Figure 5.

MD simulation of interactions of S100A9 with POMs. (A, D) Binding of Nb₁₀ and TiNb₉, respectively, to a subunit of S100A9 dimer. The electrostatic potentials on the protein surface are colored by a red–white–blue gradient with the values spanning from −5.0 to 5.0 kT/e. Nb₁₀ and TiNb₉ are shown as vdW spheres, where oxygen is presented in red, covering Nb atoms shown in blue and Ti in pink. (B, E) Magnified views of the complex formation of Nb₁₀ and TiNb₉, respectively, on the S100A9 surface based on ionic interactions. (C, F) Time dependence of the number of binding interactions of Nb₁₀ and TiNb₉ with S100A9, respectively. (G, J) The structure of S100A9 homo-dimer is shown in ribbons. S100A9 monomers, arbitrary denoted as chains A and B, are shown in yellow and green colors, respectively. Side chains of residues in the corresponding Nb₁₀ or TiNb₉ binding sites are shown in balls-and-sticks. (H) Nb₁₀ (charge, −6) forms binding interactions with Lys50, Lys51, and Lys54 on the chain A and Lys4 on the chain B. (K) TiNb₉ (charge, −7) forms binding interactions with Lys50, Lys51, Lys54, and Lys 106 on the chain A and no contacts with the chain B. (I, L) RMSF values for every amino acid in the chain A as shown in gray and on the chain B in black for the S100A9 complexes with Nb₁₀ and TiNb₉, respectively. Both chains A and B in the S100A9 complex with corresponding POM are characterized by identical RMSF values within statistical errors, except for the POM binding site (residues 50–55), the EF-hand Ca²⁺ binding sites (residues 20–30 and 62–70), and flexible C-terminal part of each monomer.⁵⁷ MD was performed in the presence of 20 mM NaCl.