H. Kandori

Structural and Dynamic Insights into the Biased Signaling Mechanism of the Human Kappa Opioid Receptor

This study investigates the structural dynamics of the human KOR-Gi signaling complex with G-protein-biased and balanced agonists, identifying key residues involved in signaling bias.

cryo-EM structure of a blue-shifted channelrhodopsin from Klebsormidium nitens.

The paper reports the cryo-EM structure of a blue-shifted channelrhodopsin from Klebsormidium nitens and develops mutants with blue-shifted action spectra.

Structural basis for ion selectivity in potassium-selective channelrhodopsins

The paper determines the cryo-EM structures of two K+-selective channelrhodopsins, revealing a unique mechanism for K+ selectivity distinct from canonical K+ channels.

Energy transfer in ubiquitous rhodopsin pumps with xanthophyll antennas

The paper detects energy transfer from hydroxylated carotenoids to rhodopsin proton pumps in marine and freshwater bacteria.

Proton-transporting heliorhodopsins from marine giant viruses

This paper identifies a light-gated proton channel in a viral heliorhodopsin from Emiliania huxleyi virus 202, showing its potential role in host manipulation and optogenetic applications.

Saccharibacteria harness light energy using Type-1 rhodopsins that may rely on retinal sourced from microbial hosts

The paper identifies Saccharibacteria using Type-1 rhodopsins that pump protons and rely on retinal from microbial hosts, suggesting a symbiotic relationship for energy generation.

Retinal vibrations in bacteriorhodopsin are mechanically harmonic but electronically anharmonic: evidence from overtone and combination bands

The paper studies retinal vibrations in bacteriorhodopsin using IR and Raman spectroscopy, finding electronic anharmonicity explains overtone band intensities better than mechanical anharmonicity.

Heliorhodopsin evolution is driven by photosensory promiscuity in monoderms

This study identifies heliorhodopsins (HeRs) as a novel type-3 rhodopsin family restricted to monoderms, likely functioning as light-dependent switches for stress mitigation and metabolic regulation.

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

The paper reports the crystal structure of schizorhodopsin, revealing its mechanism of inward proton pumping and differences from xenorhodopsins.

Structural basis for no spectral shift of heliorhodopsin by counterion mutation

The paper presents the crystal structure of a HeR mutant with an identical absorption spectrum to wild-type, revealing a unique spectral shift mechanism through counterion and serine cluster interactions.

Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K

This paper uses light-induced difference FTIR spectroscopy to study structural changes in primate blue-sensitive visual pigment (MB) at 163 K, revealing insights into its photochromic properties and structural dynamics.

Unique retinal binding pocket of primate blue-sensitive visual pigment

The paper investigates the unique photochemistry of primate blue-sensitive visual pigment by showing that 9-cis retinal does not form in monkey blue pigment at low temperatures, suggesting structural constraints in its chromophore binding pocket.

Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design

The paper uses a machine learning model to identify red-shifted rhodopsins, finding 80% of selected candidates show red-shift gains, with some having desirable ion-transporting properties.

Structural insights into the mechanism of rhodopsin phosphodiesterase

This study presents the structural and functional analysis of Rh-PDE from Salpingoeca rosetta, revealing its photoactivation mechanism and expanding the definition of rhodopsins.

The sunlit microoxic niche of the archaeal eukaryotic ancestor comes to light

The paper uses phylogenetic analyses and metabolic reconstructions to infer the lifestyle and metabolic environment of the closest archaeal relatives of eukaryotes, revealing microoxic lifestyles and novel metabolic pathways.

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity

The paper examines the presence of heliorhodopsins in diderm bacteria using metagenomic data and finds they are absent, suggesting a possible role in light-driven transport of amphiphilic molecules.