Protective antigen (PA) is a central virulence factor of Bacillus anthracis and a key component in anthrax vaccines. PA binds to target cell receptors, is cleaved by the furin protease, self-aggregates to heptamers, and finally internalizes as a complex with either lethal or edema factors. Under mild room temperature storage conditions, PA cytotoxicity decreased (t1 ⁄ 2 ≈ 7 days) concomitant with the generation of new acidic isoforms, probably through deamidation of Asn residues. Ranking all 68 Asn residues in PA based on their predicted deamidation rates revealed five residues with half-lives of <60 days, and these residues were further analyzed: The Gram-positive spore-forming bacterium Bacillus anthracis, the causative agent of anthrax, produces a bipartite A/B-type toxin. The B subunit is the 83-kDa protective antigen (PA) 3 receptor-binding moiety (named for its use as a vaccine), and the two catalytic A subunit moieties are edema factor (EF; 89 kDa) and lethal factor (LF; 90 kDa) (1). EF is a Ca 2ϩ -and calmodulin-dependent adenylate cyclase (2). LF is a Zn 2ϩ protease that cleaves and inactivates mitogen-activated protein kinase kinase-1 and -2 (3, 4). Following PA binding to cell receptors (5-8), it is cleaved by a furin family protease (9) to a 20-kDa N-terminal fragment with no known further function and to a 63-kDa fragment that forms ring-shaped heptamers on the cell surface (10). The heptamers then bind up to three molecules of EF or LF (11,12). Following binding, the heptamer-LF/EF complex undergoes endocytosis, and LF or EF is released to the cytosol (13-15). The crystal structure (16) and functional studies (11,12,(17)(18)(19)(20) have demonstrated that the PA polypeptide is folded into four distinct domains with well defined functions. Domain I (residues 1-258) prevents premature PA polymerization and harbors the furin cleavage site, which is located in an unstructured flexible loop; domain II (residues 259 -487) is involved in heptamerization and is in the membrane insertion loop; domain III (residues 488 -595) is also involved in heptamerization (18) PA has been reported previously to be a thermally unstable protein, losing its in vitro cytotoxic activity upon storage at 37°C within 48 h (32) or within few minutes above 40°C as a result of aggregation (33). Protein loss of function under mild storage conditions is generally attributed to a variety of nonenzymatic modifications such as deamidation, isomerization, oxidation, and alternative disulfide pairings (34, 35). Spontaneous deamidation, which occurs mainly at Asn side chains and at a much slower rate at Gln residues (36), is a major and well documented degradation pathway in proteins. Deamidation rates depend on pH, temperature, primary sequence ("nearest neighbor" effect), and protein conformation (37-40). Deamidation proceeds by nucleophilic attack on the side chain carbonyl carbon of Asn by the nitrogen of the adjacent peptide bond, resulting in the formation of an unstable five-member succinimide ring, which is hydrolyzed to produce m...