Folding of the Apolipoprotein A1 Driven by the Salt Concentration as a Possible Mechanism to Improve Cholesterol Trapping - Selected Topics of Computational and Experimental Fluid Mechanics - page 272

The simulations were carried out under the thermodynamic conditions known as the
canonical ensemble, where the number of particles, volume of the simulation box,
and temperature ( NVT ) are constant; the latter was fixed at 300K using the V-rescale
method (Buss et al. 2007 ). To bring the system to equilibrium we ran the simulations
for up to 200ps, after which we switched to the NPT ensemble (where the pressure
is held constant, in addition to the number of particles and the temperature) to fix
the pressure at 1 bar, using the Parrinello-Rahman method (Parrinello and Rahman
1981 ), again for 200ps. Once the pressure of the system is equilibrated under these
conditions, we ran the simulations for an additional 5ns for the equilibriumphase and
another 5ns for the production phase, during which we performed the calculation of
the properties of interest. The time step for the integration of the equation of motion
was equal to 2 fs. We worked on a cubic simulation box with lateral size equal to
10nm.
3 Results and Discussion
Since we are interested in determining howAPOA1 folds, we performed simulations
to calculate its radius of gyration ( R g ) at each of the salt concentrations we modeled.
R g is calculated from the center of mass of the molecule, as is done in polymer
science (Grosberg and Khokhlov 1994 ). Figure 1 shows the values of R g for every
Fig. 1 a Gyration radius of APOA1 as a function of NaCl concentrations. The error bars represent
the standard deviation of the data point averaged over 5ns. The snapshots shown at the top and
bottom of the data correspond to the open and close conformation of APOA1, respectively. The
arrows identify each conformation with its salt concentration. The line is only a guide for the eye.
b Typical APOA1 open (0.5M) and closed (0.6M) conformations.