Article
Chemistry, Inorganic & Nuclear
Chaemin Lee, Sung Chul Ha, Zhili Rao, Yunha Hwang, Da Som Kim, So Young Kim, Heeseon Yoo, Chungwoon Yoon, Jeong-Geol Na, Jung Hee Park, Seung Jae Lee
Summary: MMOR-a reductase plays a crucial role in the catalytic cycle of soluble methane monooxygenase by facilitating electron transfer to the hydroxylase diiron center. The X-ray structure analysis of the FAD-binding domain of MMOR identified crucial residues and their influence on the catalytic cycle.
DALTON TRANSACTIONS
(2021)
Article
Biotechnology & Applied Microbiology
Peng Peng, Junwon Yang, Alan A. Dispirito, Jeremy D. Semrau
Summary: The oxidation of methane by aerobic methanotrophs is regulated by the availability of copper. MmoD plays a critical role in the maturation of soluble methane monooxygenase and controls the expression of methanobactin. These findings provide insights into the components of the copper switch and offer new strategies for manipulating methanotrophic activity.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Olivia M. Manley, Haoyu Tang, Shan Xue, Yisong Guo, Wei-chen Chang, Thomas M. Makris
Summary: BesC is a member of an emerging family of diiron enzymes that catalyze an unusual type of carbon-carbon cleavage reaction. It activates O-2 in a substrate-gated manner to generate a diferric-peroxo intermediate, initiating a unique reaction trajectory by cleaving the C4-H bond as the rate-limiting step in a single turnover reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biotechnology & Applied Microbiology
Chaemin Lee, Yunha Hwang, Hyun Goo Kang, Seung Jae Lee
Summary: The hydroxylation of methane is crucial in environmental microbiology, and soluble methane monooxygenase (sMMO) plays a significant role in this process. The interaction between MMOH and MMOR, as well as the key residues in MMOR, are important for the electron transfer pathway.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Panu Pimviriyakul, Aritsara Jaruwat, Penchit Chitnumsub, Pimchai Chaiyen
Summary: The X-ray structure of wild-type HadA co-complexed with reduced FAD and 4-nitrophenol was solved, providing insights into its catalytic mechanism. The study also identified a novel structural motif of quadruple pi-stacking and highlighted the importance of specific residues for catalysis. The disruption of the pi-stacking motif in a variant increased enzyme activity, suggesting potential applications for future improvement of HadA's biocatalytic capabilities.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Inorganic & Nuclear
Han Sol Jeong, Sugyeong Hong, Hee Seon Yoo, Jin Kim, Yujeong Kim, Chungwoon Yoon, Seung Jae Lee, Sun Hee Kim
Summary: Methane monooxygenase plays a crucial role in the global carbon cycle by converting methane to methanol, reducing greenhouse effects. This study investigated the electronic structures of two cofactors in MMOR and unveiled their catalytic mechanisms in methane hydroxylation through EPR spectroscopy analysis.
INORGANIC CHEMISTRY FRONTIERS
(2021)
Article
Biochemistry & Molecular Biology
Michael A. Hough, Robin L. Owen
Summary: Approximately half of proteins contain metal, with X-ray crystallography being the major method for obtaining high-resolution structures of these metalloproteins. Serial crystallography offers the potential to determine low-dose synchrotron or XFEL structures and enables time-resolved or dose-resolved approaches.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
Atiya Banerjee, Qun Liu, John Shanklin, Mehmed Z. Ertem
Summary: This study investigates the electronic structures of nonheme diiron complexes by evaluating two key parameters, namely isomer shift (δ) and quadrupole splitting (ΔE(Q)), using density functional theory. The results show that the B97-D3/def2-TZVP model accurately predicts the δ and ΔE(Q) values for nonheme diiron complexes.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Inorganic & Nuclear
Williamson N. Oloo, Miklos Szavuly, Jozsef Kaizer, Lawrence Que
Summary: This study describes a substrate oxidation reaction catalyzed by [Fe-II(IndH)(CH3CN)(3)](ClO4)(2) with H2O2, involving a spectroscopically characterized intermediate capable of olefin epoxidation and alkane hydroxylation. The research identified a direct nucleophilic attack of the substrate carbonyl group by the peroxo species. Additionally, the study found that the high-valent iron-oxo oxidant derived from O-O bond cleavage of the peroxo intermediate contributes to the oxidative reactivities associated with nonheme diiron enzymes.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Williamson N. Oloo, Miklos Szavuly, Jozsef Kaizer, Lawrence Que
Summary: This study elucidates the substrate oxidations catalyzed by [Fe-II(IndH)(CH3CN)(3)](ClO4)(2) with H2O2, resulting in the formation of a spectroscopically characterized (mu-oxo)(mu-1,2-peroxo)diiron(III) intermediate capable of various oxidative reactions including epoxidation and hydroxylation.
INORGANIC CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Yunha Hwang, Jeong-Geol Na, Seung Jae Lee
Summary: This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. The purified enhancer-binding protein (MmoR) and transcription factor (s54) were used to elucidate the mechanism of transcription regulation in sMMO. Characterization studies identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. The findings demonstrate that MmoR functions as a trigger for sMMO expression due to its high specificity and selectivity for enhancer-binding sequences. The binding events of both MmoR and s54 are influenced by copper ion concentration.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Anirban Chandra, Mursaleem Ansari, Ines Monte-Perez, Subrata Kundu, Gopalan Rajaraman, Kallol Ray
Summary: The study explores the reactivity of mu-1,2-peroxo-bridged diiron(III) intermediates P as reactive intermediates in various biological oxidation reactions, showcasing both electrophilic and nucleophilic reactions. It also highlights the ability of mu-1,2-peroxo-bridged dimetal complexes to effect deformylation of aldehydes in biomimetic studies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Engineering, Environmental
Yixiang Wang, V. Joseph Puthussery, Haoran Yu, Yicen Liu, Sudheer Salana, Vishal Verma
Summary: The study revealed that urban cellular oxidative potential is mainly influenced by secondary organic aerosols, while rural and roadside areas are primarily affected by agricultural activities and road dust, respectively. However, these sources contribute minimally to PM2.5 mass.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Review
Chemistry, Multidisciplinary
Rahul Banerjee, John D. Lipscomb
Summary: Rigorous substrate selectivity in enzyme catalysis is attributed to the favorable process of substrate binding to the enzyme active site based on complementary physiochemical characteristics. However, this selectivity becomes more difficult to rationalize for diminutive molecules with too narrow a range of physical characteristics.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jason C. Jones, Rahul Banerjee, Ke Shi, Manny M. Semonis, Hideki Aihara, William C. K. Pomerantz, John D. Lipscomb
Summary: This study investigates the interactions between MMOR and MMOB with sMMOH by specific modifications and F-19 NMR technology. The findings suggest a new regulatory model for the methane conversion cycle, where MMOR and MMOB competitively bind to sMMOH with similar affinity, allowing the transient formation of reactive complexes to advance the reaction cycle.
Article
Chemistry, Multidisciplinary
Saikat Bag, Himadri Sekhar Sasmal, Sonu Pratap Chaudhary, Kaushik Dey, Dominic Blaette, Roman Guntermann, Yingying Zhang, Miroslav Poloz, Agnieszka Kuc, Ankita Shelke, Ratheesh K. Vijayaraghavan, Thalasseril G. Ajithkumar, Sayan Bhattacharyya, Thomas Heine, Thomas Bein, Rahul Banerjee
Summary: We successfully synthesized uniform covalent organic framework (COF) thin films using a solution-processable sphere transmutation process, which exhibited good crystallinity, porosity, and uniform thickness on a fluorine-doped tin oxide (FTO) surface. Four different COF thin films with different functional backbones were synthesized, and the TpEtBr COF film showed the lowest optical band gap and highest excited-state lifetime. All of the COF films exhibited significant photocurrent after illumination with visible light, indicating good photoactive characteristics. The out-of-plane photodetector device based on the TpEtBr COF thin film showed high photocurrent density and hole mobility, demonstrating the best photoactive properties.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Asmit Bhowmick, Rana Hussein, Isabel Bogacz, Philipp S. Simon, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D. Doyle, Mun Hon Cheah, Thomas Fransson, Petko Chernev, In-Sik Kim, Hiroki Makita, Medhanjali Dasgupta, Corey J. Kaminsky, Miao Zhang, Julia Gaetcke, Stephanie Haupt, Isabela I. Nangca, Stephen M. Keable, A. Orkun Aydin, Kensuke Tono, Shigeki Owada, Leland B. Gee, Franklin D. Fuller, Alexander Batyuk, Roberto Alonso-Mori, James M. Holton, Daniel W. Paley, Nigel W. Moriarty, Fikret Mamedov, Paul D. Adams, Aaron S. Brewster, Holger Dobbek, Nicholas K. Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan Kern, Junko Yano, Vittal K. Yachandra
Summary: In natural photosynthesis, the light-driven splitting of water is the first step in converting solar energy into chemical energy. The reaction occurs in photosystem II, where the Mn4CaO5 cluster plays a crucial role in storing oxidizing equivalents and catalyzing the O-O bond formation. By using X-ray crystallography, we observed the structural changes during the S-3 ->[S-4]-> S-0 transition, which is the final step of the Kok's photosynthetic water oxidation cycle. Our findings provide insights into the complex events that occur during this process, including changes in the Mn4CaO5 cluster, ligands, water pathways, and proton release mechanism.
Review
Plant Sciences
Dmitry Shevela, Jan F. Kern, Govindjee Govindjee, Johannes Messinger
Summary: Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process that sustains life on Earth and provides a blueprint for renewable energy applications. In the past two decades, significant progress has been made in the biophysical, computational, and structural understanding of PSII, including high-resolution crystal structures of stable and intermediate states. This article summarizes the current knowledge on PSII, emphasizing the basic principles of energy conversion and molecular structures involved. Remaining questions and a potential molecular pathway for biological water oxidation are discussed.
PHOTOSYNTHESIS RESEARCH
(2023)
Review
Plant Sciences
Rana Hussein, Mohamed Ibrahim, Asmit Bhowmick, Philipp S. Simon, Isabel Bogacz, Margaret D. Doyle, Holger Dobbek, Athina Zouni, Johannes Messinger, Vittal K. Yachandra, Jan F. Kern, Junko Yano
Summary: One reason for the efficiency and selectivity of biological catalysts is their ability to control the pathways of substrates and products using protein channels and modulate transport through interaction with protein residues and the water network. This is demonstrated in Photosystem II (PS II), where the water oxidation reaction occurs deep inside the protein complex and requires transport of water molecules and protons. Structural studies of PS II from different organisms reveal conserved and variable channels for mass transport, suggesting the functionality of these channels in substrate intake and proton release. The O4 channel may play a significant role in proton release based on the hydrogen-bonded water wire connected to the Mn4CaO5 cluster.
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Isabel Bogacz, Hiroki Makita, Philipp S. S. Simon, Miao Zhang, Margaret D. D. Doyle, Ruchira Chatterjee, Thomas Fransson, Clemens Weninger, Franklin Fuller, Leland Gee, Takahiro Sato, Matthew Seaberg, Roberto Alonso-Mori, Uwe Bergmann, Vittal K. K. Yachandra, Jan Kern, Junko Yano
Summary: X-ray crystallography and X-ray spectroscopy are important in understanding the interplay of structural changes in proteins and chemical changes at metal active sites. In this study, we developed methods for X-ray absorption spectroscopy (XAS) to study dilute biological samples using X-ray free electron lasers. Our focus was on Photosystem II (PS II), a membrane protein complex, which catalyzes water oxidation using a Mn4CaO5 cluster. We describe our method for collecting XAS data using PS II samples with a low Mn concentration, employing a drop-on-demand sample delivery method.
PURE AND APPLIED CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Robert B. B. Weakly, Chelsea E. E. Liekhus-Schmaltz, Benjamin I. I. Poulter, Elisa Biasin, Roberto Alonso-Mori, Andrew Aquila, Sebastien Boutet, Franklin D. D. Fuller, Phay J. J. Ho, Thomas Kroll, Caroline M. M. Loe, Alberto Lutman, Diling Zhu, Uwe Bergmann, Robert W. W. Schoenlein, Niranjan Govind, Munira Khalil
Summary: Femtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to study complex electronic and structural dynamics in solvated molecular, biological, and material systems. In this study, the authors successfully realized an ultrafast two-color X-ray pump X-ray probe transient absorption experiment in solution, allowing for the investigation of core-valence interactions in a solvated molecular complex. The results provide valuable insight into the correlated interactions of valence 3d with 3p and deeper-lying electrons, which is crucial for accurate modeling and synthesis of transition metal complexes with various applications.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Marco Reinhard, Alessandro Gallo, Meiyuan Guo, Angel T. Garcia-Esparza, Elisa Biasin, Muhammad Qureshi, Alexander Britz, Kathryn Ledbetter, Kristjan Kunnus, Clemens Weninger, Tim van Driel, Joseph Robinson, James M. Glownia, Kelly J. Gaffney, Thomas Kroll, Tsu-Chien Weng, Roberto Alonso-Mori, Dimosthenis Sokaras
Summary: The authors use femtosecond Fe K beta main line and valence-to-core x-ray emission spectroscopy to characterize a short-lived intermediate of the aqueous ferricyanide photo-aquation reaction.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Margaret D. D. Doyle, Asmit Bhowmick, David C. C. Wych, Louise Lassalle, Philipp S. S. Simon, James Holton, Nicholas K. K. Sauter, Vittal K. K. Yachandra, Jan F. F. Kern, Junko Yano, Michael E. E. Wall
Summary: The structural dynamics of water and its hydrogen-bonding networks are crucial for enzyme function. This study used crystalline molecular dynamics simulations to investigate the water oxidation reaction in Photosystem II (PS II). The simulations provided insights into water mobility and hydrogen-bonding networks, revealing potential pathways for proton transfer during the reaction cycle of PS II. These findings contribute to our understanding of the specific roles of each channel in the water oxidation reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Hugo Lebrette, Vivek Srinivas, Juliane John, Oskar Aurelius, Rohit Kumar, Daniel Lundin, Aaron S. Brewster, Asmit Bhowmick, Abhishek Sirohiwal, In-Sik Kim, Sheraz Gul, Cindy Pham, Kyle D. Sutherlin, Philipp Simon, Agata Butryn, Pierre Aller, Allen M. Orville, Franklin D. Fuller, Roberto Alonso-Mori, Alexander Batyuk, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Ville R. I. Kaila, Britt-Marie Sjoberg, Jan Kern, Katarina Roos, Martin Hogbom
Summary: This study presents a high-resolution room temperature structure of the class Ie R2 protein radical in RNR, revealing conformational reorganization and restructuring of the hydrogen bond network. These findings help explain radical handling and transfer mechanisms in RNR and have implications for radical transfer in proteins more generally.
Review
Chemistry, Multidisciplinary
Asmit Bhowmick, Philipp S. Simon, Isabel Bogacz, Rana Hussein, Miao Zhang, Hiroki Makita, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D. Doyle, Mun Hon Cheah, Petko Chernev, Franklin D. Fuller, Thomas Fransson, Roberto Alonso-Mori, Aaron S. Brewster, Nicolas K. Sauter, Uwe Bergmann, Holger Dobbek, Athina Zouni, Johannes Messinger, Jan Kern, Vittal K. Yachandra, Junko Yano
Summary: This review summarizes recent studies on the catalytic reaction in photosystem II (PS II) using XFELs and X-ray crystallography. The structural changes along the reaction pathway were investigated, including notable changes in the Mn complex, such as the insertion and disappearance of a new water molecule, indicating its involvement in the O-O bond formation reaction. The structural dynamics of the protein coordinating with the catalytic complex and the channels important for substrate and product transport were also observed.
