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

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 sol...

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Bibliographic Details
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
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Summary: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.
ISSN:2075-1729
2075-1729
DOI:10.3390/life13122288