Fig. 7.

AhLap calcium coordination and molecular dynamics. (A) The coordination of inter-repeat Ca²⁺ in the AhLap tetra-tandemer. Ca²⁺ are shown as gold spheres, and residues binding to them are numbered as follows: 1 = Asp₁₄₄, 2 = Gln₂₀₂, 3 = Glu₁₄₃, 4 = Gln₂₀₂, 5 = Leu₂₀₄, 6 = Asp₂₆₈, 7 = Glu₂₇₂, 8 = Asp₂₆₆, 9 = Asp₃₂₆, 10 = Asp₂₃₅, 11 = Asn₂₃₄, 12 = Val₂₃₃, 13 = Asp₂₃₅, 14 = water, 15 = water. Water molecules participating in the coordination sphere are shown as cyan spheres. (B) The di-tandemer in silico construct used for molecular dynamics simulations. The Bend and Twist angles to be monitored throughout the simulations are shown, and the termini are labelled as in Fig. 5. (C) The Bend angle throughout the simulations, depicted in two ways. Left: a plot of deviation from start angle over frame number. Right: a radial plot where the Bend angle every 250 frames is denoted by a line. Simulations with (blue) and without (red) the coordinated Ca²⁺ ions are shown. (D) The Twist angle throughout the simulations, depicted the same way as the Bend angle.