Paper Citing NAMD - Abstract
Chen, Rong; Chung, Shin-Ho
Binding Modes and Functional Surface of Anti-mammalian Scorpion alpha-Toxins to Sodium Channels
BIOCHEMISTRY, 51:7775-7782, OCT 2 2012
Scorpion alpha-toxins bind to the voltage-sensing domains of voltage-gated sodium (Na-v) channels and interfere with the inactivation mechanisms. The functional surface of alpha-toxins has been shown to contain an NC-domain consisting of the five-residue turn (positions 8-12) and the C-terminus (positions 56-64) and a core-domain centered on the residue 18. The NC- and core-domains are interconnected by the linker-domain (positions 8-18). Here with atomistic molecular dynamics simulations, we examine the binding modes between two alpha-toxins, the anti-mammalian AahII and the anti-insect Lqh alpha IT, and the voltage-sensing domain of rat Na(v)1.2, a subtype of Na-v channels expressed in nerve cells. Both toxins are docked to the extracellular side of the voltage-sensing domain of Na(v)1.2 using molecular dynamics simulations, with the linker-domain assumed to wedge into the binding pocket. Several salt bridges and hydrophobic clusters are observed to form between the NC- and core-domains of the toxins and Na(v)1.2 and stabilize the toxin-channel complexes. The binding modes predicted are consistent with available mutagenesis data and can readily explain the relative affinities of AahII and Lqh alpha IT for Na(v)1.2. The dissociation constants for the two toxin-channel complexes are derived, which compare favorably with experiment. Our models demonstrate that the functional surface of anti-mammalian scorpion alpha-toxins is centered on the linker-domain, similar to that of beta-toxins.
