Apamin is a polypeptide possessing an amino acid sequence of H-Cys-Asn-Cys-Lys-Ala-Pro-Glu-Thr-Ala-Leu-Cys-Ala-Arg-Arg-Cys-Gln-Gln-His-NH (one-letter sequence CNCKAPETALCARRCQQH-NH, with disulfide bonds between Cys-Cys and Cys-Cys). Apamin is very rigid because of the two disulfide bridges and seven hydrogen bonds. The three-dimensional structure of apamin has been studied with several spectroscopical techniques: HNMR, Circular Dichroism, Raman spectroscopy, FT-IR. The structure is presumed to consist of an alpha-helix and beta-turns, but the exact structure is still unknown.
By local alterations it is possible to find the amino acids that are involved in toxicity of apamin. It was found by Vincent et al. that guanidination of the ε-amino group of lysine does not decrease toxicity. When the ε-amino group of lysine and the α-amino group of cysteine are acetylated or treated with fluorescamine, toxicity decreases with a factor of respectively 2.5 and 2.8. This is only a small decrease, which indicates that neither the ε-amino group of lysine nor the α-amino group of cysteine is essential for the toxicity of apamin. Glutamine was altered by formation of an amide bond with glycine ethyl ester, this resulted in a decrease in toxicity of a factor 2.0. Glutamine also doesn't appear to be essential for toxicity. When histidine is altered by carbethoxylation, toxicity decreases only by a factor 2.6. But when histidine, the ε-amino group of lysine and the α-amino group of cysteine all are carbethoxylated and acetylated toxicity decreases drastically. This means that these three amino acids are not essential for toxicity on their own, but the three of them combined are. Chemical alteration of arginine and arginine by treatment of 1,2-cyclohexanedione and cleavage by trypsin decreases toxicity by a factor greater than 10. The amino acids that cause toxicity of apamin are cysteine, lysine, arginine, arginine and histidine.