Fig 1.
Lichenicidin Lantibiotic is composed by Lchα and Lchβ peptides [16]. Bliα is the α-component produced by B. Licheniformis I89. Both α-peptides differ in the A-ring being β-peptides identical.
Fig 2.
Structural formula for the dehydrobutyrine (left) and dehydroalanine (right) molecules.
Fig 3.
Secondary structure evolution of the peptides.
Evolution of the secondary structure during the 2 μs MD trajectory is shown for (A) Lchα, (B) Bliα and (C) Lchβ. The following color code is used: pink for α-helix; yellow for β-sheet, blue for a 310 helix, red for a π-helix, turquoise for a turn, light green for an isolated bridge and white for random coil. These plots were generated with the STRIDE tool of the VMD software [31, 40]
Fig 4.
Root mean square deviation of lichenicidin.
The RMSD with respect to initial configuration of the backbone atoms for Lchα (blue color); Bliα (green color); Lchβ (magenta) peptides is plotted. Terminal residues were excluded for the evaluation.
Fig 5.
Markov State Model of Lchα peptide.
MSM network is based on the information listed in Table 1. The 14 states are depicted as beads with size proportional to their occupation, arrows represent allowed transitions between states according to the corresponding transition matrix in Fig 8.
Fig 6.
Markov State Model of Bliα peptide.
MSM network is based on the information listed in Table 1. The 9 states are depicted as beads with size proportional to their occupation, arrows represent allowed transitions between states according to the corresponding transition matrix in Fig 9.
Fig 7.
Markov State Model of Lchβ peptide.
MSM network is based on the information listed in Table 1. The seven states are depicted as beads with size proportional to their occupation, arrows represent allowed transitions between states according to the corresponding transition matrix in Fig 10.
Fig 8.
Transition matrix of Lchα peptide.
The transition matrix elements are given in S2 File.
Fig 9.
Transition matrix of Bliα peptide.
The transition matrix elements are given in S2 File.
Fig 10.
Transition matrix of Lchβ peptide.
The transition matrix elements are given in S2 File.
Table 1.
MSM properties of the Lchα, Bliα and Lchβ peptides.
Occupation of each state πi; root mean square deviation, RMSD; average escape time, te; free energy differences between states, ΔGij calculated with respect to the most occupied state; entropy, S; average of the dipolar moment, <μ>. Standard errors associated with each quantity are indicated in gray.
Fig 11.
Cα-Root mean square fluctuations for all residues of MSM states.
(A) Lchα, (B) Bliα and (C) Lchβ. Black traces represent for each peptide the sum of the RMSF over all MSM states.