APBSmem: A Tool for the Analysis of Membrane Protein Electrostatics

Abstract

Electrostatic forces orchestrate the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular means for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available for carrying out these calculations on soluble proteins. We have developed a tool called APBSmem that performs these calculations in the presence of a membrane. Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement and shape relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane and the resulting electrostatic potential. We demonstrate the use of our software with three examples involving the calculation of the protein transfer free energy from water to membrane, solvation energy required to move an ion into a channel, and the gating charge of a molecular motion. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. In particular, our built-in protocols should be appealing to researchers studying ion channel and transporter function.