Paper Citing NAMD - Abstract
Gumbart, J.; Schulten, K.
Molecular dynamics studies of the archaeal translocon
BIOPHYSICAL JOURNAL, 90:2356-2367, APR 2006
The translocon is a protein-conducting channel conserved over all domains of life that serves to translocate proteins across or into membranes. Although this channel has been well studied for many years, the recent discovery of a high-resolution crystal structure opens up new avenues of exploration. Taking advantage of this, we performed molecular dynamics simulations of the translocon in a fully solvated lipid bilayer, examining the translocation abilities of monomeric SecYE beta by forcing two helices comprised of different amino acid sequences to cross the channel. The simulations revealed that the so-called plug of SecYE beta swings open during translocation, closing thereafter. Likewise, it was established that the so-called pore ring region of SecYE beta forms an elastic, yet tight, seal around the translocating oligopeptides. The closed state of the channel was found to block permeation of all ions and water molecules; in the open state, ions were blocked. Our results suggest that the SecYE beta monomer is capable of forming an active channel.
DOI:10.1529/biophysj.105.075291
