Unveiling protein-protein interaction potential through Monte Carlo simulation combined with small-angle X-ray scattering

Abstract

Protein interactions are investigated under different conditions of lysozyme concentration, temperature and ionic strength by means of in-solution small angle X-Ray scattering (SAXS) experiments and Monte Carlo (MC) simulations. Initially, experimental data were analysed through a Hard-Sphere Double Yukawa (HSDY) model combined with Random Phase Approximation (RPA), a closure relationship commonly used in the literature for monodisperse systems. We realized by means of MC that the HSDY/RPA modelling fails to describe the protein-protein pair potential for moderated and dense systems at low ionic strength, mainly due to inherent distortions of the RPA approximation. Our SAXS/MC results thus show that lysozyme concentrations between 2 (diluted) and 20 mg/mL (not crowded) present similar protein-protein pair potential preserving the values of surface net charge around 7 e, protein diameter of 28 Å, decay range of attractive well potential of 3 Å and a depth of the well potential varying from 1 to 5 kBT depending on temperature and salt addition. Noteworthy, we here propose a novel method to analyse the SAXS data from interacting proteins through MC simulations, which overcomes the deficiencies presented by the use of a closure relationship. Furthermore, this new methodology of combining SAXS with MC simulations gives a step forward to investigate more complex systems as those composed of a mixture of proteins of distinct species presenting different molecular weights (and hence sizes) and surface net charges at low, moderate and very dense systems.