Llized without ligand, the regions which comprise the dimerization interface cannot be defined in the X-ray experiment probably due to an increased mobility of this zone [12]. The root mean square deviation (RMSD) of the Ca was calculated relative to the starting structures to assess the stability of the systems. When the first 12 and 9 residues of PaNTD and EcNTD respectively were not taken into account (given the high mobility of these regions), both proteins showed a similar behavior, reaching values between 0.30 and 0.35 nm after 200 ns (FigurePLOS ONE | www.plosone.orgMutL N-Terminal Domain InterfacesS1A). These values over 0.30 nm indicate that the proteins suffer some (minor) global conformational change during the simulations and are in line with the idea that the crystal structure is achieved only in the dimeric state. Taking into account that the starting model of PaNTD has a RMSD of 0.2 nm from the EcNTD initial structure, the similar behavior for both proteins observed in Figure S1A supports the validity of the model created for PaNTD.Galiximab A noticeable jump in the RMSD curve of apo EcNTD is observed between 5 and 25 ns, where it reaches values near 0.Blinatumomab 4 nm (Figure S1A). After that time, the RMSD curve returns to values near 0.PMID:23460641 3 nm. This jump would indicate that the apo EcNTD can explore conformations which are not readily available to either the holo EcNTD or the PaNTD in both states (apo and holo). The difference in total secondary structure content between the holo and apo forms of both proteins is shown in Figure S1B. These curves consistently decrease as a function of time, which indicates that for both proteins the apo form has less secondary structure than the holo form. Between both proteins there were no noticeable differences. This decrease in secondary structure when the ATP is removed from both proteins could be related to the aforementioned [12]. In order to compare the four protein systems, a cluster analysis was carried out for each protein using the 200 ns and a cut-off of 0.2 nm. The central structure from the main cluster of the ATPbound PaNTD and EcNTD were determined. These structures can be superimposed using the Ca of their respective ATP binding motifs (I V) with a RMSD value of 0.15 nm (Figure 2A). This measure of the local similarity of PaNTD model indicates a rather small divergence in the position of residues responsible for ATP hydrolysis between these two structures. Also, the conserved residue lysine of motif V (K307 in EcNTD and 310 in PaNTD) maintains its relative position in both proteins (Figure 2B). This residue inserts into the active site where it contacts the cphosphate and is key for the correct work of the enzyme [15]. The central structure from the main cluster of apo EcNTD and the one corresponding to the cluster that appears during the first 25 ns were compared in order to determine the main changes that are produced in this protein structure and are responsible for the jump observed in the RMSD curve in Figure S1A. These structures can be superimposed with an RMSD of 0.4 nm, with noticeable differences in the dimerization interface, principally in the conformation of the ATP lid (data not shown). The RMSD is a global measure of the similarity between structures, and some important but more subtle structural changes could be masked by values of around 0.3 nm. The same masking effect could be taking place when analyzing the total secondary structure. A careful analysis of the trajectories.