Table 3.
Analysis of the interaction of three proteins by operations on reporter outputs in two- and one-bait cells
| Reporter output
|
Physical interpretation (one-bait and two bait data combined) | Physical interpretation (one-bait data only) | ||||
|---|---|---|---|---|---|---|
| One-bait cells
|
Two-bait cells
|
|||||
| A1 | A2 | A3 | A1 | A2 | ||
| Ba(X) | Ba(Y) | Ba(X) | Ba1(X) | Ba2(Y) | ||
| P(Z) | P(Z) | P(Y) | P(Z) | P(Z) | ||
| 0 | 0 | 0 | 0 | 0 | X, Y, Z do not interact | X, Y, Z do not interact |
| 0 | 0 | 0 | 0 | 1 | X, Y, Z associate weakly, modified Y and/or Z interact | X, Y, Z do not interact |
| 0 | 0 | 0 | 1 | 0 | X, Y, Z associate weakly, modified X and/or Z interact | X, Y, Z do not interact |
| 0 | 0 | 0 | 1 | 1 | X, Y, Z form trimer, requires X, Y, and Z | X, Y, Z do not interact |
| 0 | 0 | 1 | 0 | 0 | X, Y form dimer | X, Y form dimer |
| 0 | 0 | 1 | 0 | 1 | X modifies Y, modified Y binds Z | X, Y form dimer |
| 0 | 0 | 1 | 1 | 0 | Y modifies X, modified X binds Z | X, Y form dimer |
| 0 | 0 | 1 | 1 | 1 | X, Y form dimer, Z binds X/Y dimer to form X/Y/Z trimer | X, Y form dimer |
| 0 | 1 | 0 | 0 | 0 | X breaks Y/Z dimer | Y, Z form dimer |
| 0 | 1 | 0 | 0 | 1 | Y, Z form dimer, Z discriminates between X and Y | Y, Z form dimer |
| 0 | 1 | 0 | 1 | 0 | Y modifies Z, modified Z binds X | Y, Z form dimer |
| 0 | 1 | 0 | 1 | 1 | Y, Z form dimer, X binds to Y/Z dimer to form X/Y/Z trimer | Y, Z form dimer |
| 1 | 0 | 0 | 0 | 0 | Y breaks X/Z dimer | X, Z form dimer |
| 1 | 0 | 0 | 0 | 1 | X modifies Z, modified Z binds Y | X, Z form dimer |
| 1 | 0 | 0 | 1 | 0 | X, Z form dimer, Z discriminates between X and Y | X, Z form dimer |
| 1 | 0 | 0 | 1 | 1 | X, Z form dimer, Y binds to X/Z dimer to form X/Y/Z trimer | X, Z form dimer |
| 0 | 1 | 1 | 0 | 0 | X, Y and Y, Z form dimers, X/Y dimer precludes Y binding Z | Y, Z and Y, X form dimers |
| 0 | 1 | 1 | 0 | 1 | X, Y and Y, Z form dimers, Y/Z dimer precludes X binding Y | Y, Z and Y, X form dimers |
| 0 | 1 | 1 | 1 | 0 | Y modifies X, modified X binds Z | Y, Z and Y, X form dimers |
| 0 | 1 | 1 | 1 | 1 | X/Y and Y/Z dimers interact through Y to form X/Y/Z trimer | Y, Z and Y, X form dimers |
| 1 | 0 | 1 | 0 | 0 | X, Y and X, Z form dimers, X/Y dimer precludes X binding Z | X, Z and X, Y form dimers |
| 1 | 0 | 1 | 0 | 1 | X modifies Y, modified Y binds Z | X, Z and X, Y form dimers |
| 1 | 0 | 1 | 1 | 0 | X, Y and X, Z form dimers, X/Z dimer precludes X binding Y | X, Z and X, Y form dimers |
| 1 | 0 | 1 | 1 | 1 | X/Z and X/Y dimers interact through X to form X/Y/Z trimer | X, Z and X, Y form dimers |
| 1 | 1 | 0 | 0 | 0 | X, Z and Y, Z form dimers, dimers inactivate one another | X, Z and Y, Z form dimers |
| 1 | 1 | 0 | 0 | 1 | X, Z and Y, Z form dimers, Y/Z dimer precludes X binding Z | X, Z and Y, Z form dimers |
| 1 | 1 | 0 | 1 | 0 | X, Z and Y, Z form dimers, X/Z dimer precludes Y binding Z | X, Z and Y, Z form dimers |
| 1 | 1 | 0 | 1 | 1 | X, Z and Y, Z dimers form | X, Z and Y, Z form dimers |
| 1 | 1 | 1 | 0 | 0 | X, Y forms dimer, X/Y dimer inactivates Z | X, Y and X, Z and Y, Z form dimers, X/Y/Z trimer may form (16) |
| 1 | 1 | 1 | 0 | 1 | X, Y and X, Z and Y, Z form dimers, Y modifies X, modified X binds Z poorly | X, Y, and X, Z, and Y, Z form dimers, X/Y/Z trimer may form (16) |
| 1 | 1 | 1 | 1 | 0 | X, Y and X, Z and Y, Z form dimers, X modifies Y, modified Y binds Z poorly | X, Y, and X, Z and Y, Z, form dimers, X/Y/Z trimer may form (16) |
| 1 | 1 | 1 | 1 | 1 | X, Y and X, Z and Y, Z form dimers, X/Y/Z trimer may form | X, Y and X, Z and Y, Z form dimers, X/Y/Z trimer may form (16) |
“Reporter output” shows the state of the touching relationships registered by outputs of the reporters in three one-bait cells and a single two-bait cell. In the one-bait cells, the reporter output shows the touching relationships A1, A2, and A3 for different combinations of proteins X, Y, and Z. Here, X and Z are fused to an activation domain to form preys [P(X) or P(Z)], and Y and X are fused to a DNA binding domain to form baits [Ba(X), Ba(Y)]. In a two-bait cell, the outputs of the reporters show the state of the touching relationship for proteins X, Y and Z where they are fused with one of two DNA binding domains [Ba1(X) or Ba2(Y)] and an activation domain [P(Z)]. “Physical interpretation” shows one possible biological interpretation of this set of reporter outputs for possible combinations of one- and two-bait data, or for one-bait data alone. Although all patterns here may not have biological correlates, many have been observed, for example, the interaction of Bait1 and prey depends on the presence of Bait2 (P. King, personal communication).