Computational protocol: Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

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Protocol publication

[…] The GROMACS simulation package with version 4.0 was used in the simulations . In atomistic studies, we used the Nose-Hoover thermostat , with a coupling constant of 1.0 ps to set the temperature to 330 K in which the particle core is certainly in liquid state. The pressure was set to 1 bar using the Parrinello-Rahman barostat with isotropic pressure coupling and a coupling constant of 0.1 ps. The van der Waals interactions were chosen to have a cutoff at 1.0 nm. Electrostatic interactions were evaluated by the particle mesh Ewald technique with a real space cut-off of 1.0 nm . Water molecules were described using the SPC water model. All non-water bonds were constrained using the LINCS algorithm and the SETTLE algorithm was used to constrain water molecules, allowing the use of a time step of 2 fs in the integration of equations of motion. Berger parameters were used for lipids, while the GROMOS53A6 force-field was employed for the protein. Combination rules were introduced for the interactions between lipids and the protein. The four leading atomistic systems (A1–A4) were simulated for 100 ns, and the last two ones that focused on helix X for 80 ns. The total simulation time of atomistic simulations was 0.56 µs.CG simulations were also carried out with GROMACS, using the Martini force field with an extension to proteins , . The ElNeDyn elastic network model was used to keep the structure of CETP stable . The Berendsen thermostat and barostat were used with time constants of 1.0 ps. Temperature was set to 320 K and isotropic pressure coupling was used with pressure set to 1 bar. Cut-off distance for electrostatic interactions was set to 1.2 nm. For Lennard-Jones interactions we used a cut-off of 1.2 nm, and Lennard-Jones interactions were shifted to zero from 0.9 nm. Time step was 25 fs. The simulation time of each CG system was beyond 2 µs, and the times reported here are given in units of the effective Martini time. All rendered figures were done by VMD . […]

Pipeline specifications

Software tools GROMACS, P-LINCS, VMD
Application Protein structure analysis
Diseases Coronary Disease
Chemicals Cholesterol Esters, Triglycerides