Molecular dynamics and small-angle neutron scattering of lysozyme aqueous solutions

Abstract

Molecular dynamics simulations of a coarse-grained, embedded-charge model of lysozyme aqueous solutions are compared with small-angle neutron scattering experiments. Measures concern different solutions with a 10% by weight protein concentration and an increasing pH in the range 2–6. The model is based on a soft-core modification of the original Carlsson–Malmsten–Linse model, where in particular all residues carrying an appreciable amount of residual charge, as a function of the pH, are explicitly taken into account in the overall macromolecular interaction. Simulations reproduce qualitatively the experimental trend of the structure factor such as, in particular, the observed change from a low-pH regime, dominated by repulsive interactions, to behaviour mainly determined by attractive forces, at higher pH. Possible improvements of the model, towards a better reproduction of the structural properties of the real solution, are proposed.

Keywords:

• coarse-grained models
• proteins
• molecular dynamics
• SANS

Acknowledgements

We gratefully acknowledge the computer time and technical support provided by the Centro di Calcolo Elettronico dell'Università di Messina ‘A. Villari’ and by the PI2S2 Project, managed by the Consorzio COMETA (more information is available at http://www.pi2s2.it and http://www.consorzio-cometa.it). We thank Prof. P. Linse and the American Chemical Society for granting us the permission to reprint the picture in Figure 2.