Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations

• Published in: Life (Basel, Switzerland) Switzerland), 2023-11, Vol.13 (12), p.2288
• Main Authors: Tyagi, Chetna, Marik, Tamás, Szekeres, András, Vágvölgyi, Csaba, Kredics, László, Ötvös, Ferenc
• Format: Article
• Language: English
• Subjects: Amino acids; Antimicrobial agents; bilayer membrane; Chlorine compounds; Chloroform; Clustering; Conformation; Folding; Hydrophobicity; Lipids; Membranes; Molecular dynamics; molecular dynamics simulations; Molecular structure; peptaibol; Peptides; Proteins; Simulation; Solvents; Trichoderma
• ISSN: 2075-1729; 2075-1729
• DOI: 10.3390/life13122288

We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus . We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN in water and chloroform solvents. Peptaibols, in general, are insoluble in water, as they are amphipathic and may prefer hydrophobic environments like transmembrane regions. In this study, we attempted to use aMD simulations to model an all-atom bacterial membrane system while placing a TPN molecule in its vicinity. The results highlighted that TPN was able to introduce some disorder into the membrane and caused lipid clustering. It could also enter the transmembrane region from the water-bilayer interface. The structural dynamics of TPN in the transmembrane region revealed a single energetically stable conformation similar to the one obtained from water and chloroform solvent simulations reported by us previously. However, this linear structure was found to be at the local energy minimum (stable) in water but at a metastable intermediate state (higher energy) in chloroform. Therefore, it could be said that the water solvent can be successfully used for folding simulations of peptaibols.