Article
Biochemistry & Molecular Biology
Yusuke Nakasone, Hiroto Murakami, Shunrou Tokonami, Takashi Oda, Masahide Terazima
Summary: The signaling route and dynamics of photoactivated adenylate cyclases (PACs) from Oscillatoria acuminata (OaPAC) were studied. It was found that the diffusion coefficient and enzymatic activity of OaPAC were dependent on light intensity, and a mutation in the W90 residue suppressed these changes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Shunrou Tokonami, Morihiko Onose, Yusuke Nakasone, Masahide Terazima
Summary: The study revealed slow reaction kinetics in milliseconds for all examined BLUF proteins, contrary to previous beliefs of nanosecond red shifts. The slower dynamics in the tau(2)-phase were found to be strongly influenced by the size and nature of the C-terminal region adjacent to the BLUF domain, indicating its importance for biological functions. These results highlight the significance of Trp in the BLUF domain and propose a reaction scheme for BLUF reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biology
Masaki Tsujimura, Yoshihiro Chiba, Keisuke Saito, Hiroshi Ishikita
Summary: This study investigates proton transfer and induced structural changes in heliorhodopsin using quantum mechanical/molecular mechanical approach and molecular dynamics simulations. The results suggest that light-induced proton transfer occurs from the Schiff base to Glu107, followed by reorientation of Ser76 and subsequent proton transfer to His80. Protonation of His80 induces reorientation of Trp246 on the extracellular surface and structural fluctuation on the intracellular side.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zijing Chen, Xiu-Wen Kang, Yalin Zhou, Zhongneng Zhou, Siwei Tang, Shuhua Zou, Kailin Wang, Jiulong Huang, Bei Ding, Dongping Zhong
Summary: Proton relays through H-bond networks are crucial in protein machines. In this study, we designed a proton rocking blue light and used ultrafast spectroscopy to analyze the individual proton-transfer steps. We found that the proton jumps from E-COOH to FMN- rapidly, followed by a second proton transfer from WH+ to E-COO-, which immediately rocks back to W•. Our findings provide insights into the Grotthuss mechanism on the ultrafast timescale.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Dale Green, Palas Roy, Christopher R. Hall, James N. Iuliano, Garth A. Jones, Andras Lukacs, Peter J. Tonge, Stephen R. Meech
Summary: Flavoproteins that absorb blue light play crucial roles in various photobiological processes. Detailed studies on the excited state structure and dynamics have been conducted, especially through time-resolved vibrational spectroscopy. Although there is generally good agreement between calculated and observed enhancements, some prominently enhanced bands are absent from the calculations, indicating the need for further theoretical development.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Biochemistry & Molecular Biology
Jinnette Tolentino Collado, James N. Iuliano, Katalin Pirisi, Samruddhi Jewlikar, Katrin Adamczyk, Gregory M. Greetham, Michael Towrie, Jeremy R. H. Tame, Stephen R. Meech, Peter J. Tonge, Andras Lukacs
Summary: This study investigates the photoactivation mechanism of OaPAC and reveals the direct connection between BLUF photoactivation and the structural and functional implications on the partner protein. The results demonstrate the formation of an intermediate species on the photoactivation pathway and highlight the essential role of proton transfer in initiating structural reorganization and AC activity.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: A novel strategy was designed to compute TRIR spectra of photoreceptors by combining different types of molecular dynamics, revealing that the dynamic Stokes shift of flavin is ultrafast and mainly driven by the internal reorganization of the chromophore.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Mingzhen Zhang, Hyunbum Jang, Zhigang Li, David B. Sacks, Ruth Nussinov
Summary: In the presence of 14-3-3, the interaction with B-Raf stabilizes the RBD-CRD-KD interaction, interfering with the KD dimerization. The release of RBD-CRD promotes KD fluctuations and reorientation for dimerization, suggesting a mechanism where one KD monomer is donated by 14-3-3-free B-Raf KD and the other by 14-3-3-bound KD.
Article
Microbiology
Jihye Yang, Sohyeon Yun, Woojun Park
Summary: The presence or absence of BlsA protein in Acinetobacter species genomes has raised curiosity about its role in regulating bacterial lifestyle under light. Genetic and transcriptomic analyses revealed the loss of BlsA in several multidrug-resistant strains and the light-mediated induction of blsA. Furthermore, the study identified a potential interaction partner of BlsA, BipA, and confirmed their direct interactions under specific conditions.
Article
Chemistry, Physical
Patrizia Mazzeo, Shaima Hashem, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: In this study, we propose a new method that combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method to investigate the excited-state dynamics of molecules embedded in complex matrices. We apply this method to the photoactivation of the blue-light-using flavin (BLUF) domain of the AppA protein and demonstrate the presence of a proton-coupled electron transfer (PCET) process, which has been suggested in other BLUF proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Chemistry, Multidisciplinary
Andras Lukacs, Peter J. Tonge, Stephen R. Meech
Summary: Researchers used time-resolved infrared experiments to investigate the signaling mechanism of light activated proteins. They discovered that the photosensing mechanism of blue light using flavin (BLUF) domain proteins involves non-single-exponential relaxation and a sequential electron and double proton transfer. They also achieved control over the photoactivation process through mutagenesis and unnatural amino acid substitution, and observed real-time changes in protein structural dynamics.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Isabella M. Acquistapace, Emma J. Thompson, Imke Kuhn, Mike R. Bedford, Charles A. Brearley, Andrew M. Hemmings
Summary: The role of the proton donor residue in determining the stereospecificity of the AppA phytase enzyme was investigated. Mutations in the proton donor residue strongly influenced the enzyme's activity and preference for different substrates. High-resolution crystal structures provided evidence for the importance of the proton donor residue in regulating specificity pockets A and B.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Katalin Pirisi, Lipsa Nag, Zsuzsanna Fekete, James N. Iuliano, Jinnette Tolentino Collado, Ian P. Clark, Ildiko Pecsi, Pierre Sournia, Ursula Liebl, Gregory M. Greetham, Peter J. Tonge, Stephen R. Meech, Marten H. Vos, Andras Lukacs
Summary: Tryptophan and tyrosine radical intermediates are crucial in biological charge transfer processes and can be studied using ultrafast visible and infrared spectroscopy. Recent studies have observed the formation of neutral tyrosine radicals in biological processes and, in a few systems, the formation of cation tyrosine radicals. Transient infrared spectroscopy shows sensitivity to specific radicals at low concentrations, as demonstrated in various studies.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Regine Hengge
Summary: Bacteria use a combination of local and global c-di-GMP signaling to create a complex signaling network, allowing for specific parallel pathways. Local c-di-GMP signaling is defined by specific knockout phenotypes, direct protein interactions, and cellular c-di-GMP levels remaining below a certain threshold. Adaptive changes in signaling network architecture can further enhance signaling flexibility.
TRENDS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Jennifer Boehm, Soenke Scherzer
Summary: The article summarizes the significant advances in plant electrical signal transduction, focusing on the carnivorous Venus flytrap. It examines different types of electrical signals, their underlying ion fluxes, and summarizes the carnivorous processes downstream of the electrical signals.
Article
Plant Sciences
Ivo H. M. van Stokkum, Michal Gwizdala, Lijin Tian, Joris J. Snellenburg, Rienk van Grondelle, Herbert van Amerongen, Rudi Berera
PHOTOSYNTHESIS RESEARCH
(2018)
Article
Plant Sciences
Alonso M. Acuna, Claire Lemaire, Rienk van Grondelle, Bruno Robert, Ivo H. M. van Stokkum
PHOTOSYNTHESIS RESEARCH
(2018)
Article
Plant Sciences
Lucyna M. Wlodarczyk, Joris J. Snellenburg, Jan P. Dekker, Ivo H. M. Stokkum
PHOTOSYNTHESIS RESEARCH
(2018)
Article
Plant Sciences
Alonso M. Acuna, Pascal van Alphen, Filipe Branco dos Santos, Rienk van Grondelle, Klaas J. Hellingwerf, Ivo H. M. van Stokkum
PHOTOSYNTHESIS RESEARCH
(2018)
Article
Multidisciplinary Sciences
Lijin Tian, Wojciech J. Nawrocki, Xin Liu, Iryna Polukhina, Ivo H. M. van Stokkum, Roberta Croce
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Plant Sciences
Avratanu Biswas, Xinpeng Huang, Petar H. Lambrev, Ivo H. M. van Stokkum
PHOTOSYNTHESIS RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
Juan M. Artes Vivancos, Ivo H. M. Van Stokkum, Francesco Saccon, Yusaku Hontani, Miroslav Kloz, Alexander Ruban, Rienk van Grondelle, John T. M. Kennis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Multidisciplinary Sciences
Patrick E. Konold, Enis Arik, Jorn Weissenborn, Jos C. Arents, Klaas J. Hellingwerf, Ivo H. M. van Stokkum, John T. M. Kennis, Marie Louise Groot
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Physical
Ivo H. M. van Stokkum, Chanelle C. Jumper, Tia S. Lee, Mykhaylo Myahkostupov, Felix N. Castellano, Gregory D. Scholes
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Ivo H. M. van Stokkum, Miroslav Kloz, Dario Polli, Daniele Viola, Jorn Weissenborn, Ebo Peerbooms, Giulio Cerullo, John T. M. Kennis
Summary: A new methodology is presented to fully describe the time evolution of electronically and vibrationally excited states detected by ultrafast transient absorption in various systems. By global fit of experimental data, important vibrational frequencies in molecular systems are revealed. The enhanced method provides a balanced approach between theoretical description and fit of experimental data, aiding in the interpretation of molecular dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Nanoscience & Nanotechnology
Simon Christian Boehme, Nadine Tchamba Yimga, Achidi Frick, Susann Gunst, Harald Untenecker, John T. M. Kennis, Ivo H. M. van Stokkum, Peer Kirsch, Elizabeth von Hauff
Summary: The chemical structure at the molecular scale does not influence the molecular frontier orbitals or ultrafast dynamics of the FFPTB backbone, but does result in differences in structural and electrical properties of the FFPTB films at the macroscale. The altered location of the fluorine substitution allows for control of the electrostatic potential along the molecular backbone, impacting molecular interactions and achieving ambipolar transport in FFPTB films.
ADVANCED ELECTRONIC MATERIALS
(2021)
Article
Chemistry, Physical
Ivo H. M. van Stokkum, Yusaku Hontani, Johannes Vierock, Benjamin S. Krause, Peter Hegemann, John T. M. Kennis
Summary: In this study, the reaction dynamics of Chrimson channelrhodopsin were analyzed from femtoseconds to seconds. Multiple phases in the decay of excited state were identified, and early dynamics of K-like species on a 10 ps time scale were observed. Selective excitation at different wavelengths resulted in distinct spectral features, which gradually became indistinguishable over time. Protein motions underlying inhomogeneous broadening were resolved, demonstrating a dynamic interconversion between protein substates.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Ivo H. M. van Stokkum, Jorn Weissenborn, Sebastian Weigand, Joris J. J. Snellenburg
Summary: This article introduces a Python framework for global and target analysis of time-resolved spectra, demonstrating its ability to resolve vibrational wavepackets and associated spectra and phases. The framework has reliability and usability, making it an important tool for understanding complex molecular systems.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Ivo H. M. Van Stokkum, Marc G. Mueller, Jorn Weissenborn, Sebastian Weigand, Joris J. Snellenburg, Alfred R. Hozwarth
Summary: This study establishes a general kinetic scheme for energy transfer and trapping in cyanobacterial PSI under different light conditions. The results show that the presence of Chl f compartments in PSI under far-red light conditions leads to a decrease in charge separation rate and delayed trapping.
Article
Biochemistry & Molecular Biology
Joris J. Snellenburg, Matthew P. Johnson, Alexander V. Ruban, Rienk van Grondelle, Ivo H. M. van Stokkum
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2017)