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Proteins made up of more than one polypeptide chain also have quaternary structure. Such proteins are called multimeric proteins. When the polypeptides are the same, the protein is a homomultimer. When they are different, the protein is a heteromultimer. Other names reflect the number of polypeptides in the protein. For example, the term homodimer describes a protein made of two identical polypeptides, whereas heterodimer describes a protein made of two different polypeptides. The names trimer, tetramer, and so on refer to increasing numbers of polypeptides. Hence, the ρ transcription termination factor is a homohexamer (see above).

The polypeptide chains in a protein are usually held together by hydrogen bonds. The only covalent chemical bonds in most proteins are the peptide bonds that link adjacent amino acids to form the polypeptide chains. As a result, if a multimeric protein is heated, it falls apart into its individual polypeptide chains. However, some proteins are unusually stable; these include extracellular enzymes, which must be able to function in the harsh environment outside the cell. Such proteins are often also held together by disulfide bonds between cysteine amino acids in the protein.