Review
Engineering, Chemical
Victoria V. Shumyantseva, Polina I. Koroleva, Tatiana V. Bulko, Lyubov E. Agafonova
Summary: The functional significance of cytochrome P450s (CYP) enzymes lies in their ability to catalyze the transformation of foreign and endogenous compounds. They can selectively oxidize C-C and C-H bonds in the presence of oxygen. This review paper discusses alternative handmade electron sources to support P450 catalysis, such as modified electrodes. Solar-powered photobiocatalysis and photoelectrochemical biosensors are also promising light-driven systems.
Article
Chemistry, Physical
Lan Zhang, Christophe V. F. P. Laurent, Lorenz Schwaiger, Lushan Wang, Su Ma, Roland Ludwig
Summary: Direct bioelectrocatalysis involves efficient electron transfer between enzymes and electrodes without the use of redox mediators, and has applications in biosensors, biofuel cells, and bioelectrosynthesis. Cellobiose dehydrogenase (CDH) is a well-studied multidomain bioelectrocatalyst with a catalytic flavodehydrogenase domain and a mobile, electron-transferring cytochrome domain linked by a flexible linker. This study investigates the regulatory mechanism of the linker on electron transfer in CDH and proposes a function-based definition of the linker region. The findings provide insights into optimizing electron transfer rates in multidomain enzymes and enhancing their bioelectrocatalytic performance through rational design of the interdomain linker.
Article
Multidisciplinary Sciences
Philippe Urban, Denis Pompon
Summary: Conformational dynamics is crucial for the function of multidomain electron transfer complexes. Cryo-electron microscopy provides more information on dynamics compared to crystallographic or NMR approaches. AlphaFold has successfully predicted protein complexes, but its ability to address large conformational changes involved in catalysis has been unclear. In this study, a competitive modelling approach (CMA) was used to assess alternate conformations of the bacterial CYP102A1 monooxygenase homodimer. The predictions were compared to crystallographic and cryo-EM data, showing consistencies and allowing reinterpretation of experimental data.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Andre Gemuende, Jonas Gail, Dirk Holtmann
Summary: Vibrio natriegens shows great potential as a biotechnological organism due to its fast growth, high productivity, and availability of genomic tools. It was found that V. natriegens possesses a similar extracellular electron transfer pathway as other electroactive organisms. This study demonstrated for the first time that V. natriegens can transfer electrons to an electrode through direct contact and an artificial redox mediator, highlighting its superior electron-transfer capabilities and metabolism.
Article
Chemistry, Physical
Michael J. Martinez, Jessica D. Carder, Evan L. Taylor, Eric P. Jacobo, ChulHee Kang, J. A. Brozik
Summary: This study measured the thermodynamic driving forces responsible for how strongly CPR partitions into a biomimetic ER with the same lipid composition. Results showed that the redox states of CPR have a significant impact on these driving forces.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Ephrahime S. Traore, Aimin Liu
Summary: This study analyzes the choice of the first coordination shell of the metal center in nonheme iron oxygenases from the perspective of charge maintenance. The importance of charge maintenance after substrate binding is highlighted, and the charge analysis is extended to different types of nonheme iron oxygenases. The concept of charge maintenance is significant in promoting the reaction of the iron center and may be applicable to other oxygen-activating metalloenzymes systems.
Article
Biophysics
Madhura De, Mehmet Ali Ozturk, Sebastian Isbaner, Katalin Toth, Rebecca C. Wade
Summary: This study investigated the effect of linker DNA sequence on the binding of linker histones to nucleosomes. The results showed that linker DNA containing A-tract sequence consistently exhibited higher binding efficiency compared to pure-GC sequences. Furthermore, the study proposed a model to explain the binding mechanism of the globular domain of linker histones with different DNA sequences.
BIOPHYSICAL JOURNAL
(2021)
Editorial Material
Biochemistry & Molecular Biology
F. Peter Guengerich
Summary: The paper introduces the concept of cytochrome b(5) as an auxiliary protein facilitating cytochrome P450 reactions, providing important insights for future research.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Chemistry, Physical
Shaoguang Zhang, Serge Ruccolo, Anna Fryszkowska, Artis Klapars, Nicholas Marshall, Neil A. Strotman
Summary: An electrochemical activation method for galactose oxidase (GOase) was developed to replace the expensive horseradish peroxidase activator in large-scale pharmaceutical processes. The study showed that the electron-transfer rates between GOase and various mediators depend on both the redox potential of the mediator and the pH. The electrochemical GOase activation method was successfully applied to the aerobic oxidation of benzyl alcohol derivatives and other compounds, including a key step in the biocatalytic cascade for the HIV therapeutic islatravir.
Article
Chemistry, Multidisciplinary
Jatin J. Patil, Zhengmao Lu, Michael J. Zachman, Ningxin Chen, Kimberly S. Reeves, Asmita Jana, Griselda Revia, Brandon MacDonald, Brent D. Keller, Edgar Lara-Curzio, Jeffrey C. Grossman, Nicola Ferralis
Summary: Graphene oxide (GO) is a promising membrane material that can be used for chemical separations, including water treatment. However, often chemical modifications are needed to improve the permeability, performance, or mechanical integrity of GO membranes. In this study, we explore two different feedstocks of GO and observe significant improvements in permeability and chemical stability. These findings are connected to differences in sheet stacking and oxide functional groups through various characterization approaches.
Article
Chemistry, Multidisciplinary
Yuan-Yang Guo, Ze-Hua Tian, Yu-Chen Han, Dandan Ma, Tianju Shao, Zhiyong Jiang
Summary: Biocatalysis is a valuable tool for industrial and academic societies, especially in the field of bioredox reactions. The cost of cofactors, especially those that need to be replenished in stoichiometric amounts, is a major concern. This study verifies a readily accessible, inexpensive, and stable Hantzsch ester as an efficient NAD(P)H mimic, which can significantly reduce the costs of NAD(P)H-relying bioredox reactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Organic
Yinghua Li, Jiang Jin, Weibin Fan, Deguang Huang
Summary: A simple method for the synthesis of indolo-[3,2-a]-carbazole-6-carbaldehydes by the pi-extension of indoles with acrolein is reported. The scope and versatility of the method are demonstrated with 33 examples. The resulting products exhibit high activities in advanced synthesis and have proven to be capable of producing valuable natural products, dyes, and organic fluorescent materials. Additionally, the alkaloid racemosin B can be efficiently prepared using this method with a relatively high overall yield of approximately 50%.
Review
Biochemistry & Molecular Biology
Michael E. Runda, Niels A. W. de Kok, Sandy Schmidt
Summary: This review provides a general overview of enzymes that rely on sophisticated electron transfer via ferredoxins (Fds) for catalytic capabilities, with a focus on the Rieske non-heme iron-dependent oxygenases (ROs) family. It discusses the electron transfer principles, catalytic potential, structure-function relationships, and the mode of interaction between redox partner proteins. The review also highlights key catalyzed transformations and explores the engineerability of these enzymes for biocatalytic applications, aiming to stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
Article
Chemistry, Multidisciplinary
Pengkun Su, Heyuan Liu, Li Shen, Jun Zhou, Weijie Wang, Shanshan Liu, Xinyu Nie, Zhi Li, Zhaobin Liu, Yanli Chen, Xiyou Li
Summary: In this study, three dimers with different orientations were synthesized to control the electronic coupling strength and symmetry breaking charge separation (SB-CS) process. The o-dimer could achieve fast SB-CS in weakly polar solvents, while the m-dimer only showed slow SB-CS process in polar solvents. These results are of great importance for developing novel SB-CS materials for practical applications.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Biochemistry & Molecular Biology
Bernadius Agustinus, Elizabeth M. J. Gillam
Summary: With the increasing focus on green chemistry, biocatalysis is being widely used in industries for sustainable production of complex chemicals. Cytochrome P450 monooxygenases (P450s) are attractive biocatalysts that can transform a wide range of substrates in a specific manner. However, their industrial application is limited by the need for costly cofactors. Coupling P450s to plant photosynthesis allows light-generated electrons to drive catalysis, offering new opportunities for carbon-negative and sustainable chemical production.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Guobing Wei, Wenxing Zhang, Hanfeng Cui, Fusheng Liao, Lin Cheng, Guangqiang Ma, Hao Fan, Nian Hong, Jing Zhang
Summary: A novel electrochemical DNA sensor utilizing catalytic hairpin assembly (CHA) and tetraferrocene as a signal marker was developed to achieve signal amplification efficiency. The sensor showed good linear correlation and low detection limit under optimal conditions, with excellent selectivity, reproducibility, and stability.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2022)
Article
Chemistry, Applied
Elisa Vignali, Loredano Pollegioni, Giovanna Di Nardo, Francesca Valetti, Silvia Gazzola, Gianfranco Gilardi, Elena Rosini
Summary: This study reported the first multi-enzymatic, one-pot bioconversion process of vanillin into ccMA, achieving high yield in a lab-scale procedure within 30 hours. This research demonstrates a sustainable alternative for producing high value added products from renewable resources.
ADVANCED SYNTHESIS & CATALYSIS
(2022)
Article
Environmental Sciences
Marta Gea, Chao Zhang, Roberta Tota, Gianfranco Gilardi, Giovanna Di Nardo, Tiziana Schiliro
Summary: The study evaluated the interference of five pesticides on estrogen biosynthesis and estrogen signaling, finding that while the pesticides did not impact aromatase activity, Methiocarb was able to alter estrogen signaling at high doses. This suggests that Methiocarb should be considered a potential endocrine disruptor.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Gianluca Catucci, Alberto Ciaramella, Giovanna Di Nardo, Chao Zhang, Silvia Castrignano, Gianfranco Gilardi
Summary: This study further characterized the 3A4-BMR chimera using differential scanning calorimetry and evaluated the stabilizing role of BMR. The fusion to BMR was found to have a significant effect on thermal stability but a minimal effect on catalytic activity. Different linker loop lengths had an impact on both activity and stability of the chimera, highlighting the importance of careful design and evaluation of P450-BMR chimeras.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Antonino Famulari, Danilo Correddu, Giovanna Di Nardo, Gianfranco Gilardi, Mario Chiesa, Ines Garcia-Rubio
Summary: This study characterized the coordination environment of iron in the isolated CYP116B5 heme domain using continuous wave and advanced EPR techniques. It found that the electronic ground state of CYP116B5hd is similar to classical P450 monooxygenases rather than peroxygenases. The detection of nitrogen-mediated axial coordination explains the similarity to peroxygenases. The findings contribute to the understanding of the distinguishing features between classical P450 enzymes and peroxygenases.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Antonino Famulari, Danilo Correddu, Giovanna Di Nardo, Gianfranco Gilardi, Mario Chiesa, Ines Garcia-Rubio
Summary: This paper documents a dataset obtained from an Electron Paramagnetic Resonance (EPR) study on the electronic properties of a self-sufficient cytochrome P450, CYP116B5hd, which has potential catalytic activity for synthetic purposes. The paper provides raw data, supplementary data, simulation scripts, and detailed descriptions of experimental procedures and instrumental details.
Article
Biochemistry & Molecular Biology
Chao Zhang, Gianfranco Gilardi, Giovanna Di Nardo
Summary: This study reports the capture and spectroscopic characterization of compound I (Cpd I) of human aromatase, highlighting its importance in aromatization reaction. Mutagenesis experiments confirm the involvement of specific residues in proton delivery for Cpd I generation. The data provide new evidences on the role of threonine in oxygen activation in cytochromes P450.
Article
Biotechnology & Applied Microbiology
Gianluca Catucci, Simone Turella, Hanna Cheropkina, Melissa De Angelis, Gianfranco Gilardi, Sheila J. Sadeghi
Summary: In this study, an enzyme with an active site mutation was used to transform indole into indigo or indirubin, providing a green alternative for the production of indigoids.
BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hanna Cheropkina, Gianluca Catucci, Federico Cesano, Arianna Marucco, Gianfranco Gilardi, Sheila J. Sadeghi
Summary: It is advantageous to develop an in vitro platform for predicting the complexity of in vivo systems. The initial step involves identifying a xenobiotic that undergoes monooxygenation through two sequential enzymatic reactions. Pesticides, specifically metabolized by human flavin-containing monooxygenase 1 (hFMO1) and cytochrome P450 (CYP), serve as a suitable model for tandem reactions. By immobilizing hFMO1 on glassy carbon electrodes modified with graphene oxide (GO) and cationic surfactant didecyldimethylammonium bromide (DDAB), the feasibility of the in vitro platform is demonstrated. The bioelectrode successfully catalyzes the expected sulfoxide products of three pesticides and exhibits the ability to mimic complex metabolic reactions of xenobiotics within the human body when tested in a tandem system with hFMO1 and CYP3A4.
BIOELECTROCHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Danilo Correddu, Sabrina Helmy Aly, Giovanna Di Nardo, Gianluca Catucci, Cristina Prandi, Marco Blangetti, Chiara Bellomo, Elisabetta Bonometti, Guido Viscardi, Gianfranco Gilardi
Summary: This study found that the cytochrome P450 BM3 mutants have enhanced and specific epoxidation activity for geraniol and linalool, forming valuable oxidized derivatives, highlighting the significance of these enzymes for industrial applications.