Fig 1.
HisJ structural analysis reveals that conserved proline 16 displays different isomeric states in closed versus open structures.
In (A) and (B) are ribbon representations of the solved structures for closed/with ligand (1HSL) and open/empty (2M8C) HisJ. Residues Tyr14, Ala15 and Pro16 are in sticks. (C) and (D) are close-ups to the boxed regions in A and B, pointing out the differences in residue conformation: the closed/with ligand structure has a cis Pro16 (A, C) while the open/empty form has a trans Pro16 (B, D). The isomerization state changes the position of Tyr14's side chain. (E) Shows the residue conservation in 450 PBP sequences obtained and aligned as described in Materials. Only non-redundant sequences with more than 30% and less than 95% homology were used. Pro16 (arrow) and 20 neighboring residues are shown.
Fig 2.
LAO domain separation during simulation at 300 K, monitored through distances, angles and dihedral between domains as a function of Pro16 isomerization state.
(A-D) show distance, (E-H) show angles (I-L) show dihedral angles between domains. The starting structure used for each set of simulations is indicated at the top of each column. Boxes represent quartiles (upper, median and lower), while whiskers are maximum and minimum values for the initial and the final 5 ns of each 50 ns simulated. One value point was extracted for every 20 picoseconds of simulation, thus 2,500 values are represented in each box. Dotted and solid lines across the graphs represent the reference values for the open and closed states, respectively, calculated from structures PDB ID 2LAO (open) and PDB ID 1LAF (closed).
Fig 3.
HisJ domain separation during simulations at 300 K, monitored through distances, angles and dihedrals between domains as a function of Pro16 isomerization state.
Data were obtained, processed and presented as in Fig 2. Dotted and solid lines across the graphs correspond to the reference values calculated from open (PDB ID 2M8C) or closed (PDB ID 1HSL) structures.
Fig 4.
LAO domain separation during simulations at 323 K, monitored through distances, angles and dihedral between domains, as a function of Pro16 isomerization state.
Data were obtained, processed and presented as in Fig 2.
Fig 5.
HisJ domain separation during simulations at 323 K, monitored through distances, angles and dihedral between domains as a function of Pro16 isomerization state.
Data were obtained, processed and presented as in Fig 3.
Fig 6.
Changes in seven metrics during simulations of the closed/empty LAO with cis or trans Pro16 at 300 K.
Ten different trajectories were concatenated and changes in distance, angle, RMSD, Rg, SAS, Q(NC) and q(similarity) were calculated. Each trajectory is separated by a vertical line. Distances and angles were measured as in Fig 2. Q(NC) and q(similarity) were ploted using the closed PDB ID 1LAF (black line) or the open 2LAO (red line), as reference. Simultaneous changes in the metrics that coincide with crossovers in q(similarity) are indicated by black bars at the bottom of the figure. LAO with cis Pro16 (A) displayed two concurrent changes in the metrics whereas with trans (B), seven concurrent peaks were detected.
Fig 7.
Changes in seven metrics during simulations of the open/with ligand LAO with cis or trans Pro16 at 323 K.
Ten different trajectories were concatenated and metrics were calculated as in Fig 6. Independent trajectories are divided by vertical lines. LAO with cis Pro16 (A) displayed one crossover in q(similarity) values, whereas five were detected with trans Pro16, concurrent with dips in distance and angle (indicated with black bars at the bottom of the figure).