Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA

Abstract

Molecular dynamics (MD) simulations are used to explore the dynamics of a membrane protein in its crystal environment. A 50-ns-duration simulation (at a temperature of 300 K) is performed for the crystallographic unit cell of the bacterial outer membrane protein OmpA. The unit cell contains four protein molecules, plus detergent molecules and water. An excellent correlation between simulated and experimental values of crystallographic B factors is observed. Effectively, 0.2 micros of protein trajectories are obtained, allowing a critical assessment of simulation quality. Some deficiency in conformational sampling is demonstrated, but averaging over multiple trajectories improves this limitation. The previously undescribed structure and dynamics of detergent molecules in a unit cell are reported here, providing insight into the interactions important in the formation and stabilization of the crystalline environment at room temperature. In particular, we show that at room temperature the detergent molecules form a dynamic, extended micellar structure spreading over adjacent OmpA monomers within the crystal.

Fig. 1.

Maintenance of protein structure and crystal contacts. (A) The crystallographic unit cell (a = 6.51 nm, b = 7.97 nm, c = 5.02 nm, and β = 94.3°) of OmpA (blue cartoons format), with chain identifiers labeled, and detergent molecules [Corey–Pauling–Koltun (CPK) spacefilling format]. The crystal contact between loop L3 and turn T2 is labeled for one pair of protein molecules. Solvent molecules are omitted for clarity. The c-axis dimension of the unit cell is indicated. (B) C^α rmsd as a function of time for all atoms (upper four lines) and for the β-barrel region only (lower four lines) for OmpA chains A to D (black, red, green, and blue lines, respectively). All structures were fitted to their respective β-barrel region in the simulation starting structure.

Fig. 2.

Average fluctuations and correlated motions. (A) Time-averaged (excluding the first 5 ns) simulation C^α B factors compared with experimental (i.e., x-ray) B factors. The x-ray B factors are shown as a gray line; the simulation B factors obtained by averaging the four simulation B-factor curves for the individual chains are shown as a broken line; and the simulation B factors derived from a trajectory composed of the average structure of all four OmpA chains at each point in time are shown as a solid black line. (B) Schematic “porcupine plot” diagram of the first principal component of the simulated motion of OmpA chain C (shown in C^α trace format). The cones represent fluctuations, with their orientation indicating the direction of motion of the C^α atom to which they are attached and their length indicating the amplitude of this motion. The figure was made by using dynamite (21).

Fig. 3.

Superimposed snapshots of detergent molecules (Corey–Pauling–Koltun bonds format) around OmpA (blue cartoons format). In A, a detergent molecule translates around the barrel surface, perpendicular to the barrel axis, whereas in B, a detergent molecule translates up and down the barrel surface, parallel to the barrel axis.

Fig. 4.

Interactions between protein and detergent. (A) Superimposed 0.5-ns snapshots of detergent molecules (Corey–Pauling–Koltun spacefilling format) around adjacent OmpA chains (green or blue cartoons format), observed perpendicular to the c-axis (labeled). (B) Number of interactions (defined as an interatomic distance of <0.4 nm) along the OmpA chain C β-barrel axis with detergent oxyethylene moieties over time. The figure was made by using proximus (S.S.D. and M.S.P.S., unpublished results) and xfarbe 2.5 (35).