A Neutral View Of CASK

The distal binding pocket in the T monomer is represented ... The direct simulations identified a novel alternative uptake path, which is not visible in the crystal structure. This third path goes along the bottom of the porter domain toward PC1 and could be validated by site-directed mutagenesis of AcrB in E. coli. Mutations of residues located along the path significantly impaired the e?ux efficiency. The work of Yao et al. (2013) is of great interest because it combined different techniques to gain insight into an important step of the e?ux process. However, it has to be noted that the authors made several approximations. As in all the computational studies described in this review, the partners of the RND transporter (i.e., AcrA and TolC in the present case) were missing. It was also assumed that the drug uptake was mainly driven by hydrophobic interactions. Finally, some of the physicochemical properties such as the ordering of amphiphilic drugs in the lipid bilayer and the conformational flexibility of drugs with rotatable bonds were neglected. Despite of the necessary approximations, the work of Yao et al. (2013) was an important contribution to the understanding of drug RND e?ux. The structures of the L monomers and ligand conformations in co-crystals suggest interesting mechanistic differences between MexB and AcrB (Sennhauser et al., 2009; Nakashima et al., 2013). Thus, a similar study on MexB would be of great interest. Conclusion Much progress has been made in the understanding of the transport mechanism of RND e?ux pumps since they were discovered. Genetic and biochemical investigations have provided a good survey of the substrate specificity of different pump complexes in various bacteria. It has become accepted that RND pumps evolved as a first line of bacterial defense against exogenous substances, allowing the development of additional defense strategies (Olivares et al., 2013). Molecules that are able to penetrate the OM are potentially problematic for Gram-negative bacteria. Many sophisticated studies have supported this view as they have indicated that amphiphilic molecules (such as many antibiotics), which are able to pass the OM, are good substrates for export systems (Nikaido, 2011; Nikaido and Pages, 2012). X-ray crystallography has provided highly detailed structural information on binding interactions between pump subunits and substrates (Ruggerone et al., 2013a). It is intriguing that only a Ulixertinib order handful of a large number of known e?ux substrates could be co-crystallized with e?ux pumps. Although X-ray structures provide snap-shots of a complex transport mechanism, they have been crucial for the setup of a transport model. Concerning specific experiments aiming at a more direct investigation of e?ux dynamics, studies with whole bacteria have been performed.