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APBSmem: A graphical interface for electrostatic calculations at the membrane

Callenberg, KM and Choudhary, OP and de Forest, GL and Gohara, DW and Baker, NA and Grabe, M (2010) APBSmem: A graphical interface for electrostatic calculations at the membrane. PLoS ONE, 5 (9).

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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. © 2010 Callenberg et al.

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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Callenberg, KM
Choudhary, OP
de Forest, GL
Gohara, DW
Baker, NA
Grabe, Mmdgrabe@pitt.eduMDGRABE
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorFlower, Darren R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 29 September 2010
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 5
Number: 9
DOI or Unique Handle: 10.1371/journal.pone.0012722
Schools and Programs: School of Medicine > Computational Biology
Refereed: Yes
MeSH Headings: Computer Graphics; Membranes, Artificial; Models, Molecular; Molecular Conformation; Protein Binding; Proteins--chemistry; Software; Static Electricity; User-Computer Interface
Other ID: NLM PMC2947494
PubMed Central ID: PMC2947494
PubMed ID: 20949122
Date Deposited: 22 Aug 2012 21:50
Last Modified: 02 Feb 2019 13:55
URI: http://d-scholarship.pitt.edu/id/eprint/13555

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