2015
DOI: 10.1016/j.jmgm.2015.04.003
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Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane

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Cited by 6 publications
(7 citation statements)
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“…Prior to building the protein−lipid systems, the initial orientation of R1attached VSD in the membrane was the same as the optimal spatial position of unlabeled KvAP-VSD published previously. 17 In brief, the orientation of the VSD within the membrane was evaluated by calculating the solvation energy with the Poisson−Boltzmann solvent continuum approach. We computed the difference in electrostatic solvation energies of the protein in implicit water and membrane at various positions using the programs APBS and APBSmem.…”
Section: ■ Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Prior to building the protein−lipid systems, the initial orientation of R1attached VSD in the membrane was the same as the optimal spatial position of unlabeled KvAP-VSD published previously. 17 In brief, the orientation of the VSD within the membrane was evaluated by calculating the solvation energy with the Poisson−Boltzmann solvent continuum approach. We computed the difference in electrostatic solvation energies of the protein in implicit water and membrane at various positions using the programs APBS and APBSmem.…”
Section: ■ Methodsmentioning
confidence: 99%
“…Prior to building the protein–lipid systems, the initial orientation of R1-attached VSD in the membrane was the same as the optimal spatial position of unlabeled KvAP-VSD published previously . In brief, the orientation of the VSD within the membrane was evaluated by calculating the solvation energy with the Poisson–Boltzmann solvent continuum approach.…”
Section: Methodsmentioning
confidence: 99%
“…The protein structure quality was subsequently validated by the program PROCHECK . Prior to insertion of the protein into an explicit membrane environment, the optimal spatial position of the protein in membranes was determined using the calculation of the electrostatic solvation free energy approach previously described . In brief, all the missing hydrogen atoms were added to the protein structure using the program PDB2PQR. , Partial atomic charges and radii of the protein were taken from the PARSE parameter sets .…”
Section: Methodsmentioning
confidence: 99%
“…The combined model of mHv1cc-VSD/hHv1-CTD (Figure S1C) and the truncated C-terminal domain model in the dimer form were built using visual molecular dynamics (VMD) . The favorable position of protein in the lipid bilayer was carefully predicted by a method previously developed, using the adaptive Poisson–Boltzmann solver (APBS) software package, with PARSE partial charges . The hydrogen atoms and atomic charges were assigned with the PDB2PQR program. , …”
Section: Methodsmentioning
confidence: 99%