Protein control of photochemistry and transient intermediates in phytochromes

Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome

(2022) Jakub Rydzewski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization

(2022) Dmitry Morozov et al.   Journal of Physical Chemistry Letters

Ultrafast proton-coupled isomerization in the phototransformation of phytochrome

(2022) Yang Yang et al.   Nature Chemistry

Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model

(2022) Ludmila A. Kasatkina et al.   Nature Communications

Improved fluorescent phytochromes for in situ imaging

(2022) Soshichiro Nagano et al.   Scientific Reports

A red light–responsive photoswitch for deep tissue optogenetics

(2022) Yuto Kuwasaki et al.   NATURE BIOTECHNOLOGY

High-resolution crystal structures of transient intermediates in the phytochrome photocycle

(2021) Melissa Carrillo et al.   STRUCTURE

The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

(2021) Kun Tang et al.   CHEMICAL REVIEWS

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

(2021) Lisandro H. Otero et al.   Science Advances

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Optogenetic regulation of endogenous proteins

(2020) Taras A. Redchuk et al.   Nature Communications

The Lumi-R Intermediates of Prototypical Phytochromes

(2020) Francisco Velazquez Escobar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

(2020) Elin Claesson et al.   eLife

The Origin of Ultrafast Multiphasic Dynamics in Photoisomerization of Bacteriophytochrome

(2020) Dihao Wang et al.   Journal of Physical Chemistry Letters

Signaling Mechanism of Phytochromes in Solution

(2020) Linnéa Isaksson et al.   STRUCTURE

Bacteriophytochromes – from informative model systems of phytochrome function to powerful tools in cell biology

(2019) Geoffrey Gourinchas et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching

(2019) Emil Gustavsson et al.   BIOPHYSICAL JOURNAL

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

(2019) Martina Legris et al.   Nature Communications

On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome

(2018) Heikki Takala et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Coordination of the biliverdin D-ring in bacteriophytochromes

(2018) Nils Lenngren et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) Tai-Sung Lee et al.   Journal of Chemical Information and Modeling

Tinker 8: Software Tools for Molecular Design

(2018) Joshua A. Rackers et al.   Journal of Chemical Theory and Computation

Chromophore–Protein Interplay during the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy

(2018) Janne A. Ihalainen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome

(2018) Nicole C. Woitowich et al.   IUCrJ

The photocycle of orange carotenoid protein conceals distinct intermediates and asynchronous changes in the carotenoid and protein components

(2017) E. G. Maksimov et al.   Scientific Reports

Bacteriophytochrome Photoisomerization Proceeds Homogeneously Despite Heterogeneity in Ground State

(2016) Cheng Wang et al.   BIOPHYSICAL JOURNAL

Steric Effects Govern the Photoactivation of Phytochromes

(2016) Olle Falklöf et al.   CHEMPHYSCHEM

Crystal Structure of Deinococcus Phytochrome in the Photoactivated State Reveals a Cascade of Structural Rearrangements during Photoconversion

(2016) E. Sethe Burgie et al.   STRUCTURE

Light-induced structural changes in a monomeric bacteriophytochrome

(2016) Heikki Takala et al.   Structural Dynamics

Structural photoactivation of a full-length bacterial phytochrome

(2016) A. Bjo rling et al.   Science Advances

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful

(2015) Katrin Anders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes

(2015) Francisco Velazquez Escobar et al.   Nature Chemistry

Crystallographic and Electron Microscopic Analyses of a Bacterial Phytochrome Reveal Local and Global Rearrangements during Photoconversion

(2014) E. Sethe Burgie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Femto- to Microsecond Photodynamics of an Unusual Bacteriophytochrome

(2014) Tilo Mathes et al.   Journal of Physical Chemistry Letters

Signal amplification and transduction in phytochrome photosensors

(2014) Heikki Takala et al.   NATURE

Phytochromes: An Atomic Perspective on Photoactivation and Signaling

(2014) E. Sethe Burgie et al.   PLANT CELL

An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces

(2014) Maurizio Persico et al.   THEORETICAL CHEMISTRY ACCOUNTS

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

Fluorescence Properties of the Chromophore-Binding Domain of Bacteriophytochrome from Deinococcus radiodurans

(2013) Heli Lehtivuori et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Real-Time Tracking of Phytochrome’s Orientational Changes During Pr Photoisomerization

(2012) Yang Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bacterial phytochromes: More than meets the light

(2011) Michele E. Auldridge et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Phytochrome signaling: solving the Gordian knot with microbial relatives

(2011) Richard D. Vierstra et al.   TRENDS IN PLANT SCIENCE

Structure and Function of Plant Photoreceptors

(2010) Andreas Möglich et al.   Annual Review of Plant Biology

A Brief History of Phytochromes

(2010) Nathan C. Rockwell et al.   CHEMPHYSCHEM

Engineered photoreceptors as novel optogenetic tools

(2010) Andreas Möglich et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome

(2010) K. C. Toh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

(2009) X. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct classes of red/far-red photochemistry within the phytochrome superfamily

(2009) N. C. Rockwell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromophore Heterogeneity and Photoconversion in Phytochrome Crystals and Solution Studied by Resonance Raman Spectroscopy

(2008) David von Stetten et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Mutational Analysis ofDeinococcus radioduransBacteriophytochrome Reveals Key Amino Acids Necessary for the Photochromicity and Proton Exchange Cycle of Phytochromes

(2008) Jeremiah R. Wagner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY