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 274

Fig. 3 Histograms of the distance between one end and the other of APOA1, for various concentra-
tions of salt ions. Open conformations correspond to salt concentrations of 0.5, 0.9, 1.4 and 1.8M,
while the rest belongs to closed configurations

An inspection of Fig. 2 shows that most conformations are stable throughout the
production phase of the simulation, which indicates that they correspond to situations
of thermodynamic equilibrium of the system at those salt concentrations. Although
in some cases one observes an increase (as in, for example, the cyan and black curves)
or a decrease (red and purple curves) of R g with time, the fluctuations are to no more
than a few percent change of the averaged R g .
It should be stressed that both open and closed configurations have a distribution
of values of the radius of gyration rather than a single value. To prove this fact we
calculate the end-to-end distance distribution and depict it in Fig. 3 . The end-to-end
distance is the distance from the first to the last residues in the protein. The curves
seen in Fig. 3 represent histograms of the distribution of end-to-end distances found at
various salt concentrations. The so-called open configurations have larger end-to-end
distances, as expected, corresponding to the concentrations 0.5M (black line), 0.9M
(green), 1.4M (yellow) and 1.8M (purple). The closed conformations have smaller
end-to-end distances, as given by the lines for 0.6M (red line in Fig. 3 ), 1.0M (blue),
1.7M (gray), and 2.0M (cyan). Most of this information was known at this point,
particularly from the analysis of Figs. 1 and 2 . However, the added value of Fig. 3 is
that it provides a quantitative estimate of the average distance between the ends of
APOA1, where we find open (the largest being ∼ 5 . 3nm) and closed configurations

as well (the smallest being 1.6nm).
The structural characteristics of APOA1 are further analyzed through the so-
called “mean smallest distance matrix” (msdm), which is obtained from the averaged
distance between each residue and all other residues in the protein. In Fig. 4 ,the x
and y axes indicate the index that identifies each residue of the protein, and each data
point in Fig. 4 register the distance between each pair of residues. Such distance is