Paper Citing NAMD - Abstract
Supunyabut, Chirayut; Fuklang, Sunit; Sompornpisut, Pornthep
Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 59:81-91, JUN 2015
Orientations of proteins in the membranes are crucial to their function and stability. Unfortunately the exact positions of these proteins in the lipid bilayer are mostly undetermined. Here, the spatial orientation of membrane proteins within the lipid membrane was evaluated using a Poisson-Boltzmann solvent continuum approach to calculate the electrostatic free energy of the protein salvation at various orientations in an implicit bilayer. The solvation energy was obtained by computing the difference in electrostatic energies of the protein in water and in lipid/water environments, treating each as an implicit solvent model. The optimal position of transmembrane proteins (TIVIP) in a lipid bilayer is identified by the minimum in the "downhill" pathway of the salvation energy landscape. The energy landscape pattern was considerably conserved in various TMP classes. Evaluation of the position of 1060 membrane proteins from the orientations of proteins in membranes (OPM) database revealed thaf most of the polytopic and 3-barrel proteins were in good agreement with those of the OPM database. The study provides a useful scheme for estimating the membrane solvation energy made by lipid-exposed amino acids in membrane proteins. In addition, our results tested with the bacterial potassium channel model demonstrated the potential usefulness of the approach in assessing the quality of membrane protein models. The present approach should be applicable for constructing transmembrane proteins-lipid configuration suitable for membrane protein simulations and will have utility for the structural modeling of membrane proteins. (C) 2015 Elsevier Inc. All rights reserved.
