Referenced in: none

Automatically associated channels: TRP , TRPV , TRPV1

Title: Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations.

Authors: Frank V Marcoline, Neville Bethel, Christopher J Guerriero, Jeffrey L Brodsky, Michael Grabe

Journal, date & volume: Structure, 2015 Aug 4 , 23, 1526-37

PubMed link: http://www.ncbi.nlm.nih.gov/pubmed/26118532

Abstract
The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information.