Homodimer

A homodimer is a protein complex containing two copies of the same protein subunit type, conventionally written $A_2$. A heterodimer instead contains two different types, $AB$. Identical subunit type does not require the copies to occupy identical conformations or environments in every instant of the complex's motion.

Assembly is part of protein quaternary structure, rather than a claim that the two chains have become one longer polypeptide. If each subunit contains 100 amino acid residues, the homodimer contains 200 residues across two chains. Association alone need not add a peptide bond between them.

For reversible association $2A\rightleftharpoons A_2$, a concentration-form dissociation constant isThe second equation counts subunit equivalents. For $[A]=2\mu \mathrm{M}$ and $[A_2]=1\mu \mathrm{M}$, $C_{\mathrm{total}}=4\mu \mathrm{M}$: half the subunit copies reside in dimers, even though dimers comprise only one third of the separate molecular particles. The written $K_d$ uses the usual macroscopic concentration convention.

HIV-1 protease supplies an experimentally important example. Recombinant enzyme had reported molecular masses of approximately 11,000 under denaturing conditions and 22,000 under nondenaturing conditions; chemical crosslinking provided additional evidence consistent with an active two-subunit enzyme. Comparing several measurements was more informative than assigning a homodimer solely from an apparent mass in one assay.^[ref]