Free-energy contributions to complex formation between botulinum neurotoxin type B and synaptobrevin fragment

Free-energy terms that contribute to complex formation between the catalytic domain of botulinum neurotoxin type B (BoNT/B-L(C)) and a 36-residue synaptobrevin fragment were estimated by using a combination of microscopic simulations and continuum methods. The complex for a non-hydrolyzed substrate was calculated by optimizing an energy function applied to the X-ray co-crystal structure of BoNT/B-L(C) bound with reaction products from a cleaved synaptobrevin peptide, refined to high crystallographic thermal factors. The estimated absolute binding affinity of the simulation structure is in good qualitative agreement with the experimental free energy of Michaelis complex formation, given the approximations of the model calculations. The simulation structure revealed significant complex stabilization from the hydrophobic effect, while the electrostatic cost of releasing water molecules from the interface determined to be highly unfavorable. By partitioning the total electrostatic and hydrophobic terms into residue free-energy contributions, a binding-affinity 'signature' for synaptobrevin was developed from the optimized conformation. The results demonstrate the effect of substrate length on complex formation and identify a peripheral high-affinity binding site near the N-terminal region that might initiate cooperative activation responsible for the large minimal substrate length requirement. The so-called SNARE motif is observed to contribute negligible free energy of binding.