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The DNA-binding domain supports site occupancy, while the region for homotypic protein interaction permits much larger assemblies. With the truncated protein, the faster complex 4 appears at low protein:DNA ratios and gives way to the slower complex 3 as protein increases. A natural assignment is occupancy of one and then both recognition repeats by functional binding units. A binding unit could itself be a protein dimer; a native gel does not determine the number of polypeptide chains from mobility alone. Loss of free probe with increasing protein supports binding, and failure to shift the zero-repeat probe supports sequence preference under these conditions.

Full-length protein instead produces the very slow complex 1 already at relatively low ratios, followed by more of complex 2 at high ratios. homotypic protein interactions can make cooperative higher-order assemblies and can bridge different probe molecules. At protein excess, separate saturation of available sites can reduce productive bridging, explaining why the largest species need not increase monotonically. Complex 2 is compatible with a smaller saturated full-length assembly; assigning its exact stoichiometry requires an independent measurement. protein size also contributes to the difference between full-length and truncated complexes, but size alone does not explain the concentration-dependent redistribution into the exceptionally slow species. The experiment supports assembly dependent on protein oligomerization rather than a unique structure for every numbered band.

Protein oligomerization associates several protein subunits into a defined assembly, such as a protein dimer. It can create cooperative binding sites, regulate activity or build structural units. A measured assembly depends on concentration and conditions: a dimer can dissociate on dilution. Determining subunit count therefore requires an assay model as well as a measured size or signal. ^[ref]

T. M. Weaver is the published author name credited on the 1995 structural study of Fumarase C from Escherichia coli. The paper lists a University of Minnesota biochemistry affiliation. Its initials are retained here as the verified scientific byline.^[ref]

The study determined the four-subunit protein complex at $2.0$ ångströms crystallographic resolution. A tungstate derivative, acting as a competitive inhibitor, helped locate an active site containing contributions from three of the four protein subunits. Thus, the site was not simply a pocket belonging to one isolated chain.^[ref]

This gives an illuminating reason to distinguish folding from assembly. A purified protein subunit could retain its own folded shape yet fail to form a complete active site if a neighboring contribution is missing. Conversely, identifying a conserved catalytic group in a sequence does not establish that the required protein complex has assembled.

An original probability model illustrates the possible amplification. Suppose an idealized site requires three independently functional subunit contributions, each present with probability $p$. Its probability of being complete is $p^3$. With $p=0.9$, this is $0.729$, rather than $0.9$. In that model, losing $10\%$ of individual contributions leaves $27.1\%$ of sites incomplete. This is not a measured activity law for Fumarase C: independent availability, random assembly and all-or-nothing site function are explicit assumptions. A real defect could affect assembly, chemical turnover or both.

The structural observation motivates complementary measurements: assess protein oligomerization separately from reaction rate, then ask whether altered assembly accounts for altered catalysis. A crystal structure supplies a concrete spatial hypothesis about these relationships, while functional measurements test its consequences.