Earlier biochemical in vitro studies suggest that each Dscam1 isoform has extracellular domains that prefer to bind to itself (self-binding or homophilic binding), while heterophilic binding (binding between different isoforms) tends to be weak or below the detection limit of the assays used [ 9].
Some proteins may actually prefer to bind shorter stems and/or may bind 1-1 bulges.
This view is consistent with the result of recent high-resolution single molecule fluorescence microscopic assays that showed that free cofilin molecules prefer to bind within 65 nm of an already bound cofilin molecule, but not necessarily to the site immediately neighboring the already bound molecule (Hayakawa et al., 2014).
We have shown that transport vesicles can bind to GCC185's N-terminus, and seem to prefer to bind to splayed ends of this dimeric, coiled coil tether.
MBD1, MBD2 and MBD4 preferentially bind methylated DNA, in contrast to MBD3, MBD5 and MBD6 that prefer to bind to non-methylated DNA [ 47], although MBD5 and MBD6 associate with heterochromatin [ 48].
Jun-Jun and Jun-Fos dimers preferentially bind to the phorbol ester tumor promoter response element (TRE) while Jun-ATF dimers prefer to bind to c-AMP-responsive element (CRE) [ 9].
c-Jun/c-Fos heterodimers bind to the AP-1 site (5′-TGACTCA-3′) with high affinity, whereas c-Jun/ATF2 heterodimers prefer to bind to ATF sites (5′-TGACGTCA-3′).
If Fj inhibits Ds binding and promotes Ft binding more strongly to the right, Ft molecules in each cell prefer to bind to Ds in the next left-most cell (with which they have a stronger binding interaction), and so preferentially accumulate at left cell edges; similarly Ds molecules prefer to associate with Ft in the next right-most cell and in turn accumulate at right cell edges.
In the ground state, they prefer to bind bromide ion.
SAR demonstrated that the S2 and S3 pockets of FVIIa prefer to bind small, lipophilic groups.
Actors prefer to bind their various social practices into a reasonably coherent unit.
