The dissociation constant (K d) in the unit of molar is estimated to be [37, 45, 46]: (1) where W(z) is the 1D PMF with the zero point located at the bulk, 1,000 N A is used to convert from cubic meter to liter per mole, k B and T are Boltzmann’s constant and temperature, respectively, z 1 is in the binding pocket, and z 2 is in the bulk [46]. Although Equation 1 was originally derived for the binding of an ion to a channel [45], it has also been successfully applied to www.selleckchem.com/products/CP-673451.html toxin binding [16, 37, 43]. Note that the windows at 38.5 and 42.0 Å for NavAb and Kv1.3, respectively, are assumed to be bulk, and the PMF is therefore set to zero at this z position. The fullerene is docked to NavAb and Kv1.3 at z = 20.5 Å and z = 23.0 Å, respectively, and the center of mass is located at z = 0 Å. A hydrogen bond is assumed to be formed if the donor-acceptor distance is within 3.0 Å and the donor-hydrogen-acceptor angle is ≥150. A salt bridge is formed between the fullerene and ion channel if the distance between any of the nitrogen atoms on the fullerene side chains and the oxygen atoms of an acidic residue on the ion channel AZD5582 chemical structure is <4 Å. Results and discussion Figure 2 illustrates the PMF for the cleavage of [Lys]-fullerene from the NavAb and Kv1.3 channels. The axial position in Figure 2 is measured

from the center of mass of the channel to that of the [Lys]-fullerene. The PMF reaches a minimum at 20.5 Å for NavAb, with a well depth of −18.7 kT. For Kv1.3, the PMF reaches a minimum at 23.0 Å, with a well depth of −7.1 kT. We find that the binding between [Lys]-fullerene and both NavAb and Kv1.3 is stable and so all 5 ns of umbrella sampling is used. It is assumed that the properties for the window at 38.5 and 42.0 Å for NavAb and Kv1.3, respectively, are similar to those in bulk, and therefore, the PMF is set to 0 at this point. Figure 2 Potential of mean force LY294002 (PMF). PMF for the cleavage of [Lys]-fullerene from the NavAb and Kv1.3 channels. Using Equation 1, we obtain dissociation constants, K d,

of 46 nM and 3 mM for the NavAb and Kv1.3 channels, respectively. In comparison, in MD simulations, Chen and Chung [16] found that μ-conotoxin binds to NavAb with a well depth of approximately −25 kT and a binding affinity of 0.1 nM. French and colleagues [17] have recently confirmed this result experimentally and obtained a binding affinity of 0.005 nM for the NaChBac, a bacterial channel closely related to NavAb. This [Lys]-fullerene mimic of μ-conotoxin is specific to NavAb over Kv1.3 and presents exciting opportunities for future drug development research. To characterize the interactions between the [Lys]-fullerene and the two channels, we examine the umbrella sampling window located at the minimum of the PMF, 20.5 and 23.0 Å in NavAb and Kv1.3, respectively.