Paper Citing NAMD - Abstract
He, Yi; Prieto, Lidia; Lazaridis, Themis
Modeling peptide binding to anionic membrane pores
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:1463-1475, JUN 30 2013
Peptide-induced pore formation in membranes can be dissected into two steps: pore formation and peptide binding to the pore. A computational method is proposed to study the second step in anionic membranes. The electrostatic potential is obtained from numerical solutions to the PoissonBoltzmann equation and is then used in conjunction with IMM1 (implicit membrane model 1). A double charge layer model is used to incorporate the effects of the membrane dipole potential. Inhomogeneity of the charge density in the pore, characterized by explicit membrane simulations of toroidal pores, is included in the model. This approach was applied to two extensively studied peptides, magainin and melittin. In agreement with previous work, binding to toroidal pores is more favorable than binding to the flat membrane. The dependence of binding energy on anionic content exhibits different patterns for the two peptides, in correlation with the different lipid selectivity that has been observed experimentally. (c) 2013 Wiley Periodicals, Inc.
