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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.

SUBMITTER: Gumbart J

PROVIDER: S-EPMC1403164 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature

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Molecular dynamics studies of the archaeal translocon.

Gumbart James J Schulten Klaus K

Biophysical journal 20060113 7

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 ...[more]

PMID: 16415058

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Project description:BACKGROUND: Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO2 or urea. Recently, the identification and characterization of a number of archaeal and bacterial aquaporins suggested the existence of a third sub-family; one that is neither a strict aquaporin nor an aquaglyceroporin. The function and phylogeny of this third family is still a matter of debate. RESULTS: Twenty nanosecond molecular dynamics (MD) simulation of a fully hydrated tetramer of AqpM embedded in a lipid bilayer permitted predictions to be made of key biophysical parameters including: single channel osmotic permeability constant (pf), single channel diffusive permeability constant (pd), channel radius, potential water occupancy of the channel and water orientation inside the pore. These properties were compared with those of well characterized representatives of the two main aquaporin sub-families. Results show that changes in the amino acid composition of the aromatic/arginine region affect the size and polarity of the selectivity filter (SF) and could help explain the difference in water permeability between aquaporins. In addition, MD simulation results suggest that AqpM combines characteristics of strict aquaporins, such as the narrow SF and channel radius, with those of aquaglyceroporins, such as a more hydrophobic and less polar SF. CONCLUSIONS: MD simulations of AqpM extend previous evidence that this archaeal aquaporin exhibits hybrid features intermediate between the two known aquaporin sub-families, supporting the idea that it may constitute a member of a novel class of aquaporins.

Dataset Information

Molecular dynamics studies of the archaeal translocon.

Publications

Molecular dynamics studies of the archaeal translocon.

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