Paper Citing NAMD - Abstract
Jang, Hyunbum; Ma, Buyong; Lal, Ratnesh; Nussinov, Ruth
Models of Toxic beta-Sheet Channels of Protegrin-1 Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer beta-Amyloid Ion Channels
BIOPHYSICAL JOURNAL, 95:4631-4642, NOV 15 2008
Antimicrobial peptides (AMPs) induce cytotoxicity by altering membrane permeability. The electrical properties of membrane-associated AMPs as well as their cellular effects have been extensively documented; however their three-dimensional structure is poorly understood. Gaining insight into channel structures is important to the understanding of the protegrin-1 (PG-1) and other AMP cytolytic mechanisms, and to antibiotics design. We studied the beta-sheet channels morphology using molecular dynamics simulations. We modeled PG-1 channels as intrinsic barrel-stave and toroidal membrane pores, and simulated them in zwitterionic and anionic lipid bilayers. PG-1 channels consist of eight beta-hairpins in a consecutive NCCN (N and C represent the beta-hairpin's N-and C-termini) packing organization yielding antiparallel and parallel b-sheet channels. Both channels preserve the toroidal, but not the barrel-stave pores. The two lipid leaflets of the bilayer bend toward each other at the channels' edges, producing a semitoroidal pore with the outward-pointing hydrophobic residues preventing the polar lipid headgroups from moving to the bilayer center. In all simulated lipid environments, PG-1 channels divide into four or five beta-sheet subunits consisting of single or dimeric b-hairpins. The channel morphology with subunit organization is consistent with the four to five subunits observed by NMR in the POPE/POPG bilayer. Remarkably, a b-sheet subunit channel motif is in agreement with Alzheimer ion channels modeled using the universal U-shape beta-strand-turn-beta-strand structure, as well as with high resolution atomic force microscopy images of beta-amyloid channels with four to six subunits. Consistent with the toxic b-amyloid channels that are ion-conducting, the PG-1 channels permeate anions.
