Shaker pore structure as predicted by annealed atomic simulation using symmetry and novel geometric restraints

Abstract

Recent studies making use of channel-blocking peptides as molecular calipers have revealed the architecture of the pore-forming region of Shaker-type potassium channels. Here we show that the low-resolution, experimentally derived geometric information can be incorporated as restraints within the context of an annealed molecular dynamics simulation to predict an atomic structure for the channel pore which, by virtue of restraints, conforms to the experimental evidence. The simulation is reminiscent of the computational method employed by nuclear magnetic resonance (NMR) spectroscopists to resolve solution structures of biological macromolecules, but in lieu of restraints conventionally derived from NMR spectra, novel restraints are developed that include side-chain orientation of amino acid residues and assumed symmetry of protein subunits. The method presented here offers the possibility of expanding cooperation between simulation and experiment in developing structural models, especially for systems such as ion channels whose three-dimensional structures may not be amenable to determination by direct methods at the present time.

Synergistic Biophysical Techniques Reveal Structural Mechanisms of Engineered Cationic Antimicrobial Peptides in Lipid Model Membranes

“…Natural antimicrobialp eptides (AMPs) like colistin and LL-37 have been well studied. [5,[7][8][9][10][11] SomenaturalA MPs kill eukaryotic as well as bacterial cells, or they kill only one type of bacteria or only in specified environments. Colistin, for example, only kills Gram-negative (G(À)) but not Gram-positive (G(+ +)) bacteria and displays ad ecrease in antimicrobial activity when in the presence of divalent cations.…”

Solution Structure of Two New Toxins from the Venom of the Chinese Scorpion Buthus martensi Karsch Blockers of Potassium Channels,

“…Beyond a simple explanation of the mechanism of the blocking phenomenon, the structures of scorpion toxins directed against potassium channels were used as molecular calipers to precisely map their binding site (18)(19)(20)(21). There-fore, different models of pore-forming regions of the voltagegated Shaker-related potassium channels were defined (22)(23)(24). While the interaction of the scorpion toxins with the voltage-gated potassium channels is well-known, the interaction of other scorpion toxins with the large-and smallconductance calcium-activated potassium channels (BK Ca and SK Ca respectively) is still unclear.…”