OmpT: molecular dynamics simulations of an outer membrane enzyme

Abstract

Five molecular dynamics simulations (total duration >25 ns) have been performed on the Escherichia coli outer membrane protease OmpT embedded in a dimyristoylphosphatidylcholine lipid bilayer. Globally the protein is conformationally stable. Some degree of tilt of the beta-barrel is observed relative to the bilayer plane. The greatest degree of conformational flexibility is seen in the extracellular loops. A complex network of fluctuating H-bonds is formed between the active site residues, such that the Asp210-His212 interaction is maintained throughout, whereas His212 and Asp83 are often bridged by a water molecule. This supports a catalytic mechanism whereby Asp83 and His212 bind a water molecule that attacks the peptide carbonyl. A configuration yielded by docking calculations of OmpT simulation snapshots and a model substrate peptide Ala-Arg-Arg-Ala was used as the starting point for an extended Huckel calculation on the docked peptide. These placed the lowest unoccupied molecular orbital mainly on the carbon atom of the central C=O in the scissile peptide bond, thus favoring attack on the central peptide by the water held by residues Asp83 and His212. The trajectories of water molecules reveal exchange of waters between the intracellular face of the membrane and the interior of the barrel but no exchange at the extracellular mouth. This suggests that the pore-like region in the center of OmpT may enable access of water to the active site from below. The simulations appear to reveal the presence of specific lipid interaction sites on the surface of the OmpT barrel. This reveals the ability of extended MD simulations to provide meaningful information on protein-lipid interactions.

FIGURE 1

(A) OmpT fold showing: 1), the four active site residues (i.e., Asp⁸³, Asp⁸⁵ on the left, and Asp²¹⁰, His²¹² on the right) in red; 2), the basic lipid binding sites formed by Arg and Lys residues in orange; and 3), the upper and lower amphipathic aromatic belts formed by Trp and Tyr residues in green. The position of the lipid bilayer is delineated by horizontal lines, with the extracellular space located at the top and the periplasm at the bottom. (B) A schematic cross section of OmpT indicating the approximate position of a potential tetrapeptide substrate (in black). (C) Snapshots from the OMPT2 simulation at t = 0 and 10 ns. The protein is blue (cartoon representation), the lipid bilayer polar headgroups are shown as red and orange spheres, the hydrophobic tails as green lines, water molecules as blue dots, and Na⁺ and Cl⁻ ions as purple and cyan spheres, respectively. Three regions are indicated: w, water; i, interface; and h, hydrophobic core.

FIGURE 2

Root mean-square deviation (RMSD) of Cα atoms from the starting structure versus time for the OmpT1 (A) and OmpT2 (B) simulations. The RMSD for all residues (solid lines, labeled all), for the loop and turn residues (light shaded lines, labeled loops) and for secondary structure (i.e., β-sheet) elements (dark shaded lines, labeled barrel) are shown.

FIGURE 3

(A) Root mean-square fluctuations (RMSF) of Cα atoms versus residue number for the OmpT1 simulation (solid line) compared to fluctuations derived from the crystallographic B-factors (blue line). The background of the graph is colored according to secondary structure (pink, β-strand; yellow, loop) and the β-strands are labeled. (B) Superimposed protein structures from the OMPT1 and OMPT2 trajectories (showing frames saved every 0.4 ns) highlighting regions of high flexibility. Structures are colored according to the frame number from blue (start, 0 ns) via green to red (end, 10 ns). (C) Dominant secondary structure analysis for simulations OMPT1, OMPT2, and OMPT3 showing residues that maintain their secondary structure as determined via DSSP (Kabsch and Sander, 1983) for >90% of the total simulation time. (Red, β-strand; green, bend; yellow, turn; and light shaded, coil.) The β-strands and extracellular loops are labeled.

FIGURE 4

(A) Selected snapshot of important active site residues (D83, D85, H212, D210, E27, D208, and S99) in a representative conformation, in particular showing the interactions E27-D208, H212-water-D83, and D83-water-D85. (B) Superposed on a line representation of the conformation shown in A are snapshots of an E27-water-D210 interaction (in purple); a conformation where H212 is more distant from D83 which, in turn, is interacting with S99 (in orange); and a conformation where D85 is far from D83 (in brown). (C) Interaction existence plot where a given H-bonding interaction is plotted versus time. The first three lines correspond to interactions of D83 with H212 via a water bridge, with S99 and with D85 via water bridges. (The colors are black for a single interaction; red for two bridging waters; and blue for three and green for four water bridges.) The last two lines show the possible interactions of E27, with either D208 or via water bridges with D210.

FIGURE 5

Results of docking calculations, showing a selected OmpT-ARRA complex in which interacting protein residues are in light blue, the peptide is in green, and the scissile peptide bond is highlighted in yellow. D83 is protonated and a water molecule between D83 and H212 is shown. The putative catalytic mechanism is indicated via arrows. The I170 residue is not shown for clarity, but its approximate side-chain position is indicated by an asterisk.

FIGURE 6

(A) Diagram of the cumulative water density inside the OmpT barrel, taken from the OMPT1 trajectory. Two orthogonal views are shown. (B) Trajectory of a single water molecule leaving the central pocket toward the periplasmic space. (C) Selected water trajectories from the OMPT1 simulation projected onto the z axis. The approximate limits of the transmembrane region are shown as solid horizontal lines. The solid black trajectory corresponds to the water molecule shown in B.

FIGURE 7

The number of OmpT/lipid H-bonds versus time for simulations OMPT1 (solid line) and OMPT2 (shaded line).

FIGURE 8

(A) Comparison of the covalent structures of DMPC versus Lipid-A (the latter after Ferguson et al., 2000). (B) Snapshots showing the interactions between basic residues and DMPC at the putative Lipid-A binding site for the three residues Arg¹⁷⁵, Lys²²⁶, and Arg¹³⁸.

FIGURE 9

Contour plot of the number of interactions (≤3.5 Å) of the amphipathic aromatic (i.e., Tyr, Trp) residues of OmpT with lipid polar headgroups as a function of position in the bilayer versus time for simulations (A) OMPT1 and (B) OMPT2.