Figure 4.

(A) The ribbon representation of the fifty-four homolog (Ffh) M-domain is enclosed by a molecular surface in white. The polypeptide chain is ramp-colored from red (N-terminal) to orange (C-terminal). The five alpha helices are rendered and colored accordingly (αh1—red, αh2—pink, αh3—green, αh4—golden, αh5—orange). The missing disordered region near the peptide binding groove is predicted by comparative homology modeling using HHpred and colored blue with the curved red line indicating the modeled portion. The two alpha helices (αh1 and αh5) and finger loop making up a signal peptide binding groove with key residues are labeled. The right panel shows the molecular dynamics simulated complexes of M-domain with pOGH-5 (B) and pOGH-2 (C) obtained after a 200 ns production run. This is followed by root mean square deviation (RMSD) trajectories in time-dependent manner (ns) of pOGH-5 (D) and pOGH-2 (E), with red and green color representing the M-domain and docked peptide in black. The RMSDs of the reference structure (3NDB) bound to signal sequence with (blue) or without the finger loop (FL) (orange) are also displayed. (E) Per-residue fluctuations of the M-domain throughout 200 ns are plotted for pOGH-5 (red) and pOGH-2 (green) along with the error bars calculated by comparing trajectories in different time frames, while the corresponding helices and finger loop regions are underlined with the same color code.