Fig 1.
The structures of human lysozyme and sodium dodecyl sulfate.
(a) The native structure of human lysozyme represented as a new cartoon model. The α- helix structures are shown with the letter H and C6-C128, C30-C116, C65-C81, and C77-C95 represent disulfide bounds in the human lysozyme structure. (b) The structure of an SDS surfactant molecule with its polar head group (in red and green) and hydrophobic tail (in cyan and yellow) is shown as a ball and stick model.
Table 1.
Summary of MD simulations with details a.
Fig 2.
The Cα RMSD and the radius of gyration of human lysozyme.
(a) and (b) represent the time evolution of the Cα RMSD and the radius of gyration of human lysozyme in pure liquid water and aqueous SDS solution at 300 K and 370 K, respectively. (c) represents the RMSF of Cα atoms as a function of residue number.
Fig 3.
Human lysozyme secondary structure analysis with DSSP.
Left: time evolution of the secondary structure of human lysozyme through DSSP in pure liquid water or aqueous SDS solution at 300 K and 370 K. Right: a snapshot of human lysozyme extracted from last step trajectory (500000 ps) in each MD simulation. Helix and β-sheet structures are shown with the letters H and E, respectively.
Table 2.
The percentages of average secondary structure for Lysozyme during the 500 ns MD simulation.
Fig 4.
Radial distribution functions for human lysozyme.
Represents the radial distribution functions for human lysozyme in contact with water or SDS molecules in pure liquid water and the aqueous SDS solution systems at 300 K (a) and 370 K (b).
Fig 5.
Radial distribution functions for hydrophobic and hydrophilic residues of human lysozyme.
Represents the radial distribution functions for hydrophobic and hydrophilic residues of human lysozyme touching the C2 and S atoms of SDS in the aqueous SDS solution systems at 300 K and 370 K.
Fig 6.
The contribution energy per residue in the total binding free energies 1.
(a) Polar contribution of free energy per residue, (b) non-polar contribution of free energy of each residue, and (c) total contribution of free energy of per residue to the formation of the human lysozyme-SDS complex at 300 K. Left, hydrophilic residues; right, represent hydrophobic residues of human lysozyme. The critical residues for the formation of the human lysozyme-SDS complex (residues with ΔGb < -10 Kj/mol (< -2.4 Kcal/mol)) are labeled and shown with blue bars.
Fig 7.
The contribution energy per residue in the total binding free energies 2.
(a), (b), and (c) represent the polar, non-polar, and total contributions of free energy of per residue, respectively to the binding free energy at 370 K. Left, hydrophilic residues; right hydrophobic residues of human lysozyme. The critical residues for the formation of the human lysozyme-SDS complex (residues with ΔGb < -10 Kj/mol (< -2.4 Kcal/mol)) are labeled and shown with blue bars. The contribution of free energy for Lys-1 in a and c is not shown because of its high values ΔGpb < 201.05 Kj/mol and ΔGb < 72.17 Kj/mol.
Fig 8.
Energetic components of the human lysozyme-SDS complex.
All energetic components of the human lysozyme-SDS complex at (a) 300 K and (b) 370 K during the last 40000 ps of the MD simulation. (I) is polar solvation energy, (II) is electrostatic energy, (III) is polar binding energy, (IV) is van der Waals energy, (V) is non-polar solvation energy (SASA energy), (VI) is non-polar binding energy, and (VII) is Binding energy.
Fig 9.
Orientation of SDS surfactants around human lysozyme.
(a) and (b) show the first and the last frames of the trajectory in two ambient conditions (aqueous SDS solution at 300 K (upper) and 370 K (lower)).
Table 3.
The critical residues for the absorption of SDS on lysozyme, based on their total binding free energy contributions (residues with ΔG < -10 Kj/mol (< -2.4 Kcal/mol)) a.