In silico conformational features of botulinum toxins A1 and E1 according to the intraluminal acidification

Although the botulinum neurotoxins (BoNTs) are among the most toxic compounds found in nature, their molecular mechanism of action is far from being elucidated. A key event is the conformational transition due to the acidification of the interior of synaptic vesicles, and leading to the translocation of the BoNT catalytic domain into the neuronal cytosol. To investigate these conformational variations, homology modelling and atomistic simulations are combined to explore the internal dynamics of the subtypes BoNT/A1, the most-used in medical applications, and BoNT/E1, the most kinetically efficient. This first simulation study of di-chain BoNTs in closed and open states includes the effects of neutral and acidic pH. The conformational mobility is driven by domains displacements; the ganglioside binding site in the receptor binding domain, the translocation domain (HCNT) switch and the belt α helix visit multiple conformations depending on the primary sequence and on the pH. Fluctuations of the belt α helix are observed for closed conformations of the toxins and at acidic pH, and patches of more accessible residues appear in the same conditions in  the core translocation domain HCNT. These findings suggest that during translocation, the larger mobility of belt could be transmitted to HCNT, leading to a favorable interaction of HCNT residues with the non-polar membrane environment. The data deposited to Zenodo correspond to those used to produce Figures 2, 3, 4, 5, 6, 7, 9, 10 and 11, as well as representative conformations extracted from rhe molecular dynamics trajectories.