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The quantity ! E(i)
represents the intra-fragment energy gained or lost by breaking all of
the interactions between fragment 1 and fragment 2, as might occur in an opening
motion. It also includes the solvation energy which might be gained or lost. The
quantity E C is a constant independent of the cut location and can be set to zero without
consequence
Even when the actual motion of the protein is not an opening one, the method should
have predictive value because for incorrect choices of the hinge location, i.e. cut
locations that are actually inside one of the domains, many inter-fragment interactions
would be broken. Also, significant hydrophobic areas would be exposed on the surfaces
of fragments 1 and 2. In either case, ! E(i)
would be relatively high.
Clearly, we can repeat the procedure of cutting the protein before residue i and
computing ! E(i)
for values of i that are scanned from 2 through N. We then plot
! E(i)
vs. i and expect that minima on this graph will correspond to hinge locations.
It is to be expected that there exists a “single-cut” error associated with the fact that we
are cutting the backbone at only one location. In many proteins, the backbone crosses the
hinge region two or more times. Thus the single-cut predictor gives significantly clearer
results for single-stranded hinges (e.g. Lir-1, Figure 3.5) than for double, triple, etc.
stranded hinges (e.g. GluR2, Figure 3.4). We will return to this point later.
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