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compute FoldX_energy (stability of fragment 1 + fragment 2)
The free energy of folding for each of the two fragments was computed separately by
means of a ‘Stability’ run in FoldX 2.5.2. FoldX_energy is the sum of the two energies.
Once FoldX_energy was calculated for all such pairs of fragments it was plotted, with
energies coded with blue = lowest energy and yellow = highest as shown in figures 3-8.
Upon inspecting these graphs and comparing local minima of free energy to the known
hinge locations, we found that the following cases occurred:
The i, j indices of a minimum were near the diagonal, meaning the corresponding
fragment 2 was small. Such minima were discarded since the diagonal energies are
generally small and we are not interested in small fragment motions.
Both i and j were near the termini. These minima were also discarded, because the
termini are usually flexible but we are not studying those motions.
Of the minima that did not fall in cases 1 or 2, the lowest minimum sometimes had one of
its two indices near a terminus, but the other substantially far from either terminus. In
this case the former index was discarded for the reasons cited in (2) but the latter index
tended to coincide with a single-stranded hinge.
Of the minima that did not fall in cases 1, 2, or 3, the lowest very often indicated the
location of a double stranded hinge.
Lastly, on occasion the minimum reported following cases (3) or (4) did not correspond
to the known hinge location, but one of the higher minima not eliminated per cases 1 and
2, did.
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