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Figure 5
MD simulation of NZ-1 Fab–PDZ complexes. (a) Trajectories for the target PDZ structures. R.m.s.d.s were calculated for the snapshot models relative to the initial model to estimate the structural changes in the PDZ domains during the simulation trajectories. The inserted PA14 residues and the flexible N-­terminal region upstream of the PDZ-N domain were excluded from the calculation. R.m.s.d.s are plotted for trajectories of the PDZ-N domain (green) and for the PDZ-C domain in both complex 1 (cyan) and complex 2 (blue). (b) Structural fluctuations in the residues within the PA14 tag. In the r.m.s.f. calculations, the complex models within each trajectory were aligned with the initial model based on the VH region of the NZ-1 Fab, and the structural fluctuation from the averaged structure was calculated for each residue in PA14. (c) Histogram of PDZ-domain residues binned by r.m.s.f. values calculated relative to the NZ-1 Fab. Similar to the process for calculating r.m.s.f. values in (b), the snapshot models within a trajectory were aligned with the averaged structure at the respective VH regions for each of the three complexes. Subsequently, the fluctuation in the atomic coordinates was calculated for each residue. (d) The representative snapshot of PDZ-N (181-PA14-184) complexed with NZ-1 Fab from the trajectory. The snapshot at 605 ns, representing the most frequently observed conformation, is shown as a ribbon model. The PDZ-N domain is colored green. PA14 residues are colored light magenta, except for Glu1′ and Gly2′ at the N-terminus, which are colored light blue. The heavy and light chains in NZ-1 are colored dark and light orange, respectively. Glu1′ in PA14 was separated both from Arg120 in the NZ-1 heavy chain and from Arg70 in the NZ-1 light chain. Arg181 was also separated from Tyr69 in the light chain. Glu184 in PDZ-N interacted with Tyr51 and Ser119 in the NZ-1 heavy chain as opposed to the interaction with Arg70 in the NZ-1 light chain in the crystal structure (see Fig. 2[link]f). (e, f) Reorientation of the PDZ-C domains relative to the NZ-1 Fab in the MD simulations initialized from complexes 1 (e) and 2 (f). For both of the calculations, the snapshot models were aligned with the initial models of complexes 1 and 2 based on the VH region, and the r.m.s.d.s for the PDZ-C domains were calculated relative to the initial models. The r.m.s.d.s calculated using complexes 1 and 2 as references are shown in cyan and blue, respectively. The conformations of the 347 ns snapshot in (e) and the 689 ns snapshot in (f) are similar to that of complex 2, as analyzed in Supplementary Fig. S7(c).

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ISSN: 2059-7983
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