Environmental and dynamic effects explain how nisin captures membrane-bound lipid II

Abstract

Antibiotics (AB) resistance is a major threat to global health, thus the development of novel AB classes is urgently needed. Lantibiotics (i.e. nisin) are natural compounds that effectively control bacterial populations, yet their clinical potential is very limited. Nisin targets membrane-embedded cell wall precursor-lipid II-via capturing its pyrophosphate group (PPi), which is unlikely to evolve, and thus represents a promising pharmaceutical target. Understanding of exact molecular mechanism of initial stages of membrane-bound lipid II recognition by water-soluble nisin is indispensable. Here, using molecular simulations, we demonstrate that the structure of lipid II is determined to a large extent by the surrounding water-lipid milieu. In contrast to the bulk solvent, in the bilayer only two conformational states remain capable of nisin binding. In these states PPi manifests a unique arrangement of hydrogen bond acceptors on the bilayer surface. Such a "pyrophosphate pharmacophore" cannot be formed by phospholipids, which explains high selectivity of nisin/lipid II recognition. Similarly, the "recognition module" of nisin, being rather flexible in water, adopts the only stable conformation in the presence of PPi analogue (which mimics the lipid II molecule). We establish the "energy of the pyrophosphate pharmacophore" approach, which effectively distinguishes nisin conformations that can form a complex with PPi. Finally, we propose a molecular model of nisin recognition module/lipid II complex in the bacterial membrane. These results will be employed for further study of lipid II targeting by antimicrobial (poly)cyclic peptides and for design of novel AB prototypes. The widespread misuse of antibiotics (AB) results in fast development of resistance by bacteria, which presents a growing threat to global health. Discovery of new classes of antibacterial agents with alternative mode of action along with grasp of these mechanisms present the primary scientific challenges. There is a class of lanthionine-containing antimicrobial peptides (AMPs) referred to as lantibiotics, which possesses medicinal potential. Nisin, the most studied lantibiotic, was known even before A. Fleming's penicillin discovery 1. Although nisin has never been used in clinical practice due to its poor pharmacokinetics, it has been widely utilized as a food preservative since 1953 with no evidence of any resistance development 2-4. Nisin is a 34-amino acid peptide produced by certain strains of Lactococcus Lactis. Following the ribosomal synthesis, nisin prepeptide undergoes significant post-translational modifications, including proteolytic removal of a leader peptide 5 and introduction of atypical amino acids, resulting in five lanthionine rings and three unsaturated residues (Fig. 1A) 6. NMR studies of nisin and its major degradation products under various conditions revealed that the molecule is highly flexible in aqueous solution and consists of two structural domains: an amphiphilic N-terminal fragment including lanthionine rings A, B a...

Molecular Dynamics Insight into the Lipid II Recognition by Type A Lantibiotics: Nisin, Epidermin, and Gallidermin

“…Our simulations determined the structure of the nisin/lipid II complex in DMSO similar to the NMR structure [21] and predicted the alternative complex in water solution (Figure 1B), in which only ring A binds PPi, while ring B stabilizes this conformation via two inter-ring h-bonds. This configuration remained stable in a longterm MD run in the model bacterial membrane [27], and was confirmed in the NMR study on nisin1-12 in solution [34].…”

“…In this study, we performed the set of five independent MD simulations for the following solvated molecules: nisin1-12, epidermin1-12, and gallidermin1-12 without the ligand, and (in order to examine mutual adaptation of the peptides and their target) in presence of one or three DMPPi ions (Table 1). Initial coordinates of nisin1-12 were taken from MD-equilibrated states of the full-length molecule that has been published previously (NF1 state) [27]. Epidermin1-12 and gallidermin1-12 starting structures were prepared manually applying the standard mutagenesis utility of the PyMOL program version 2.5.0 (www.pymol.org) to the nisin1-12 starting conformation.…”

“…Note a single amino acid substitution, which differs gallidermin and epidermin. (B) Spatial structure of nisin/lipid II complex: obtained by NMR in DMSO [21] (wheat) and predicted by molecular dynamics simulations in water solution (pale blue) [27]. The major discrepancy (ring B relative position) is highlighted with an arrow.…”

“…MD simulations and molecular docking were used to examine interactions between lipid II and lantibiotics, such as nisin (for more details see [32]), mutacin1140 [30,33], and lacticin 3147 [33]. Our previous MD study determined that conformational space of nisin's AB-rings crucially depends on the molecular environment and is not essentially affected by the absence of the C-terminal CDE-rings [27]. Our simulations determined the structure of the nisin/lipid II complex in DMSO similar to the NMR structure [21] and predicted the alternative complex in water solution (Figure 1B), in which only ring A binds PPi, while ring B stabilizes this conformation via two inter-ring h-bonds.…”

Isolation, Characterization and Structure Elucidation of a Novel Lantibiotic From Paenibacillus sp.

“…Given that 1WCO is a structure of the complex between nisin and lipid II, while CMB001 is an apo-structure, this indicates that CMB001 undergoes a conformational change in order to bind lipid II, where rings A and B combine to bind the pyrophosphate group of lipid II. Molecular dynamic simulations indicate that rings A and B have relatively fixed backbone conformations when not bound to lipid II, however they vary in orientation with respect to one another as indicated by the simulations (Panina et al, 2020). Solid state NMR data show that the nisin rings A and B have small 15N chemical shift changes when bound to different micelles, further indicating rings A and B have only small conformational differences in DMSO and micelles (Medeiros-Silva et al, 2018).…”