Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2

Abstract

Cytochrome P450 1A2 (P450 1A2, CYP1A2) is a membrane-bound enzyme that oxidizes a broad range of hydrophobic substrates. The structure and dynamics of both the catalytic and trans-membrane (TM) domains of this enzyme in the membrane/water environment were investigated using a multiscale computational approach, including coarse-grained and all-atom molecular dynamics. Starting from the spontaneous self-assembly of the system containing the TM or soluble domain immersed in randomized dilauroyl phosphatidylcholine (DLPC)/water mixture into their respective membrane-bound forms, we reconstituted the membrane-bound structure of the full-length P450 1A2. This structure includes a TM helix that spans the membrane, while being connected to the catalytic domain by a short flexible loop. Furthermore, in this model, the upper part of the TM helix interacts directly with a conserved and highly hydrophobic N-terminal proline-rich segment of the catalytic domain; this segment and the FG loop are immersed in the membrane, whereas the remaining portion of the catalytic domain remain exposed to the aqueous solution. The shallow membrane immersion of the catalytic domain appears to induce a depression in the opposite intact layer of the phospholipids, which may help in stabilizing the position of the TM helix directly beneath the catalytic domain. The partial immersion of the catalytic domain also allows for the enzyme substrates to enter the active site from either aqueous solution or phospholipid environments via several solvent- and membrane-facing tunnels in the full-length P450 1A2. The calculated tunnel dynamics indicated that the opening probability of the membrane-facing tunnels is significantly enhanced when a DLPC molecule spontaneously penetrates into the membrane-facing tunnel 2d. The energetics of the lipid penetration process were assessed by the linear interaction energy (LIE) approximation, and found to be thermodynamically feasible.

Ligand Access Channels in Cytochrome P450 Enzymes: A Review

“…A recent study has also shown in silico that the phospholipids may modulate the dynamics of access channels in human CYP1A2 [ 66 ]. One of the results presented shows that, during molecular dynamics simulations, a molecule of 1,2-dilauroyl- sn -glycero-3-phosphocholine (DLPC) can penetrate in one of the CYP1A2 access channels (namely tunnel 2d).…”

Spontaneous Ligand Access Events to Membrane-Bound Cytochrome P450 2D6 Sampled at Atomic Resolution

“…These tunnels are believed to influence both the poorly understood substrate specificity and binding kinetics of CYPs 1,11,13,15 . As the prediction of CYP metabolism is of major importance for drug development 1 , the influence of enzyme tunnels on small molecule binding has been intensively investigated 2,10,13,16,17 . Available experimental methods have only limited applicability for the determination and characterization of enzyme tunnels or complex transport phenomena.…”

“…Various molecular dynamics (MD) simulation techniques have been applied to study the dynamic tunnels and their capability to transport ligands in CYPs 10,11,15,16,18,19 . While most groups focused on the egress routes of ligands from the active site, only a handful of studies were focused on access routes 10,18,19 which are likely to be different 13,20 . Due to the long timescale of such molecular processes 21 , biasing potentials have been applied in nearly all studies to increase the likeliness of a successful translocation.…”

Cytochrome‐P450‐Induced Ordering of Microsomal Membranes Modulates Affinity for Drugs

“…3a). [9] Under a 100 ns all-atom simulation, CYP2B4 showed no substantial alteration of protein folding around the catalytic site as revealed from its backbone RSMD. The CYP2B4 soluble domain depicted a constrained conformation with an average RMSD of 2.3 (ER), 2.0 (ER ex ) and 2.9 Å (POPC) in comparison to its full-length conformation.…”

“…Structural characterization of membrane proteins in a closely native lipid environment is not facile. [33] Alternatively, MD simulation on P450s embedded in homogeneous membrane mimetic, [9, 21, 34] has supplied insights into protein/lipid interfaces, despite not fully representing the physiological lipids. We performed both all-atom and coarse-grained (CG) simulations on CYP2B4 embedded in POPC, ER and ER ex membranes.…”