title: The roles of pore ring and plug in the SecY protein-conducting channel.
abstract: The protein-conducting channel, or translocon, is an evolutionarily conserved complex that allows nascent proteins to cross a cellular membrane or integrate into it. The crystal structure of an archaeal translocon, the SecY complex, revealed that two elements contribute to sealing the channel: a small "plug" domain blocking the periplasmic region of the channel, and a pore ring composed of six hydrophobic residues acting as a constriction point at the channel's center. To determine the independent functions of these two elements, we have performed molecular dynamics simulations of the native channel as well as of two recently structurally resolved mutants in which portions of their plugs were deleted. We find that in the mutants, the instability in the plug region leads to a concomitant increase in flexibility of the pore ring. The instability is quantified by the rate of water permeation in each system as well as by the force required for oligopeptide translocation. Through a novel simulation in which the interactions between the plug and water were independently controlled, we find that the role of the plug in stabilizing the pore ring is significantly more important than its role as a purely steric barrier.
authors.affiliation: Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: James
authors.initials: J
authors.lastname: Gumbart
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D002463:Cell Membrane Permeability; D017124:Conserved Sequence / Q000502:physiology; D018360:Crystallography, X-Ray; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure*; D016297:Mutagenesis, Site-Directed; D020836:Protein Structure, Quaternary / Q000502:physiology; D017433:Protein Structure, Secondary / Q000502:physiology; D017434:Protein Structure, Tertiary / Q000502:physiology; D021381:Protein Transport / Q000502:physiology; D000069816:SEC Translocation Channels; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014867:Water / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D029968:Escherichia coli Proteins; D026901:Membrane Transport Proteins; D046912:Multiprotein Complexes; D000069816:SEC Translocation Channels; C057841:SecY protein, E coli; D014867:Water