title: Molecular dynamics studies of the archaeal translocon.
abstract: 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 SecYEbeta by forcing two helices comprised of different amino acid sequences to cross the channel. The simulations revealed that the so-called plug of SecYEbeta swings open during translocation, closing thereafter. Likewise, it was established that the so-called pore ring region of SecYEbeta 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 SecYEbeta monomer is capable of forming an active channel.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign and Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, USA.
authors.forename: James
authors.initials: J
authors.lastname: Gumbart
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: D000409:Alanine / Q000737:chemistry; D001105:Archaea / Q000378:metabolism*; D019843:Archaeal Proteins / Q000737:chemistry*; D001216:Asparagine / Q000737:chemistry; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D003593:Cytoplasm / Q000378:metabolism; D030562:Databases, Protein; D019281:Dimerization; D005998:Glycine / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D007477:Ions; D007930:Leucine / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry*; D008055:Lipids / Q000737:chemistry; D017017:Methanococcus / Q000378:metabolism*; D008958:Models, Molecular; D008968:Molecular Conformation; D009842:Oligopeptides / Q000737:chemistry; D010713:Phosphatidylcholines / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D015203:Reproducibility of Results; D055672:Static Electricity; D013997:Time Factors; D014867:Water / Q000737:chemistry*
chemical_list: D019843:Archaeal Proteins; D007477:Ions; D008051:Lipid Bilayers; D008055:Lipids; D009842:Oligopeptides; D010713:Phosphatidylcholines; D014867:Water; D006639:Histidine; D001216:Asparagine; D006859:Hydrogen; D007930:Leucine; D000409:Alanine; D005998:Glycine; C028694:1-palmitoyl-2-oleoylphosphatidylcholine