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 277

Fig. 6 Averaged radial
distribution function of the P
residue with the both salt
ions, at different NaCl
concentrations a Open
conformation; b closed
conformation. The residue
index 24 in the sequence of
APOA1 is Proline (P)
just means that the aminoacids have values of their angles which are similar to those
found in the beta sheets. We can also see that the aminoacids having moving angles
with time are PYS, while the other ones are (H, L, A). Therefore, the Ramachandran
plot helps us identify specifically the residues that are responsible for the folding
of the protein driven by the addition of ions. Up to this point we have studied the
residues that drive APOA1 to form closed conformations.
Next, we must understand the influence of the salt ions and water. With that
purpose in mind we calculated the radial distribution function (rdf) of these residues
and their interactionwithwater and ions. The rdf is obtained from the relative distance
between a chosen particle in a fluid and all other particles that surround it; therefore
it quantifies how the local density in a fluid varies (Allen and Tildesley 1987 ). In
the case of water, we did not see any significant difference between the rdf's of the
water—open configuration, and those between the water—closed conformation, and
so we do not show them here. Instead, we focused on calculating the rdf's between
the ions and the residues. In Fig. 6 we show the rdf of the P—residue with the ions
(namely, with the sum of Na and Cl ions).