SASCUBE: An Updated Method of Cubes for Calculation of the Intensity of X-Ray Scattering by Biopolymers in Solution

Abstract

Abstract—This work describes an updated method of cubes, which allows calculation of the SAS curves for biopolymers in solution on the basis of the coordinates of their atoms without introducing any fitting parameters. The efficiency of the method was checked on a number of model systems. For eight globular proteins, the scattering intensities that were calculated using the SASCUBE software (https://sourceforge.net/projects/sascube) were compared with the corresponding experimental curves. This work addresses the contentious issue of the nature of distortions of the electron density of water near a protein surface. Molecular dynamics simulations were used to show that the electron density distribution of water in a 0.3-nm thick near-border protein layer could not be considered uniform, while its mean value could be less than the average electron density of water. It was shown that the conformational mobility significantly influenced the scattering curve of proteins. The possibility of using the method of cubes (SASCUBE software) in combination with molecular dynamics is discussed in order to find the intensities of protein scattering taking all the factors that influence the scattering curve into account (conformational mobility of proteins, distortions of water structures, etc.).