title: β-sheet structures and dimer models of the two major tyrocidines, antimicrobial peptides from Bacillus aneurinolyticus.
abstract: The structures of two major tyrocidines, antibiotic peptides from Bacillus aneurinolyticus, in an aqueous environment were studied using nuclear magnetic resonance spectroscopy, restrained molecular dynamics (MD), circular dichroism, and mass spectrometry. TrcA and TrcC formed β-structures in an aqueous environment. Hydrophobic and hydrophilic residues were not totally separated into nonpolar and polar faces of the peptides, indicating that tyrocidines have low amphipathicity. In all the β-structures, residues Trp(4)/Phe(4) and Orn(9) were on the same face. The ability of the peptides to form dimers in aqueous environment was studied by replica exchange MD simulations. Both peptides readily dimerize, and predominant complex structures were characterized through cluster analysis. The peptides formed dimers by either associating sideways or stacking on top of each other. Dimers formed through sideways association were mainly stabilized by hydrogen bonding, while the other dimers were stabilized by hydrophobic interactions. The ability of tyrocidine peptides to form different types of dimers with different orientations suggests that they can form larger aggregates, as well.
authors.affiliation: Department of Chemistry, University of Cape Town , P Bag X3, Rondebosch, Cape Town, South Africa 7701.
authors.forename: Gadzikano
authors.initials: G
authors.lastname: Munyuki
authors.forename: Graham E
authors.initials: GE
authors.lastname: Jackson
authors.forename: Gerhard A
authors.initials: GA
authors.lastname: Venter
authors.forename: Katalin E
authors.initials: KE
authors.lastname: Kövér
authors.forename: László
authors.initials: L
authors.lastname: Szilágyi
authors.forename: Marina
authors.initials: M
authors.lastname: Rautenbach
authors.forename: Barbara M
authors.initials: BM
authors.lastname: Spathelf
authors.forename: Bhaswati
authors.initials: B
authors.lastname: Bhattacharya
authors.forename: David
authors.initials: D
authors.lastname: van der Spoel
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism; D001407:Bacillus / Q000737:chemistry / Q000378:metabolism*; D019281:Dimerization; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D014440:Tyrocidine / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D014440:Tyrocidine