The human serine protease inhibitor (serpin) alpha-1 antitrypsin (alpha1-AT) protects tissues from proteases of inflammatory cells. The most common disease-causing mutation in alpha1-AT is the Z-mutation (E342K) that results in an increased propensity of alpha1-AT to polymerize in the ER of hepatocytes, leading to a lack of secretion into the circulation. The structural consequences of this mutation, however, remain elusive. We report a comparative molecular dynamics investigation of the native states of wild-type and Z alpha1-AT, revealing a striking contrast between their structures and dynamics in the breach region at the top of beta-sheet A, which is closed in the wild-type simulations but open in the Z form. Our findings are consistent with experimental observations, notably the increased solvent exposure of buried residues in the breach region in Z, as well as polymerization via domain swapping, whereby the reactive center loop is rapidly inserted into an open A-sheet before proper folding of the C-terminal beta-strands, allowing C-terminal domain swapping with a neighboring molecule. Taken together, our experimental and simulation data imply that mutations at residue 342 that either stabilize an open form of the top of beta-sheet A or increase the local flexibility in this region, may favor polymerization and hence aggregation.