Molecular dynamics simulations of highly charged green fluorescent proteins

Abstract

A recent experimental study showed that green fluorescent proteins (GFPs) that have been mutated to have ultra-high positive or negative net charges, retain their native structure and fluorescent properties while gaining resistance to aggregation under denaturing conditions. These proteins also provide an ideal test case for studying the effects of surface charge on protein structure and dynamics. Classical molecular dynamics (MD) simulations have been performed on the near-neutral wildtype GFP and mutants with net charges of −29 and +35. The resulting trajectories were analysed to quantify differences in structure and dynamics between the three GFPs. This analysis shows that all three proteins are stable over the MD trajectory, with the near-neutral wild type GFP exhibiting somewhat more flexibility than the positive or negative GFP mutants, as measured by the order parameter and changes in ϕ–ψ angles. There are more dramatic differences in the properties of the water and counter ions surrounding the proteins. The water diffusion constant near the protein surface is closer to the value for bulk water in the positively charged GFP than in the other two proteins. Additionally, the positively charged GFP shows a much greater clustering of the counter ions (Cl⁻) near its surface than corresponding counter ions (Na⁺) near the negatively charged mutant.

Keywords:

• green fluorescent protein
• molecular dynamics
• highly charged proteins
• protein hydration

Acknowledgements

This work was also supported by the US Department of Energy, Office of Science, Offices of Advanced Scientific Computing Research, and Biological & Environmental Research through the U.C. Merced Center for Computational Biology #DE-FG02-04ER25625. This work was in part performed under the auspices of the United States Department of Energy by Lawrence Livermore National Laboratory under contract number DE-AC52-07NA27344.