, 2008). Although this process might involve additional structural changes, it is nonetheless reasonable to assume that the available X-ray structures are broadly KU 55933 representative of the active state without

further information. There is currently no atomic-resolution structure of a Kv channel in the resting state. This has motivated efforts aimed at translating the results from various experiments into structural information using modeling (Jiang et al., 2003, Lainé et al., 2003, Ruta et al., 2005, Posson et al., 2005, Chanda et al., 2005, Yarov-Yarovoy et al., 2006, Campos et al., 2007, Grabe et al., 2007, Lewis et al., 2008 and Pathak et al., 2007). Despite their inherent approximate nature, such experimentally constrained structural models AZD0530 solubility dmso can serve to provide a context for the rational interpretation and design of future experiments. They can also be used to interpret and validate future experimental structures targeting the resting state of the VSD. Information about the conformation of the VSD in the resting state has come from a wide range of experiments, including mutagenesis (Starace et al., 1997, Starace and Bezanilla, 2001, Starace and Bezanilla,

2004, Ahern and Horn, 2004, Ahern and Horn, 2005, Grabe et al., 2007, Lin et al., 2010 and Tao et al., 2010), cross-linking (Jiang et al., 2003, Lainé et al., 2003, Ruta et al., 2005 and Campos et al., 2007), fluorescence (Pathak et al., 2007), resonance-energy transfer (Cha et al., 1999, Chanda et al., 2005 and Posson et al., 2005), and inhibitory toxins (Phillips et al., 2005b). Despite the wealth of experimental information, not all measurements can be easily translated into simple structural constraints. In that regard, experimental observations involving residue-residue interactions are of interest because they provide highly specific spatial constraints for the resting conformation of Kv channels (Campos et al., medroxyprogesterone 2007, Lin et al., 2010 and Tao et al., 2010). Engineered metal bridges are particularly informative because they involve strong chemically specific interactions occurring between residues that

are within atomic proximity from one another. Furthermore, the presence of a high-affinity metal bridge indirectly implies that the interaction reliably reports the protein conformation because large distortions would be expected to cause unfavorable strain energy that would result in a low-affinity site. Here, we review the available information on the resting state of the VSD and assess how its conformation is constrained by the available experimental data. We set out to explicitly simulate several of the key interactions associated with the resting state using molecular dynamics (MD). Although MD simulations are limited by approximations, the approach enables an objective evaluation of how these interactions can contribute to restricting the conformation of the VSD.