Paper Citing NAMD - Abstract
Gumbart, James; Chipot, Christophe; Schulten, Klaus
Free Energy of Nascent-Chain Folding in the Translocon
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7602-7607, MAY 18 2011
During their synthesis, many water-soluble proteins and nearly all membrane proteins transit through a protein-conducting channel in the membrane, the Sec translocon, from where they are inserted into the lipid bilayer. Increasing evidence indicates that folding of the nascent protein begins already within the ribosomal exit tunnel in a sequence- and environment-dependent fashion. To examine the effects of the translocon on the nascent-chain folding, we have calculated the potential of mean force for a-helix formation of a 10-alanine oligopeptide as a function of its position within the translocon channel. We find that the predominant conformational states, a-helical and extended, reflect those found for the peptide in water. However, the translocon, via its surface properties and its variable diameter, shifts the equilibrium in favor of the a-helical state. Thus, we suggest that the translocon facilitates not only the insertion of membrane proteins into the bilayer but also their folding.
