Figure 1.
Structures of CETP and anacetrapib and results from molecular docking.
A) X-ray structure of human CETP. The two DOPCs (gray) plug the tunnel openings that lead to the hydrophobic tunnel where two CEs (cyan spheres) are located. The sn-chains of DOPCs, the N- and C-terminals, as well as helix X are labeled. B) The atomic formula of anacetrapib. Anacetrapib is a 1–3-oxazolidin-2-one based CETP inhibitor. C) The most probable binding sites and conformations of anacetrapib within the structure of CETP obtained from molecular docking calculations. The binding energies for the binding sites of red, brown, cyan, and green ligands are −47.7 kJ mol−1, −46.4 kJ mol−1, −48.5 kJ mol−1, and −46.9 kJ mol−1, respectively. D) The most probable binding site of anacetrapib gained from docking calculations matched with the recently published X-ray structure of CETP with bound torcetrapib. Anacetrapib is presented with red and torcetrapib with blue color. E) Simulation snapshot from simulation S2-1nm. While moving at the N-terminal tunnel opening, anacetrapib aligns itself to a tighter conformation through the orientation of trifluoromethyl- and methyl groups close to each other.
Figure 2.
Initial configurations of the simulated systems.
Starting configurations of the A)–E) longer 200 ns atomistic simulations as well as the F)–M) free energy calculations where DOPCs are presented as gray stick models, CEs as cyan spheres and anacetrapibs as red stick models. For clarity, the starting configurations of the 20 ns atomistic simulations are not presented.
Table 1.
Performed simulations and their setups.
Figure 3.
Structural measures of CETP during short simulations.
RMSD and radii of gyration profiles for CETP during the short 20 simulations for three of the studied systems. Results for the other systems are largely similar.
Figure 4.
Interactions between CETP and anacetrapib.
The van der Waals and electrostatic interaction energies between CETP and anacetrapib in the simulations performed for 20 (upper three rows). Additionally also the interaction energies concerning simulations L2, L4, and L5 are presented (bottom two rows). Interaction energies for the simulation S4-3nm are not presented due to small values. Interaction energies between the molecules are observable when anacetrapib enters the 1 nm cutoff region during the course of simulations.
Table 2.
Average interaction energies and their standard deviations between CETP and anacetrapib.
Figure 5.
Free energy profiles of anacetrapib and cholesteryl ester.
Free energy profiles of the umbrella sampling simulations. Both A) anacetrapib and B) cholesteryl ester were pulled out from the structure of CETP through the N-terminal tunnel opening to the water phase. CETP residues Cysh9, Arg10, Ile11, and Thr12 were used as the reference pull group due to their parallel alignment with the N-terminal tunnel opening.
Figure 6.
Structural measures of CETP during long simulations.
RMSD and radii of gyration profiles for CETP during the long 200 simulations, the systems L1–L3 and L5 shown here being suggestive of the data. The RMSD graph illustrates separately the RMSD values for the CETP bound DOPCs.
Figure 7.
Dynamical properties of CETP bound lipids.
A) Atomic RMS fluctuation profiles for DOPCs (atoms 7441–7716) during the long 200 simulations. The peaks indicate the atoms that fluctuate the most over the course of simulations. The positions of DOPC headgroups and sn-2 chains with respect to atom numbers are labeled. The headgroup N and the sn-2N chain correspond with the headgroup and the sn-2 chain of the N-terminal DOPC, while the headgroup C and the sn-2C chain correspond with the C-terminal DOPC, see Figure 1A. B) Spatial density maps for DOPCs and CEs. The map reveals the movement of the corresponding lipid inside the binding pocket of CETP.
Table 3.
Average interaction energies and their standard deviations between different particles in longer 200 ns simulations.
Figure 8.
A) Residual RMS fluctuations for short 20 ns and long 200 ns simulations. The peaks indicate the regions of CETP that fluctuate the most over the course of simulations. These regions are found in loops marked with omegas as well as in the residues corresponding to helix X. B) Residual B-factors mapped to the backbone structure of CETP. Red color indicates the most rigid regions in the structure, whereas white and blue indicate the most flexible structural regions in the order of growing flexibility. Loop regions are marked with omegas and the region corresponding to helix X is labeled.
Figure 9.
Conformational fluctuations of helix X.
A) Secondary structure of helix X (residues 461–472) during simulations L1 and L2. B) Simulation snapshots from simulations L1 and L2. Helix X is colored to highlight the changes in the secondary structure. In the absence of anacetrapib (L1), helix X maintains the α-helical structure, whereas in the presence of anacetrapib (L2) it alternates between turn (unfolding of the helix) and 310-helix (extension of the helix). Turn-like conformation is presented in the figure.
Table 4.
Percentage values of the different secondary structure elements of helix X in shorter and longer simulations.