X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin

Scientific Reports
Takefumi MorizumiOliver P Ernst

Abstract

Gloeobacter rhodopsin (GR) is a cyanobacterial proton pump which can be potentially applied to optogenetics. We solved the crystal structure of GR and found that it has overall similarity to the homologous proton pump from Salinibacter ruber, xanthorhodopsin (XR). We identified distinct structural characteristics of GR's hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the transmembrane helices relative to those of XR. Employing Raman spectroscopy and flash-photolysis, we found that GR in the crystals exists in a state which displays retinal conformation and photochemical cycle similar to the functional form observed in lipids. Based on the crystal structure of GR, we selected a site for spin labeling to determine GR's oligomerization state using double electron-electron resonance (DEER) spectroscopy and demonstrated the pH-dependent pentamer formation of GR. Determination of the structure of GR as well as its pentamerizing propensity enabled us to reveal the role of structural motifs (extended helices, 3-omega motif and flipped B-C loop) commonly found among light-driven bacterial pumps in oligomer formation. Here we propose a new concept to classify these pumps based o...Continue Reading

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Citations

Oct 9, 2020·Scientific Reports·Masumi HasegawaSusumu Yoshizawa
Nov 12, 2020·Nature Communications·Matthias BroserPeter Hegemann
Nov 2, 2019·Biochimica Et Biophysica Acta. Biomembranes·Srividya GanapathyWillem J de Grip
Apr 3, 2020·Journal of Microbiology and Biotechnology·Soon-Kyeong KwonJihyun F Kim
Jun 3, 2020·Journal of Microbiology and Biotechnology·Soon-Kyeong KwonJihyun F Kim
Apr 1, 2021·Journal of Chemical Theory and Computation·Eric Sefah, Blake Mertz
Sep 19, 2020·The Journal of Physical Chemistry Letters·Junpei MatsuoMasashi Unno
Jun 29, 2021·Biophysics and Physicobiology·Masashi UnnoJun Tamogami
Jul 2, 2021·Communications Biology·Dmitrii ZabelskiiValentin Gordeliy
Jul 26, 2021·Current Opinion in Structural Biology·Jörg ReichenwallnerOliver P Ernst
Jul 7, 2021·Nature Communications·Stephan HirschiDimitrios Fotiadis

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Methods Mentioned

BETA
X-ray
circular dichroism
electron paramagnetic resonance
AFM
NMR
ESR
size-exclusion chromatography
electron microscopy
gel filtration
PCR

Software Mentioned

CCP4
LongDistances
Multiscale Modeling of Macromolecules ( MMM )
DEER
COOT
Phenix
LabVIEW

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