Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation

Elife. 2016 May 16;5:e15598. doi: 10.7554/eLife.15598.

Abstract

The essential process of protein secretion is achieved by the ubiquitous Sec machinery. In prokaryotes, the drive for translocation comes from ATP hydrolysis by the cytosolic motor-protein SecA, in concert with the proton motive force (PMF). However, the mechanism through which ATP hydrolysis by SecA is coupled to directional movement through SecYEG is unclear. Here, we combine all-atom molecular dynamics (MD) simulations with single molecule FRET and biochemical assays. We show that ATP binding by SecA causes opening of the SecY-channel at long range, while substrates at the SecY-channel entrance feed back to regulate nucleotide exchange by SecA. This two-way communication suggests a new, unifying 'Brownian ratchet' mechanism, whereby ATP binding and hydrolysis bias the direction of polypeptide diffusion. The model represents a solution to the problem of transporting inherently variable substrates such as polypeptides, and may underlie mechanisms of other motors that translocate proteins and nucleic acids.

Keywords: E. coli; SecA; SecYEG; biochemistry; biophysics; molecular dynamics; protein secretion; protein translocation; single molecule FRET; structural biology.

MeSH terms

  • Adenosine Diphosphate / chemistry
  • Adenosine Diphosphate / metabolism
  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism
  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / metabolism
  • Amino Acid Motifs
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Gene Expression
  • Kinetics
  • Methanocaldococcus / genetics
  • Methanocaldococcus / metabolism*
  • Models, Molecular
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Interaction Domains and Motifs
  • Protein Transport
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • SEC Translocation Channels / chemistry*
  • SEC Translocation Channels / genetics
  • SEC Translocation Channels / metabolism
  • SecA Proteins
  • Substrate Specificity
  • Thermodynamics
  • Thermotoga maritima / genetics
  • Thermotoga maritima / metabolism*

Substances

  • Bacterial Proteins
  • Recombinant Proteins
  • SEC Translocation Channels
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Adenosine Triphosphatases
  • SecA Proteins