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In protein chemistry, a heterodimer is an assembly of two different protein subunits, conventionally written $AB$. A homodimer has two copies of the same subunit type, $A_2$. Different types can have similar protein folds and nearly equal molecular masses; “different” refers to molecular identity, not simply size or shape. An $A_2{B}_2$ protein complex contains two types but four chains, so it is not itself a heterodimer.

The alpha/beta tubulin heterodimer is the repeating building block of a microtubule. The alpha and beta protein subunits have similar folds but distinct sequences and nucleotide environments. Their structural relationship was resolved by electron crystallography of zinc-induced tubulin sheets: the 1998 model reached $3.7$ angstrom resolution. This is a concrete example of a two-chain protein quaternary structure, rather than the protein tertiary structure of a single chain.^[ref]

Stoichiometry gives a useful upper bound. If an idealized mixture contains $3\mu \mathrm{mol}$ of $A$ and $2\mu \mathrm{mol}$ of $B$, and only $AB$ can assemble, at most $2\mu \mathrm{mol}$ of heterodimer can form; at least $1\mu \mathrm{mol}$ of $A$ remains outside $AB$. The actual amount also depends on binding equilibrium and experimental conditions: chain counting alone does not guarantee complete association.

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]