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Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II

Mulholland, Sam; Turpin, Eleanor R.; Bonev, Boyan B.; Hirst, J.D.

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Authors

Sam Mulholland

Eleanor R. Turpin

Boyan B. Bonev



Abstract

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.

Journal Article Type Article
Publication Date Feb 18, 2016
Deposit Date Feb 19, 2016
Publicly Available Date Feb 19, 2016
Journal Scientific Reports
Electronic ISSN 2045-2322
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 6
Issue 21185
DOI https://doi.org/10.1038/srep21185
Keywords computational biophysics, computational chemistry, membrane biophysics
Public URL https://nottingham-repository.worktribe.com/output/775877
Publisher URL http://www.nature.com/articles/srep21185

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