APBSmem: A Tool for the Analysis of Membrane Protein Electrostatics

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