Acidic Side-Chain Rotamers and their Impact on Ion Conduction through the Nicotinic Acetylcholine Receptor

Abstract

It has long been recognized that the glutamates at the intracellular mouth of the nicotinic acetylcholine-receptor (AChR) pore provide most of the stabilization to the passing cations. Moreover, it has recently been found that these “intermediate-ring” glutamates contribute asymmetrically to the single-channel conductance of the muscle receptor, with only two of the side chains being sufficient to achieve a wild-type value (Cymes and Grosman, 2012). Further single-channel recordings suggested that the difference between the two glutamates that contribute to the conductance and those that do not lies in the different conformations adopted by these side chains. To test these ideas in a framework of stereochemical rigor, we performed molecular simulations on a homology model of the open-channel muscle AChR that corrects for a register error in the original structural model. Using Brownian Dynamics, we found that different glutamate rotamers can account for dramatic changes in the computed single-channel conductance, and using Molecular Dynamics, we found that two of the four glutamates project their carboxylate oxygens into the pore while the other two glutamates project them away from the pore. In addition, using Brownian Dynamics simulations, we found that pore-facing glutamates are responsible for the majority of the single-channel conductance, whereas non-pore facing glutamates have a negligible impact on it. Overall, this configuration of glutamate side chains in the intermediate ring of charge (which is in remarkable agreement with the one we surmised on the basis of single-channel recordings) points to an unusual arrangement of acidic groups that may perhaps explain their bulk-like pKa values.