PMC

These RDFs are calculated for the last 300 ns of MD trajectory. Inset: RDF for PP_lipid-II–P_PE in PG/PE membrane for the first 50 ns of MD. The dynamic RDF picture is shown in . Dashed line corresponds to RDF = 1.

The structure of nisin complex with lipid-II fragment is taken from PDB 1WCO. Nisin is presented with semi-transparent surface colored by the Molecular hydrophobicity potential (calculated with PLATINUM): blue color corresponds to hydrophilic areas, brown — to hydrophobic ones. Inside the surface nisin backbone is presented with sticks; lanthionine and methyllanthionine rings are colored yellow. In the front of nisin surface the fragment of lipid-II molecule is shown; probable recognition determinant is presented with sticks.

(A) Radial distribution functions (RDFs) for lipid-II bacterioprenol tail segments from two different molecules. Curves are colored according to the legend, where numbers mark the tail segments (starting from the closest one to PP) in the first and the second molecule, respectively. (B) Correlation of MD distances between lipid-II PP groups and their tail segments. Inset: MD evolution of distances between PP groups of two lipid-II molecules (black) and the last (11^th) segments of their tails (red). Dashed vertical line depicts beginning of the “equilibrium” part of MD trajectory (150–500 ns), which was used for analysis of system with two lipid-II molecules. (C) MHP-map of PG/PE bilayer with the presence of two lipid-II molecules. Further details are available from the caption to .

(A) Distribution of cluster size over MD trajectories of six systems: pure POPC (black broken line), POPC+lipid-II (gray line), pure PG/PE (green broken line), PG/PE+lipid-II (green line), PG/PE+lipid-III (red line) and PG/PE+short lipid-II (yellow line). X-axis: cluster size (in nm²). Y-axis: Probability Density Function (PDF). Note that the largest clusters are observed in PG/PE with full-length tail molecule (lipid-II or -III). At the same time, the smallest clusters are observed in POPC+lipid-II system. Alternative analysis of cluster sizes (complementary cumulative PDF) is shown in . (B) Life-time distribution for hydrophobic clusters. X-axis is cluster lifetime (in ns). Y-axis is total lifetime for all clusters with the current lifetime or longer (in μs).

Lipid-II conformations are extracted from the equilibrium part (30–1000 ns) of MD trajectory with time step of 2 ns, as viewed from the membrane (A) and extracellular side (B). Gray spheres correspond to PLs' phosphorus atoms from a single MD frame and denote the water–membrane interface; PL atoms from other frames, water and ions are not shown for clarity. Lipid-II groups are colored as follows: tail, sandy; pyrophosphate, black; sugar M, red; sugar G, orange; Ala, green; γ-D-Glu, cyan; Lys, blue; 1^st D-Ala, magenta; 2^nd D-Ala, purple. Pink spheres show C-terminus of the pentapeptide. A, lower panel: Radial distribution function (RDF) of lipid-II tail terminus (S-11) with respect to PP. RDF is truncated at distance 3 nm. Note that this graph is symmetrical.

(A) Phospholipid acyl chains order parameters (S_cd) of pure PG/PE bilayer mapped on the membrane surface. Color represents MD averaged S_cd values for both PL acyl chains: from green (disordered chain) to violet (relatively ordered chain). (B) S_cd map for PG/PE bilayer with lipid-II (red). Note extended disordered area next to lipid-II molecule. (C) 2D-map of hydrophobic properties of pure PG/PE membrane (view from the “top” corresponding to panel A). Hydrophobicity is represented by the Molecular Hydrophobicity Potential (MHP), which was calculated at bilayer surface, mapped in the plane and MD-averaged. Colored circles depict projections of POPG (blue) and POPE (green) phosphorus atoms. (D) MHP-map of PG/PE bilayer with lipid-II (view corresponds to panel B). Lipid-II is shown with yellow triangles (tail segments), orange circles (phosphorus atoms), cyan circles (sugar residues) and pink circles (amino acid residues). Colored contours show areas of the most probable location of lipid-II atomic groups during MD (colored according to symbols). Note prominent hydrophobic “atoll” surrounding lipid-II which is co-localized with lipid-II tail group (marked with broken line) and partially corresponds to the disordered area in panel B. Results of the same analysis of POPC bilayer properties (pure and with lipid-II) can be found in .

(A) Chemical structure of lipid-II: peptidoglycan “building block” (shown with colored symbols) is connected via pyrophosphate moiety (orange circles) to bacterioprenol hydrophobic chain, which consists of eleven isoprenoid monomers. Lipid-III in contrast to lipid-II does not have pentapeptide moiety. “Short” lipid-II analog used in our MD-simulations has a tail comprised of only four isoprene segments. (B) Typical conformation of lipid-II in PG/PE membrane during MD simulation: tail (yellow) is “L-shaped”, pyrophosphate (orange) is partially buried into membrane–water interface, and disaccharide (cyan) is “embraced” with pentapeptide (pink). (C) “V-shaped tail” of lipid-II (the terminal group is able to emerge to the water–lipid interface). (D) Density profiles of various lipid-II groups (left axis) and solvent (violet; right axis). Results are shown for the following lipid-II groups: peptide (pink), sugar residues (cyan), pyrophosphate (orange), tail (yellow) and the terminal segment of the tail (S-11; brown). (E) Hydrogen-bonding pattern within lipid-II head group and with phospholipids' polar groups. Blue broken lines depict hydrogen bonds between head group monomers (larger thickness corresponds to high occupancy of hydrogen bonds in MD). Symbols' color indicates whether monomer is hydrogen bond donor (blue), acceptor (green), or both (magenta). Bold symbol outline points monomers that form extensive hydrogen bonding with the membrane (and therefore have low relative solvent accessibility, see ).