APBSmem: a graphical interface for electrostatic calculations at the membrane.
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.
Carnegie Mellon-University of Pittsburgh Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
Keith M
KM
Callenberg
Om P
OP
Choudhary
Gabriel L
GL
de Forest
David W
DW
Gohara
Nathan A
NA
Baker
Michael
M
Grabe
D003196:Computer Graphics; D008567:Membranes, Artificial; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D014584:User-Computer Interface
D008567:Membranes, Artificial; D011506:Proteins