Single molecule kinetics of bacteriorhodopsin by HS-AFM

Nat Commun. 2021 Dec 10;12(1):7225. doi: 10.1038/s41467-021-27580-2.


Bacteriorhodopsin is a seven-helix light-driven proton-pump that was structurally and functionally extensively studied. Despite a wealth of data, the single molecule kinetics of the reaction cycle remain unknown. Here, we use high-speed atomic force microscopy methods to characterize the single molecule kinetics of wild-type bR exposed to continuous light and short pulses. Monitoring bR conformational changes with millisecond temporal resolution, we determine that the cytoplasmic gate opens 2.9 ms after photon absorption, and stays open for proton capture for 13.2 ms. Surprisingly, a previously active protomer cannot be reactivated for another 37.6 ms, even under excess continuous light, giving a single molecule reaction cycle of ~20 s-1. The reaction cycle slows at low light where the closed state is prolonged, and at basic or acidic pH where the open state is extended.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriorhodopsins / chemistry*
  • Biophysics
  • Cytoplasm / metabolism
  • Hydrogen-Ion Concentration
  • Ion Transport
  • Kinetics
  • Light
  • Microscopy, Atomic Force / methods*
  • Molecular Dynamics Simulation
  • Nanotechnology
  • Protein Conformation
  • Proton Pumps / chemistry
  • Receptors, Opioid
  • Single Molecule Imaging / methods*


  • Proton Pumps
  • Receptors, Opioid
  • Bacteriorhodopsins