Fig 1.
Positions of EF1 and EF2 peptides in laminin.
(a) and (b) are positions of EF1 and EF2 peptide in mouse laminin α1, 2 chain LG4 module. Each site showed by green and blue color has the same sequence as EF1 and EF2, respectively.
Table 1.
Amino acid sequences of EF1 and EF2 peptides.
Table 2.
Temperature of each replica.
Table 3.
Positions of hydrogen bonds (H-bonds), characterizing β-sheet structures of EF1 and EF2.
Each of the H-bonds is defined as HB1-HB8.
Fig 2.
Autocorrelation of rate of formation of β-sheet structure.
(a) and (b) show autocorrelation of rate of formation of β-sheet structure obtained from replicas of EF1 and EF2 used for analysis. (c) shows the autocorrelation of EF1 and EF2 obtained from conventional MD.
Table 4.
Average rate of formation of β-sheet structure.
Fig 3.
Free energy landscape of EF1 obtained from REMD.
These maps indicate the existence probabilities of the EF1 peptide obtained from simulations at 300 K (a), 310 K (b), 322.5 K (c) and 343 K (d). Relative free energy change (kJ/mol) is colored as shown on the right side of the plots. RMSD and Rg are selected as the reaction coordinates. The structures in blue are taken from the vicinity of the global minimum.
Fig 4.
Free energy landscape of EF2 obtained from REMD.
These maps indicate the existence probabilities of the EF2 peptide obtained from simulations at 300 K (a), 310 K (b), 322.5 K (c) and 343 K (d). Relative free energy change (kJ/mol) is colored as shown on the right side of the plots. Reaction coordinates are RMSD and Rg. The structures in blue are selected from typical structures among conformations at the vicinity of the global minimum.
Table 5.
The range of RMSD and Rg for the region around the global minimum.
Fig 5.
Trajectories of conventional MD simulations drawn on free energy landscape at 300 K obtained from REMD.
Trajectories are plotted in purple on the free energy landscape. (a) and (b) correspond to two simulations of EF1, and (c) and (d) correspond to two simulations of EF2. Arrows indicate the areas where states were seldom observed in the time scale of the conventional MD.
Table 6.
Average values of RMSD and Rg.
Fig 6.
Free energy landscape of EF1 and EF2 obtained from conventional MD simulations.
(a) and (b) are free energy landscapes of two simulations of EF1, and (c) and (d) are free energy landscapes of two simulations of EF2. Reaction coordinates are RMSD and Rg. The displayed structures are selected from typical structures at local minima.
Fig 7.
Overall RMSF (Cα) of EF1 and EF2 (a), RMSF (Cα) for 1–10 residues (b), and RMSF (Cα) for 11–19 residues (c). Red and green lines correspond to two simulations of EF1, and black and blue lines correspond to two simulations of EF2.
Table 7.
Solvent accessible surface area (SASA) of EF1 and EF2.
Fig 8.
Number of H-bonds of EF1 and EF2 characterizing β-sheet structure.
Red and green lines correspond to two simulations of EF1, and black and blue lines correspond to two simulations of EF2. The number of H-bonds is plotted every 10 ns.
Fig 9.
Number of H-bonds and autocorrelation function of the H-bonds.
(a) and (b) indicate number of H-bonds of EF1 and EF2 for each replica (300 K, 310 K, 322.5 K and 343 K) used for analysis. The number of the H-bonds is plotted at every 1 ns. (c) is autocorrelation function of the number of the H-bonds obtained from REMD and the conventional MD. Purple and green colors are obtained from REMD at 300 K for REMD. Blue and yellow colors are obtained from the conventional MD.
Fig 10.
Length of hydrogen bonds (H-bonds), characterizing β-sheet structure of EF1 and EF2.
The lines indicate the lengths of H-bonds for each pair of EF1 and EF2 shown in Table 3. (a) and (b) correspond to two simulations of EF1, and (c) and (d) correspond to two simulations of EF2. The length of H-bonds is plotted at every 10 ns.
Table 8.
Number of H-bonds.
Table 9.
Average distance of hydrogen bonds (H-bonds), characterizing β-sheet structure for EF1 and EF2.
Fig 11.
Categorization of residues for (a) EF1 and (b) EF2 residues into four groups. Dashed lines show positions of H-bonds. Open circles are the pairs of hydrophobic amino acids.