• 1. Representations of Protein Solution and Pure Solvent Ensembles.

  • 2. MD simulation of Myoglobin & Pure Water with NAMD & VMD

  • 3. Preparing systems for X-ray Solution Scattering Curve Calculation

  • 4. Program Implementation

  • 5. Convergence of scattering curves calculated by explicit solvent models

  • 6. Checking the convergence with AXES & WAXSiS

XSoS-Explicit

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.Here two systems are considered, system A containing the N protein molecules along with a water shell and system B containing the N water droplets corresponding to the solvent-excluded volume. The atomic coordinates of the two systems, namely protein with water shell and the solvent-excluded volume, are generated from short MD simulations snapshots.

2.Perl codes were written to remove water molecules beyond 7 Angstroms from the protein water box as well as the pure water box. All the 200 snapshots were processed by the perl code to remove water molecules beyond 7 Angstroms.

3.The source codes used in this work were written in C++. The source codes were compiled and executed in the Linux platform (CentoOS 7) on a 2.2 GHz Intel Pentium 4 processor.

4.The theoretical scattering curves of the same protein structures calculated with XSoS-explicit indicate that the shapes of the static scattering curves change sensitively depending on the solvent atomic coordinate sets. The default limit includes 100 atomic coordinate sets each for the solvent-excluded volume and the hydration layer. Calculating the scattering curves with increasing number of MD snapshots reduced undesirable effects of the solvent atomic coordinate sets on the scattering curves.

5.Results indicate that the scattering curve attains convergence on increasing the number of solvent degrees of freedom to above 500 snapshots.

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.

"Simulated x-ray scattering of protein solutions using explicit-solvent models." Park S, Bardhan J P, Roux B, Makowski L. J Chem Phys., 2009, 7;130(13):134114.