Environmental Engineering Reference
In-Depth Information
Fig. 4 The mean smallest distance matrix for 0.5M ( a ) and 0.6M ( b ) concentrations of NaCl. The
axes represent the residues that conform APOA1. The maximum distance considered to be part of
the protein is 1.5nm
represented in a gray scale, with the maximum distance being 1.5nm; if a distance
between residues is larger than this value a black dot is added to this figure.
The principal diagonal line in Fig. 4 (white colored) represents a relative distance
equal to zero, because it is the distance of a residue with itself. Therefore, a protein
leaves a fingerprint of itself in a msdm graph. This is a useful tool to compare
between open and closed structures because it shows how the protein modifies its
conformations from open to closed as it evolves in time and which residues are
moving the most. In Fig. 4 we show two graphs, with the left corresponding to an
open APOA1 structure at a salt concentration equal to 0.5M, and the right for the
closed configuration at 0.6M. The left graph (Fig. 4 a) shows the msdm between the
aminoacid residues that make up APOA1, where a diagonal line across the graph
means that there are similar distances between the residues, which corresponds to
the extended protein conformation (open). In Fig. 4 b, one observes a qualitatively
different behavior from that found for the open conformation (left panel in Fig. 4 ). In
the center of the graph on the right of Fig. 4 , there is a gray area representing relative
distances between residues that are smaller than 1.5nm, meaning that the structure
of the protein is of the closed conformation and it also identifies the residues that are
closer to each other because of this folding. We selected the residues 21-26 from the
right panel of Fig. 4 because they are in the zone where the closed conformation is
formed. These residues are H (Hystidine), L (Leucine), A (Alanine), P (Proline), Y
(Tyrosine) and S (Serine). The sequence of APOA1 studied here is therefore called
HLAPYS. In the upper right corner of the right panel in Fig. 4 , we find another
zone where residues are closer than 1.5nm; these residues correspond to the end of
the protein.
Search WWH ::




Custom Search