Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation

• Published in: Journal of chemical information and modeling 2024-10, Vol.64 (20), p.7977-7986
• Main Authors: Perez, Hugo A., Wang, Zhe, Gerstman, Bernard S., He, Jin, Chapagain, Prem P.
• Format: Article
• Language: English
• Subjects: Bacteria; Computational Biochemistry; Dimers; Dynamic structural analysis; Interface stability; Lipids; Membranes; Modelling; Molecular dynamics; Molecular structure; Monomers; Nisin; Oligomerization; Peptides; Pore formation; Self-assembly; Structural integrity; Structural stability; Time
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.4c01050

The lantibiotic pore-forming peptide nisin is a promising candidate in the fight against multidrug-resistant bacteria due to its unique structure, which allows it to disrupt bacteria in two distinct waysLipid II trafficking and transmembrane pore formation. However, exactly how nisin and Lipid II assemble into oligomeric pore structures in the bacterial membrane is not known. Spontaneous peptide assembly into pores is difficult to observe in even the very long-time scale molecular dynamics (MD) simulations. In this study, we adopted an MD-guided modeling approach to investigate the nisin–nisin and nisin–Lipid II associations in the membrane environment. Through extensive microsecond-time scale all-atom MD simulations, we established that nisin monomers dimerize by forming β-sheets in a POPE:POPG lipid bilayer and oligomerize further to form stable transmembrane channels. We determined that these nisin dimers use Lipid II as a dimer interface to incur enhanced stability. Our results provide a clearer understanding of the self-assembly of nisin monomers within the membrane and insights into the role of Lipid II in the structural integrity of oligomeric structures.