Figure 1.
Structural topology of holo-Tth-MCO and superposition with others MCÓs.
A) Multinuclear metal site of the holo-Tth-MCO. B) Structural depiction of the three cupredoxin domains of holo-Tth-MCO, (domain 1, green), (domain 2, light blue) and (domain 3, yellow), the loop (β21–β24)D2 is in deep blue cartoons. C) Ribbon superposition of the holo forms of Tth-MCO (green), CueO (red, PDB entry 1N68) and CotA (blue, PDB entry 1UVW), the main differences among them are represented in cartoon structure. Mononuclear copper center (T1Cu) is shown in blue and trinuclear copper cluster (TNC) is shown in orange (T3Cu) and red (T2Cu) Van der Waals representation.
Table 1.
Selected structural properties of TthMCO apo and holo forms.
Figure 2.
Root mean square deviation (RMSD) from the crystallographic structures of the Cα atoms as a function of simulation time for apo-Tth-MCO form (black line), holo-Tth-MCO (red line) and holo-Tth-MCO without loop (β21–β24)D2 (blue line).
Figure 3.
Structural evidences of the average conformations accessible in the 38 ns MD simulation for the holo-Tth-MCO (snapshots A–C) and apo-Tth-MCO forms (snapshots D–E).
The different secondary structure elements are represented in light blue cartoons. The protein regions involved in the open-closure of the electron-transfer site are in deep blue cartoons: Loop (β21–β24)D2 and α4-helixD2 for snapshots A-B and D, loop (β21–β24)D2 and (187-α4-201)D2 for snapshot C, loop (β21–β24)D2, loop (β25–β26)D3 and loop (β28–β29)D3 for snapshot E.
Figure 4.
Root mean square deviations (RMSD) from the starting structure of the Cα atoms, as a function of the residue number, for apo-Tth-MCO (black) and holo-Tth-MCO (red) for the last 18 ns of a 38 ns-long simulation.
Deviations are averaged over Cα fragments with a homogeneous secondary structure. Error bars represent the standard deviation. Secondary structure elements are shown at top: β-sheet (black) and α-helix (grey).
Table 2.
Salt bridges found for apo-Tth-MCO and holo-Tth-MCO.
Figure 5.
Eigenvalues as a function of the first 15 eigenvectors, in the time interval 20–38 ns, for apo-Tth-MCO (blue solid square) and holo-Tth-MCO (red solid circles).
Figure 6.
Fluctuations of the Cα atoms in the first (A) and the second (B) eigenvector for the time interval 20–38 ns, as a function of the residue number, for apo-Tth-MCO form (square black symbol) and holo-Tth-MCO form (circle red symbol).
Figure 7.
Cross-correlation motions (DCCM) for apo-Tth-MCO form (panel A) and holo-Tth-MCO (panel B).
DCCM larger than 0.5 nm are shown on the upper triangle and all values on the lower triangle. Vector products representing the maxim extent of correlated motion (nm) for each Cα pair are plotted. The color scale indicates the degree of correlation: red, positively correlated; blue, negatively correlated; white, uncorrelated.
Figure 8.
RMSF analysis of the Cα atoms of TNC’s residues (A) and the second sphere carboxylate residues (B), for apo-Tth-MCO (black) and holo-Tth-MCO (red) for the last 18 ns of a 38 ns-long simulation.
Figure 9.
Average conformations of ABTS inside the electron-transfer complex formed with holo-Tth-MCO electron-transfer cavity during the last 25 ns of MD simulation. Residues in close proximity (<0.4 nm) to the ABTS (orange stick models) are represented as green stick models and coppers are shown in Van der Waals representation.
B) The non-bonded short-range Coulomb (black line) and Lennard–Jones (red line) interaction between holo-Tth-MCO and ABTS as a function of time.