• 1. X-ray Solution Scattering: An Experimental Overview.

  • 2. X-ray Solution Scattering - Information Content.

  • 3. Theoretical X-ray Solution Scattering Intensity.

  • 4. Implementation of code for making cubes around protein.

  • 5. Fitting experimental X-ray solution scattering data.

  • 6. Fitting experimental X-ray solution scattering data: Additional use cases

  • 7. Comparing chi-squared values CRYSOL, XSoS-implicit and FoXS

  • 8. Advantages of implicit solvent model.

XSoS-Implicit

Summary

XSoS-explicit is program based on explicit solvent model and uses explicit water molecules generated by molecular dynamics simulation for solvent-excluded volume and hydration layer.

1. X-ray solution scattering technique has become widely used technique for determining the structure of the molecules in the physiological condition. The X-ray solution data collected from protein solution and the buffer. The solvent intensities are then subtracted from solution intensity to obtain the scattering from the solute.

2. Computational approaches for modeling a macromolecular structure based on X-ray scattering data can be classified into Ab initio methods and Coordinate based calculation.

a. Using the Ab initio methods low resolution shapes of the macromolecules and its complexes can be determined, profile-to model approach.

b. Coordinate based calculation methods requires computing the scattering pattern of given atomic structure and its comparison with experimental data in a model to profile approach.

3. The accuracy of theoretical X-ray scattering curves of proteins is strongly dependent on the solvent contribution. Solvent can be represented as continuous electron density. XSoS-implicit is program based on implicit solvent model and uses continuous electron density for solvent-excluded volume and hydration layer.

4. Cube method is implemented for calcualting the scattering from the hydration layer.

Implementation of code for making cubes around protein

(i) Determine the maximum and minimum coordinates of the protein along x, y and z axes.

(ii) Using the maximum and minimum coordinates make a rectangular parallelepiped around the protein.

(iii) Enlarge the size of the parallelepiped, divide it into cubes and store them into an array.

(iv) Next calculate the distance of all the cubes from the protein surface to within 3Angstroms around it store them in array.

(v) The scattering curve of the hydration layer is evaluated form the cubes within 3Angstroms around the protein.

5. The source codes used in this work were written in C++. The source codes were compiled and executed in the Linux platform (CentOS 7) on a 2.2 GHz Intel Pentium 4 processor.The programs CRYSOL and FoXS are as standards checking performance of XSoS-Implicit.

6. The chi-squared values for the agreement between the experimental and the theoretical scattering curves indicate that XSoS-implicit is as accurate as, or in some cases even better than, the other methods (CRYSOL and FoXS).

References

"Implicit vs. Explicit Solvent Models for Calculating X-ray Solution Scattering Curves." Prabhakar G, Jong Goo K, Jae Hyuk L, Jeongho K, H. Ihee*, Bull. Korean Chem. Soc., 2015, 36: 955-962.