up an easy […]<\/p>\n","protected":false},"author":58,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_seopress_robots_primary_cat":"","nova_meta_subtitle":"","footnotes":""},"categories":[5572],"tags":[],"supplier":[541,7241,6679,1195],"class_list":["post-32459","post","type-post","status-publish","format-standard","hentry","category-bio-based","supplier-arizona-state-university","supplier-deutsches-elektronen-synchrotron-desy","supplier-slac-national-accelerator-laboratory","supplier-universitaet-hamburg"],"_links":{"self":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/posts\/32459","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/users\/58"}],"replies":[{"embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/comments?post=32459"}],"version-history":[{"count":0,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/posts\/32459\/revisions"}],"wp:attachment":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/media?parent=32459"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/categories?post=32459"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/tags?post=32459"},{"taxonomy":"supplier","embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/supplier?post=32459"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}