4.5 Article

Mechanisms of inward transmembrane proton translocation

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins

Valentin Borshchevskiy et al.

Summary: High-resolution structures of bacteriorhodopsin reveal the important roles of hydrogen bond chains and low-barrier hydrogen bonds in proton transport and storage, as well as long-range communication and signaling in proteins.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

Article Multidisciplinary Sciences

Dynamics and mechanism of a light-driven chloride pump

Sandra Mous et al.

Summary: By combining time-resolved crystallography, spectroscopy, and multiscale simulations, we have elucidated the molecular mechanism and structural dynamics of a chloride-pumping rhodopsin throughout the transport cycle. We identified transient anion-binding sites, provided evidence for the use of light energy in the pumping mechanism, and discovered molecular gates that ensure unidirectional transport. These findings reveal key mechanistic features that enable finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.

SCIENCE (2022)

Article Chemistry, Multidisciplinary

The Voltage Dependent Sidedness of the Reprotonation of the Retinal Schiff Base Determines the Unique Inward Pumping of Xenorhodopsin

Juliane Weissbecker et al.

Summary: The new class of microbial rhodopsins, xenorhodopsins (XeRs), extends the versatility of this family by serving as inward H+ pumps, offering an alternative optogenetic tool that can activate electrically excitable cells independently of surrounding physiological conditions. Functional and spectroscopic characterization of NsXeR reveals insights into the photodynamic behavior, pH-dependent kinetics, and potential-dependent vectoriality of photocurrent transients. Mutational studies on the putative intracellular H+ acceptor D220 provide further understanding of the kinetically independent switching mechanism.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

Article Biochemistry & Molecular Biology

Rhodopsin Channel Activity Can Be Evaluated by Measuring the Photocurrent Voltage Dependence in Planar Bilayer Lipid Membranes

Tatyana Rokitskaya et al.

Summary: The study explored the voltage-dependent characteristics of stationary photocurrents for two light-sensitive proteins, bR and ChR2, in the presence of a protonophore. Differences were observed in the photocurrent behavior, with TTFB being more efficient in maximizing stationary photocurrents compared to CCCP.

BIOCHEMISTRY-MOSCOW (2021)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Partial recovery of visual function in a blind patient after optogenetic therapy

Jose-Alain Sahel et al.

Summary: Optogenetics combined with engineered goggles enabled partial recovery of visual function in a blind patient, as demonstrated by object-related brain activity recorded through electroencephalography. This represents the first reported case of partial functional recovery in a neurodegenerative disease after optogenetic therapy.

NATURE MEDICINE (2021)

Article Chemistry, Multidisciplinary

XGANDALF - extended gradient descent algorithm for lattice finding

Yaroslav Gevorkov et al.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2019)

Article Multidisciplinary Sciences

Unique structure and function of viral rhodopsins

Dmitry Bratanov et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Structural insights into ion conduction by channelrhodopsin 2

Oleksandr Volkov et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach

Vitaly Shevchenko et al.

SCIENCE ADVANCES (2017)

Article Multidisciplinary Sciences

A three-dimensional movie of structural changes in bacteriorhodopsin

Eriko Nango et al.

SCIENCE (2016)

Review Biochemistry & Molecular Biology

Bacteriorhodopsin: Would the real structural intermediates please stand up?

Cecilia Wickstrand et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)

Article Biophysics

Crystal Structures of the L1, L2, N, and O States of pharaonis Halorhodopsin

Tsutomu Kouyama et al.

BIOPHYSICAL JOURNAL (2015)

Article Biochemical Research Methods

In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF

David von Stetten et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Review Biochemistry & Molecular Biology

The role of protein-bound water molecules in microbial rhodopsins

Klaus Gerwert et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2014)

Article Multidisciplinary Sciences

Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography

Uwe Weierstall et al.

NATURE COMMUNICATIONS (2014)

Software Review Chemistry, Multidisciplinary

CrystFEL: a software suite for snapshot serial crystallography

Thomas A. White et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2012)

Article Biochemical Research Methods

REFMAC5 for the refinement of macromolecular crystal structures

Garib N. Murshudov et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemical Research Methods

Overview of the CCP4 suite and current developments

Martyn D. Winn et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

X-ray-Radiation-Induced Changes in Bacteriorhodopsin Structure

Valentin I. Borshchevskiy et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Multidisciplinary Sciences

Proton transfer via a transient linear water-molecule chain in a membrane protein

Erik Freier et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

Know your dose: RADDOSE

Karthik S. Paithankar et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemical Research Methods

XDS

Wolfgang Kabsch

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Paul D. Adams et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Chemistry, Physical

Factors Governing Metal-Ligand Distances and Coordination Geometries of Metal Complexes

Gopi Kuppuraj et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Multidisciplinary Sciences

The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment

Luis David Alcaraz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemical Research Methods

Protein production by auto-induction in high-density shaking cultures

FW Studier

PROTEIN EXPRESSION AND PURIFICATION (2005)

Article Multidisciplinary Sciences

Anabaena sensory rhodopsin:: A photochromic color 0 sensor at 2.0 Å

L Vogeley et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Demonstration of a sensory rhodopsin in eubacteria

KH Jung et al.

MOLECULAR MICROBIOLOGY (2003)

Article Biochemistry & Molecular Biology

Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes

A Krogh et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)