Specific zinc binding to heliorhodopsin

Calcium Binding to TAT Rhodopsin

(2022) Teppei Sugimoto et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels

(2022) Andrey Rozenberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Heliorhodopsin binds and regulates glutamine synthetase activity

(2022) Shin-Gyu Cho et al.   PLOS BIOLOGY

Proton-transporting heliorhodopsins from marine giant viruses

(2022) Shoko Hososhima et al.   eLife

Heliorhodopsin Helps Photolyase to Enhance the DNA Repair Capacity

(2022) Jin-gon Shim et al.   Microbiology Spectrum

Microbial Rhodopsins: The Last Two Decades

(2021) Andrey Rozenberg et al.   Annual Review of Microbiology

Vibrational spectroscopy analysis of ligand efficacy in human M2 muscarinic acetylcholine receptor (M2R)

(2021) Kota Katayama et al.   Communications Biology

Structure‐affinity insights into the Na + and Ca 2+ interactions with multiple sites of a sodium‐calcium exchanger

(2020) Masayo Iwaki et al.   FEBS Journal

High-resolution structural insights into the heliorhodopsin family

(2020) K. Kovalev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy

(2020) Hideki Kandori   BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN

Structural basis for unique color tuning mechanism in heliorhodopsin

(2020) Tatsuki Tanaka et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Zinc Binding to Heliorhodopsin

(2020) Masanori Hashimoto et al.   Journal of Physical Chemistry Letters

Role of Gln114 in Spectral Tuning of a Long-Wavelength Sensitive Visual Pigment

(2019) Kota Katayama et al.   BIOCHEMISTRY

Crystal structure of heliorhodopsin

(2019) Wataru Shihoya et al.   NATURE

Ligand Binding-Induced Structural Changes in the M2 Muscarinic Acetylcholine Receptor Revealed by Vibrational Spectroscopy

(2019) Kota Katayama et al.   Journal of Physical Chemistry Letters

Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor

(2019) Yasuhiro Onoue et al.   Scientific Reports

Crystal structure of heliorhodopsin 48C12

(2019) Yang Lu et al.   CELL RESEARCH

“In situ” observation of the role of chloride ion binding to monkey green sensitive visual pigment by ATR-FTIR spectroscopy

(2018) Kota Katayama et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Mutation Study of Heliorhodopsin 48C12

(2018) Manish Singh et al.   BIOCHEMISTRY

Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP

(2018) Masayo Iwaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

(2018) Alina Pushkarev et al.   NATURE

Unique Hydrogen Bonds in Membrane Protein Monitored by Whole Mid-IR ATR Spectroscopy in Aqueous Solution

(2017) Shota Ito et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Infrared spectroscopic studies on the V-ATPase

(2015) Hideki Kandori et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Structural basis for Na+ transport mechanism by a light-driven Na+ pump

(2015) Hideaki E. Kato et al.   NATURE

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The role of protein-bound water molecules in microbial rhodopsins

(2013) Klaus Gerwert et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

(2013) Oliver P. Ernst et al.   CHEMICAL REVIEWS

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

(2013) Manuel Doemer et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT

(2013) S. Doki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A light-driven sodium ion pump in marine bacteria

(2013) Keiichi Inoue et al.   Nature Communications

N-Ras Forms Dimers at POPC Membranes

(2012) Jörn Güldenhaupt et al.   BIOPHYSICAL JOURNAL

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

ATR-FTIR Spectroscopy Revealing the Different Vibrational Modes of the Selectivity Filter Interacting with K+ and Na+ in the Open and Collapsed Conformations of the KcsA Potassium Channel

(2012) Yuji Furutani et al.   Journal of Physical Chemistry Letters

Sodium or Lithium Ion-Binding-Induced Structural Changes in the K-Ring of V-ATPase from Enterococcus hirae Revealed by ATR-FTIR Spectroscopy

(2011) Yuji Furutani et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Proton Release Group ofpharaonisPhoborhodopsin Revealed by ATR-FTIR Spectroscopy†

(2009) Yuya Kitade et al.   BIOCHEMISTRY

Interaction between Na+Ion and Carboxylates of the PomA−PomB Stator Unit Studied by ATR-FTIR Spectroscopy

(2009) Yuki Sudo et al.   BIOCHEMISTRY