Paper Citing NAMD - Abstract
Chen, Rong; Chung, Shin-Ho
Binding Modes of mu-Conotoxin to the Bacterial Sodium Channel (Na(v)Ab)
BIOPHYSICAL JOURNAL, 102:483-488, FEB 8 2012
Polypeptide toxins isolated from the venom of cone snails, known as mu-conotoxins, block voltage-gated sodium channels by physically occluding the ion-conducting pathway. Using molecular dynamics, we show that one subtype of mu-conotoxins, PIIIA, effectively blocks the bacterial voltage-gated sodium channel Na(v)Ab, whose crystal structure has recently been elucidated. The spherically shaped toxin, carrying a net charge of +6 e with six basic residues protruding from its surface, is attracted by the negatively charged residues on the vestibular wall and the selectivity filter of the channel. The side chain of each of these six arginine and lysine residues can wedge into the selectivity filter, whereas the side chains of other basic residues form electrostatic complexes with two acidic residues on the channel. We construct the profile of potential of mean force for the unbinding of PIIIA from the channel, and predict that PIIIA blocks the bacterial sodium channel with subnanomolar affinity.
