Using an experimental method that leverages X-rays scattered from a sample, Researchers at the Moscow Institute of Physics and Technology (MIPT) have devised a method for testing proteins that is about 50 times faster than conventional methods.
'Polynomial expansions of protein structures and interactions’- 'small-angle X-ray scattering’ (Pepsi-SAXS) is a versatile technique for swift and precise determination of small-angle X-ray scattering profiles, which are distinct signatures used to identify proteins in the same way that fingerprints are used to identify individuals.
Proteins have intricate structures and a very small size, just a few nanometres across. To better analyze them, Scientists are constantly coming up with innovative processes. One major hurdle is sensitivity, protein specimens are readily destroyed and their qualities can be disturbed by tests.
The evaluation of X-rays scattered by proteins is just one of the means used to analyze these molecules. Scientists use X-rays instead of visible light, because of the minute scale of their work, on the order of 0.1 nanometres. The smaller the sample, the shorter the wavelength of light that must be used to see it. Since X-rays have a much shorter wavelength than visible light, they can be used to analyze tiny molecular structures.
SAXS is a novel method that involves collecting scattered X-rays from a sample. After plotting scattered X-ray beam intensity against the angle of incidence, a protein sample can be compared to samples in a database and identified. Compared to other tactics used to ascertain protein structure, SAXS is much less complicated and cheaper. It calls for little sample preparation, and specimens are studied in solution, in their operational state. As a result, outcomes are much more reliable and testing is non-destructive.
While SAXS has had extremely high research potential, the technique has been held back by the amount of computer processing power required to execute it, with one experiment taking hours to process. When the technique was first developed, the quantity of computations required was exponentially higher than the number of the atoms in the sample, with samples generally containing more than 1000 atoms.
Over the years, multiple computational tools for the investigation of SAXS data were produced. According to a report recently published by the MIPT team in the journal Acta Crystallographica Section D: Structural Biology, they evaluated many computational procedures and contrasted them with their own novel method.
The new method allows us to plot scattering curves efficiently and precisely, and analyze the three-dimensional structure of a sample. Among other things, Pepsi-SAXS boosts modelling efficiency and the accuracy of three-dimensional macromolecule structure prediction.
Maria Garkavenko, Study Author
“Pepsi-SAXS can be adapted to the size of a given sample and the resolution of experimental data,” added Co-Author and PhD Student Andrei Kazennov.
In addition to devising a new computational method, the study team also developed an effective way to model the hydration shell, a covering of water molecules encompassing proteins in solution and integrated it into their software, boosting the precision of the technique.
Lead Researcher Sergei Grudinin said his team’s method was validated using a massive data set from two of the largest biological databases in the world.
We have shown that Pepsi-SAXS is five to 50 times faster than the previously used methods. At the same time, the accuracy is on a par with them.
Sergei Grudinin, Lead Researcher
The study team said their work could have major repercussions for research on the basic operations fundamental to life, along with for the creation of medications and medical treatments, including the creation of artificial organs. Understanding proteins enables new medications and treatments to be created in a more targeted manner.