Figure 12
A multi-domain protein may first associate non-specifically with the DNA predominantly through one domain facilitated by long-range electrostatics to the charged DNA backbone and then ‘slide’ along DNA until its target DNA site (green) is found where the second domain can now also bind, locking it in place. Another multi-domain protein may bind a disordered region of a protein that is enriched in charged and hydrophobic residues which would allow non-specific binding and then slide or hop along the disordered region until its binding site (green) is found where again the second domain can now also bind, locking it in place. Another multi-domain protein may bind a lipid bilayer and diffuse until the second domain binds to a target membrane protein (green). In all cases, the search would be quicker since the protein is only scanning possible areas of the cell that are more likely to lead to the correct target. This is facilitated by having a separate domain that specialises in binding either DNA, disordered protein regions or lipid bilayers possibly through forming an encounter complex. In some cases, a single domain could achieve the same effect by having two distinct regions, a non-specific and specific binding surface.
Proteins can find their partners faster by searching in 1D or 2D

A multi-domain protein may first associate non-specifically with the DNA predominantly through one domain facilitated by long-range electrostatics to the charged DNA backbone and then ‘slide’ along DNA until its target DNA site (green) is found where the second domain can now also bind, locking it in place. Another multi-domain protein may bind a disordered region of a protein that is enriched in charged and hydrophobic residues which would allow non-specific binding and then slide or hop along the disordered region until its binding site (green) is found where again the second domain can now also bind, locking it in place. Another multi-domain protein may bind a lipid bilayer and diffuse until the second domain binds to a target membrane protein (green). In all cases, the search would be quicker since the protein is only scanning possible areas of the cell that are more likely to lead to the correct target. This is facilitated by having a separate domain that specialises in binding either DNA, disordered protein regions or lipid bilayers possibly through forming an encounter complex. In some cases, a single domain could achieve the same effect by having two distinct regions, a non-specific and specific binding surface.

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