X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION

J Biol Chem. 2016 Jun 3;291(23):12223-32. doi: 10.1074/jbc.M116.719815. Epub 2016 Apr 18.


Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance.

Keywords: MD simulation; X-ray crystallography; membrane protein; optogenetics; photoreceptor; proton pump; thermal stability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Animals, Genetically Modified
  • Binding Sites / genetics
  • Caenorhabditis elegans / genetics
  • Caenorhabditis elegans / metabolism
  • Crystallography, X-Ray
  • Hot Temperature*
  • Hydrogen Bonding
  • Molecular Dynamics Simulation
  • Optogenetics / methods
  • Protein Domains*
  • Protein Stability
  • Protein Structure, Secondary*
  • Proton Pumps / chemistry
  • Proton Pumps / genetics
  • Proton Pumps / metabolism
  • Rhodopsins, Microbial / chemistry*
  • Rhodopsins, Microbial / genetics
  • Rhodopsins, Microbial / metabolism
  • Sequence Homology, Amino Acid
  • Thermus thermophilus / genetics
  • Thermus thermophilus / metabolism


  • Proton Pumps
  • Rhodopsins, Microbial

Associated data

  • PDB/1C3W
  • PDB/3DDL
  • PDB/5AZD