MSGID: 1:317/3 6476cd87   
   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    An algorithm for sharper protein films    
      
     Date:   
         May 30, 2023   
     Source:   
         Paul Scherrer Institute   
     Summary:   
         Proteins are biological molecules that perform almost all   
         biochemical tasks in all forms of life. In doing so, the tiny   
         structures perform ultra-fast movements. In order to investigate   
         these dynamic processes more precisely than before, researchers have   
         developed a new algorithm that can be used to evaluate measurements   
         at X-ray free-electron lasers.   
      
      
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   FULL STORY   
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   Proteins are biological molecules that perform almost all biochemical   
   tasks in all forms of life. In doing so, the tiny structures perform   
   ultra-fast movements. In order to investigate these dynamic processes   
   more precisely than before, researchers have developed a new algorithm   
   that can be used to evaluate measurements at X-ray free-electron lasers   
   such as the SwissFEL more efficiently. They have now presented it in   
   the journal Structural Dynamics.   
      
   Sometimes, when using the navigation system while travelling by car,   
   the device will locate you off the road for a short time. This is due to   
   the inaccuracy of the GPS positioning, which can be as much as several   
   metres. However, the algorithm in the sat nav will soon notice this   
   and correct the trajectory displayed on the screen, i.e. put it back on   
   the road.   
      
   A comparable principle for addressing unrealistic motion sequences has now   
   been successfully applied by a team of researchers led by PSI physicist   
   Cecilia Casadei. However, their objects of investigation are about a   
   billion times smaller than a car: proteins. These building blocks of   
   life fulfil crucial functions in all known organisms. In doing so, they   
   often perform ultra-fast movements. Analysing these movements precisely   
   is crucial for our understanding of proteins which can help us produce   
   new medical agents, amongst other things.   
      
   How to "film" proteins...   
      
   To further improve the understanding of protein movements, Casadei,   
   together with other PSI researchers, a researcher at DESY in Hamburg   
   and other colleagues at the University of Wisconsin in Milwaukee, USA,   
   has developed an algorithm that evaluates data obtained in experiments   
   at an X-ray free-electron laser (XFEL). An XFEL is a large-scale   
   research facility that delivers extremely intense and short flashes of   
   laser-quality X-ray light. Here, a method called time-resolved serial   
   femtosecond X-ray crystallography (TR-SFX) can be used to study the   
   ultra-fast movements of proteins.   
      
   The measurements are very complex for several reasons: the proteins are   
   much too small to be imaged directly, their movements are incredibly fast,   
   and the intense pulse of X-ray light of an FEL completely destroys the   
   proteins. On the experimental level, TR-SFX already solves all these   
   problems: no individual molecule is measured, but rather a large number   
   of identical protein molecules are induced to grow together in a regular   
   arrangement to form protein crystals.   
      
   When the FEL X-ray light shines on these crystals, the information is   
   captured in time before the crystals and their proteins are destroyed by   
   the pulse of light. The raw data from the measurements are available as   
   so-called diffraction images: light spots that are created by the regular   
   arrangement of the proteins in the crystal and registered by a detector.   
      
   ... and how to evaluate the measurement data Where the experimental   
   challenges have been overcome, the evaluation of the data is just   
   beginning. "The measurement of each individual crystal provides only   
   two percent of the data of a complete image." This incompleteness has   
   physical and experimental reasons and can only be eliminated by combining   
   the measurement data of many crystals in a meaningful way. Casadei's   
   research focuses on exactly how to go about this.   
      
   The method established so far is called "binning and merging." "A lot has   
   been achieved with this method in the last decade," says Casadei. With   
   this method, the data are divided into time intervals and all data   
   within one interval, a "bin," are averaged. However, a lot of detailed   
   information is also lost in this averaging. "You could say that the   
   individual images of the protein film are then all a bit washed out,"   
   Casadei continues. "That's why we have developed a method that allows   
   us to get more out of the measurement data."  The new method devised   
   by Casadei and her colleagues is called "low-pass spectral analysis,"   
   or LPSA for short. "Similar to electronics or audio technology, we apply   
   a low-pass filter," Casadei explains. "However, in our case it comes in   
   the form of advanced linear algebra. We apply these formulas to remove   
   unwanted noise from the data without losing the relevant details."   
   In short and simple terms, the raw data, i.e. the diffraction images of   
   the protein crystals, are tracked throughout the protein motion. This   
   movement is assumed to be smooth, i.e. jerk-free. Similar to how the   
   navigation system corrects itself when the car seemingly leaves the   
   course of the road, the new algorithm by Casadei and her colleagues   
   mitigates errors of the protein movement reconstruction.   
      
   HDR for protein films Lay people may not notice an immense difference   
   in the new protein films. But for the cineastes at X-ray free-electron   
   lasers, the improvement is comparable to switching from a DVD film to   
   HDR quality.   
      
   "Above all, the new algorithm now allows researchers here at   
   SwissFEL at PSI to extract more information from their data," says   
   Casadei. Conversely, this means the algorithm can help shorten long   
   measurement times. Since beam time is always in high demand at large-scale   
   research facilities, and in particular at SwissFEL, this is a most welcome   
   prospect for protein researchers using this highly advanced facility.   
      
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   ==========================================================================   
   Story Source: Materials provided by Paul_Scherrer_Institute. Original   
   written by Laura Hennemann. Note: Content may be edited for style   
   and length.   
      
      
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   Journal Reference:   
      1. Patrick Sharman, Alastair J. Wilson. Genetic improvement of   
      speed across   
         distance categories in thoroughbred racehorses in Great Britain.   
      
         Heredity, 2023; DOI: 10.1038/s41437-023-00623-8   
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   Link to news story:   
   https://www.sciencedaily.com/releases/2023/05/230530125358.htm   
      
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