Article
Biotechnology & Applied Microbiology
Tomoya Maeda, Abigail Koch-Koerfges, Michael Bott
Summary: The oxidation of NADH and reduction of quinone is crucial for cellular metabolism. In this study with Corynebacterium glutamicum, Ndh was found to be the main enzyme for NADH oxidation, while Mdh and LdhA can functionally replace Ndh. The study also showed that Mdh and LdhA, along with Mqo and LldD, play active roles in NADH oxidation and menaquinone reduction.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Franziska Hoeser, Hannes Tausend, Sinja Gotz, Daniel Wohlwend, Oliver Einsle, Stefan Gunther, Thorsten Friedrich
Summary: Energy-converting NADH: ubiquinone oxidoreductase, respiratory complex I, plays a crucial role in coupling NADH oxidation to proton translocation in cellular energy metabolism. The membrane arm of complex I contains a unique axis of polar and charged amino acid residues that are proposed to catalyze proton translocation. However, our study shows that charge asymmetry is not essential for proton translocation, casting doubts on the previous suggestion of an asynchronous operation of the subunits involved. Our findings highlight the importance of a balanced charge distribution in the protein for directional proton transfer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Chemistry, Multidisciplinary
Etienne Galemou Yoga, Jonathan Schiller, Volker Zickermann
Summary: Complex I is the first enzyme complex of the respiratory chain, functioning as a redox-driven proton pump to generate proton motive force for ATP synthase. The structure of Complex I has been well described, with the ubiquinone reduction site located in the peripheral arm and accessed through a tunnel-like structure. Recent studies have shown interactions between Complex I and ubiquinone at various binding positions along the tunnel and at the reduction site.
FRONTIERS IN CHEMISTRY
(2021)
Review
Chemistry, Medicinal
Jonathan Schiller, Volker Zickermann
Summary: This article summarizes the structure and redox mechanism of respiratory complex I, as well as the binding modes and inhibitory mechanisms of inhibitors in the Q reduction site and Q access pathway. It provides important insights into the crucial protein complex involved in mitochondrial oxidative phosphorylation.
Article
Biochemistry & Molecular Biology
Alexei A. Stuchebrukhov, Tomoyuki Hayashi
Summary: Using quantum chemistry and electrostatic calculations, the pKa of the reduced quinone in the catalytic cavity of complex I is found to be very high, indicating that a single protonation reaction can drive four protons across the membrane. Based on these calculations, a possible scheme of redox-linked proton pumping by complex I is proposed.
Article
Biochemistry & Molecular Biology
Jann-Louis Hau, Susann Kaltwasser, Valentin Muras, Marco S. Casutt, Georg Vohl, Bjoern Claussen, Wojtek Steffen, Alexander Leitner, Eckhard Bill, George E. Cutsail, Serena Debeer, Janet Vonck, Julia Steuber, Guenter Fritz
Summary: This study reveals that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. This mechanism is of significant importance for NADH oxidation in the human pathogen Vibrio cholerae.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Environmental Sciences
Jinghao Wang, Huimin Liu, Song Song, Yuancai Chen, Yongyou Hu
Summary: Microbial electron output capacity is crucial for the degradation of organic contaminants. The incorporation of Pd(0) has been found to enhance electron output and improve the degradation ability of C. freundii JH towards sulfamethoxazole (SMX). The presence of Pd(0) alters the electron flow, resulting in intensified electron output and reduced ecotoxicity of SMX in the environment.
Article
Microbiology
Bo-Chen Chen, Zhi-Shan Ding, Jian-Sheng Dai, Ni-Pi Chen, Xing-Wen Gong, Lie-Feng Ma, Chao-Dong Qian
Summary: Cryptotanshinone (CT) is a bacteriostatic agent that targets the cell membrane and may act as a respiratory chain inhibitor, specifically by targeting type II NADH:quinone dehydrogenase (NDH-2). Combination therapy involving CT and other inhibitors targeting different components of the bacterial respiratory chain shows promising synergistic activities against Staphylococcus aureus.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Renata Plocinska, Karolina Wasik, Przemyslaw Plocinski, Ewelina Lechowicz, Magdalena Antczak, Ewelina Blaszczyk, Bozena Dziadek, Marcin Slomka, Anna Rumijowska-Galewicz, Jaroslaw Dziadek
Summary: This study investigates the role of the orphan response regulator Rv3143 in the physiology of Mycobacterium tuberculosis and Mycobacterium smegmatis. The results suggest that Rv3143 interacts with NuoD and modulates its activity. Deletion of Rv3143 and msmeg_2064 leads to increased sensitivity to reactive nitrogen species and valinomycin, as well as increased reduction of the electron acceptor TTC. Silencing of ndh expression affects cell survival under limited oxygen conditions.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Plant Sciences
J. S. Amthor
Summary: This study investigates the mechanism and factors influencing the ATP yield of plant respiration through a numerical balance sheet model. The results suggest that the ATP yield is often lower than previously estimated, leading to an underestimation of substrate requirements for active processes. Further research is needed to determine the size of the plant mitochondrial ATP synthase c-ring and the bypasses of energy-conserving reactions in the respiratory chain, as well as the magnitude of leaks in the inner mitochondrial membrane.
Article
Biochemistry & Molecular Biology
Franziska Hoeser, Maximilian Weiss, Thorsten Friedrich
Summary: NADH:ubiquinone oxidoreductase (respiratory complex I) is crucial for cellular energy metabolism, and deficiencies in complex I are often associated with mitochondrial dysfunction. In this study, researchers used Escherichia coli as a model system to investigate the effects of a 7 bps inversion in mtND1, which resulted in a triple mutation. The triple mutant showed poor growth and lacked enzymatic activity.
Review
Biology
Flora Kahlhoefer, Max Gansen, Volker Zickermann
Summary: NADH:ubiquinone-oxidoreductase (complex I) is the largest membrane protein complex in the respiratory chain, with mutations in the accessory subunit NDUFS4 in the matrix arm associated with neuromuscular and neurodegenerative diseases.
Article
Chemistry, Multidisciplinary
Franziska Nuber, Luca Merono, Sabrina Oppermann, Johannes Schimpf, Daniel Wohlwend, Thorsten Friedrich
Summary: Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is crucial in cellular energy metabolism by oxidizing NADH and reducing quinone while translocating protons across the membrane. It has an overall L-shaped structure with electron transfer catalyzed by a peripheral arm and proton translocation by a membrane arm. The spatially separated reactions are tightly coupled through a mechanism that is not fully understood.
FRONTIERS IN CHEMISTRY
(2021)
Article
Endocrinology & Metabolism
Tao Yu, Quanli Liu, Xiang Wang, Xiangjian Liu, Yun Chen, Jens Nielsen
Summary: This study demonstrates the establishment of a synthetic decarboxylation cycle in the yeast cytosol, which enhances the production of reduced chemicals. By implementing rational design, metabolic rewiring, and recombinant expression, the researchers achieved a significant increase in free fatty acid yield.
Article
Multidisciplinary Sciences
Bo Zhang, Christopher Lingga, Hannah De Groot, Timothy J. Hackmann
Summary: Propionate, a microbial metabolite formed in the gastrointestinal tract, affects host physiology. This study identifies Rnf as a key oxidoreductase in rumen bacteria, which solves the imbalance of electron carriers and cofactors by oxidizing ferredoxin and reducing NAD.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Joana S. Sousa, Filipa Calisto, Julian D. Langer, Deryck J. Mills, Patricia N. Refojo, Miguel Teixeira, Werner Kuehlbrandt, Janet Vonck, Manuela M. Pereira
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Filipa V. Sena, Filipe M. Sousa, A. Sofia F. Oliveira, Claudio M. Soares, Teresa Catarino, Manuela M. Pereira
Article
Biochemistry & Molecular Biology
Cecilia Jonsson, Ana P. Castor Batista, Preben Kjolhede, Peter Stralfors
BIOCHEMICAL JOURNAL
(2019)
Article
Entomology
Sofia Branco, Eduardo Pires Mateus, Marco Diogo Richter Gomes da Silva, Davide Mendes, Maria Manuela Araujo Pereira, Stefan Schutz, Maria Rosa Paiva
JOURNAL OF APPLIED ENTOMOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Filipe M. Sousa, Patricia N. Refojo, Manuela M. Pereira
Summary: DHOQOs are membrane bound enzymes responsible for oxidizing DHO to orotate and have potential therapeutic applications in cancer, immunological disorders and infections. A thorough bioinformatic study on their structural conservation and taxonomic distribution was conducted, revealing the presence of DHOQOs in Archaea, Eukarya and Bacteria, with proposed new findings on quinone binding motifs.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Review
Chemistry, Multidisciplinary
Filipa Calisto, Filipe M. Sousa, Filipa Sena, Patricia N. Refojo, Manuela M. Pereira
Summary: Life depends on energy transduction, where different membrane proteins exhibit either direct or indirect coupling mechanisms for charge translocation.
Article
Chemistry, Medicinal
Filipe M. Sousa, Luis M. P. Lima, Clement Arnarez, Manuela M. Pereira, Manuel N. Melo
Summary: This work developed coarse-grained parameters for 79 key metabolites/cofactors in different oxidation and protonation states, aiming to boost the biochemical application of coarse-grained simulations by covering important gaps in nucleotide characterization through the measurement of partition and acid-base physicochemical data.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Analytical
Susana A. Lobo, Paulina Baczyk, Brigitte Wyss, Jasmin C. Widmer, Lidia P. Jesus, Joana Gomes, Ana P. Batista, Steffen Hartmann, Paul Wassmann
Summary: Identification of molecular liabilities and implementation of mitigation strategies are essential for pharmaceutical companies developing therapeutic proteins. Streamlined processes like developability assessment are used in selecting the fittest candidate, especially in the field of monoclonal antibodies. Different protein modalities may require a paradigm change towards candidate enabling, with early assessment of liabilities being crucial for project success.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Chemistry, Multidisciplinary
Filipa Calisto, Manuela M. Pereira
Summary: The NrfD-like subunits, connected to the membrane through an integral membrane protein, may act as ion-pumping modules in various microbial enzymes, featuring ion-conducting pathways and quinone/quinol binding sites.
FRONTIERS IN CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Filipa Calisto, Manuela M. Pereira
Summary: Energy transduction is the process of converting energy from one form to another, enabling life to exist. The transmembrane difference of electrochemical potential serves as a universal energy currency. Modular enzymes allow for different catalytic and charge-translocating modules to combine, forming energy-transducing complexes.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Andreia Barreto, Filipe M. Sousa, Manuela M. Pereira
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Manuela M. Pereira
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Filipa Calisto, Simone Graf, Christoph von Ballmoos, Manuela M. Pereira
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Patricia Pires, Filipe M. Sousa, Patricia N. Refojo, Andreia Barreto, Manuela M. Pereira
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Meeting Abstract
Biophysics
Filipe M. Sousa, Patricia N. Refojo, Andreia Barreto, Patricia Pires, Micael Silva, Pedro Fernandes, Ana P. Carapeto, Tiago T. Robalo, Mario S. Rodrigues, Mariana G. Pinho, Eurico J. Cabrita, Manuela M. Pereira
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Brandon P. Russell, David J. Vinyard
Summary: The Mn4CaO5 oxygen-evolving complex in Photosystem II is crucial for water oxidation. D1 residue R334 participates in proton release and interacts with PsbO. A D1-R334G mutant destabilizes the OEC but stabilizes the S2 intermediate.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Alexander A. Bulychev, Tatiana S. Strelets
Summary: Excitable cells of higher plants and characean algae respond to stressful stimuli by generating action potentials that influence chlorophyll fluorescence and photosynthesis for an extended period of time. While plant leaves exhibit a reversible depression in the efficiency of photosystem II reaction after an individual action potential, characean algae show long-lasting oscillations of photosystem II reaction efficiency after firing an action potential. This study investigates the possible mechanisms behind these oscillations and suggests that they are a result of metabolic rearrangements in chloroplasts and the cyclosis cessation-recovery cycle induced by calcium influx during action potentials. The findings also indicate that fluidic communications between different cell regions play a role in these oscillations, and the inhibition of oscillations occurs when these communications are restricted or eliminated.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Dmitry Zlenko, Elena A. Protasova, Georgy Tsoraev, Nikolai N. Sluchanko, Dmitry A. Cherepanov, Thomas Friedrich, Baosheng Ge, Song Qin, Eugene G. Maksimov, Andrew B. Rubin
Summary: The conformation of chromophores in isolated phycobiliproteins is heterogeneous, but not in the entire phycobilisome (PBS). Under low-energy excitation, there is no significant uphill energy transfer from the core to the peripheral rods of the PBS, while transfer from the terminal emitters to bulk allophycocyanin chromophores is highly probable.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Makio Yokono, Chiyo Noda, Jun Minagawa
Summary: This paper investigates the energy transfer between Photosystem II and Photosystem I in Arabidopsis thaliana, and finds that the fast spillover is reversibly regulated depending on pH.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)