Abstract
Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method 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 that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement 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 before the calculation and the electrostatic potential after completing the computation. 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. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated.
Highlights
The relationship between the electric field and the charge in a system is determined by Maxwell’s equations; several factors contribute to making these equations difficult to solve in a heterogeneous, condensed phase
Very recently, an online web server was created to facilitate PB calculations on membrane proteins using the PBEQ module [42], and here, we present our program, APBSmem, which combines an easy to use interface with Adaptive Poisson-Boltzmann Solver (APBS) to allow non-experts to calculate the electrostatic properties of membrane proteins
APBSmem was developed in Java and requires Java Runtime Environment 5.0 or later and APBS version 1.2.0 or later which can be downloaded from http://java.sun.com/ and http://www. poissonboltzmann.org/, respectively
Summary
The relationship between the electric field and the charge in a system is determined by Maxwell’s equations; several factors contribute to making these equations difficult to solve in a heterogeneous, condensed phase. The most popular method for carrying out electrostatic calculations in a biological setting is to solve the Poisson-Boltzmann (PB) equation. Starting from a known protein structure, this method treats the protein and water as distinct dielectric environments, and the charges on the protein give rise to the electric field. PB theory implicitly accounts for counter-ions in solution via a non-linear term that depends on the bulk counter-ion concentration and the electrostatic potential. {+:1⁄2E(~r)+w(~r)zk2(~r) sinh1⁄2w(~r)~ e 4pr(~r), ð1Þ kBT where w~eW=kBT is the reduced electrostatic potential and W is the electrostatic potential, k2 is the Debye-Huckel screening parameter, which accounts for ionic shielding, E is the dielectric constant for each of the distinct microscopic regimes in the system, and r is the density of charge within the protein moiety.
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