Predicting Bound Ions on the Protein Surface

Abstract

Biological macromolecules exist in the complex environment of the cell, constantly interacting with other molecules and ions. Some of the ions may bind directly to proteins affecting their structure and thus altering their function. Though the X-ray crystallography remains to be one of the most popular methods of proteins structure determination, typically the positions of bound ions are not routinely revealed. Here we report a development of an approach, based on numerical solutions of the Poisson-Boltzmann equation (PBE) as implemented in DelPhi, which predicts the positions of surface bound ions taking into account geometrical considerations as well. The method is tested against existing experimental data of proteins with different types of ions on the surface and it is shown that it the electrostatic potential is the dominant factor for ion binding not involving chemical interactions. We further outline the importance of such an approach with respect to relaxing the limits of Poisson-Boltzmann formalism in describing the perturbation of ion's concentration in the space regions with large local electrostatic potential. The work is supported by NIH, NIGMS, grant number 1R01GM093937-01.