| Abstract
| - Brownian dynamics (BD) and molecular dynamics (MD) simulations and electrostatic calculationswere performed to study the binding process of κ-PVIIA to the Shaker potassium channel and the structureof the resulting complex. BD simulations, guided by electrostatic interactions, led to an initial alignmentbetween the toxin and the channel protein. MD simulations were then carried out to allow for rearrangementsfrom this initial structure. After ∼4 ns, a critical “induced fit” process was observed to last for ∼2 ns. In thisprocess, the interface was reorganized, and side chains were moved so that favorable atomic contactswere formed or strengthened, while unfavorable contacts were eliminated. The final complex structurewas stabilized through electrostatic interactions with the positively charged side chain of Lys7 of κ-PVIIAdeeply inserted into the channel pore and other hydrogen bonds and by hydrophobic interactions involvingPhe9 and Phe23 of the toxin. The validity of the predicted structure for the complex was assessed bycalculating the effects of mutating charged and polar residues of both the toxin and the channel protein,with the calculated effects correlating reasonably well with experimental data. The present study suggestsa general binding mechanism, whereby proteins are pre-aligned in their diffusional encounter by long-range electrostatic attraction, and nanosecond-scale rearrangements within the initial complex then leadto a specifically bound complex.
|
