Editorial Material
Chemistry, Multidisciplinary
Fahmi Himo, Sam P. de Visser
Summary: The article discusses the use of the cluster approach in elucidating enzyme reaction mechanisms, highlighting its strengths and weaknesses, and advocates for its preference as the method of choice in investigating enzymatic reaction mechanisms.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Xiaolu Chen, Dongru Sun, Lanping Gao, Yufen Zhao, Sam P. de Visser, Yong Wang
Summary: DFT calculations reveal that the iodine of cobalt(ii)-iodylarene complexes acts as a directing group via halogen bonding interaction to substrates. A transient 3c-4e bond is formed during oxidation reactions to decrease the activation energy by electron delocalization. Dehydrogenation of dihydroantharacene proceeds via a novel concerted hydride transfer/proton transfer mechanism.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Thien-Kim Le, Jinhyun Kim, Ngoc Anh Nguyen, Thi Huong Ha Nguyen, Eun-Gene Sun, Su-Min Yee, Hyung-Sik Kang, Soo-Jin Yeom, Chan Beum Park, Chul-Ho Yun
Summary: Photobiocatalysis is a green platform for driving redox enzymatic reactions using solar energy without high-cost cofactors. Natural flavins were used as photosensitizers to develop a visible light-driven whole-cell platform for human cytochrome P450 (CYP) photobiocatalysis. The research showed that flavins can mediate light-driven biocatalysis by human CYPs in whole-cell systems, demonstrating the general applicability of solar-powered P450 photobiocatalytic system.
Article
Chemistry, Multidisciplinary
Alecia R. Gee, Isobella S. J. Stone, Tegan P. Stockdale, Tara L. Pukala, James J. De Voss, Stephen G. Bell
Summary: We have achieved efficient oxidation reactions on unactivated carbon-hydrogen bonds by modifying the enzyme structure.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Bashu Dev Pardhe, Kyoung Pyo Kwon, Jong Kook Park, Jun Hyuck Lee, Tae-Jin Oh
Summary: In this study, CYP105D18 was used as a catalyst for the hydroxylation of steroids with H2O2 as a co-substrate. The hydroxylation positions of different steroids were predicted based on experimental data and molecular docking. Mutations in the substrate access channel were performed to improve substrate conversion. The findings provide a basis for the potential application and further engineering of CYP105D18.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Cenyang Han, Wenyou Zhu, Guangcai Ma, Yewen Chen, Xinqi Li, Xiaoxuan Wei, Haiying Yu
Summary: This study elucidates the biotransformation routes of halophenols (XPs) to produce epoxides through cytochrome P450 enzymes (CYPs) and identifies the key factors influencing the epoxidation reactivity, contributing to a comprehensive understanding of the metabolic fate and toxicity of XPs.
Article
Biochemistry & Molecular Biology
Paula Bracco, Hein J. Wijma, Bastian Nicolai, Jhon Alexander Rodriguez Buitrago, Thomas Kluenemann, Agustina Vila, Patrick Schrepfer, Wulf Blankenfeldt, Dick B. Janssen, Anett Schallmey
Summary: By utilizing protein engineering and substrate modifications based on the crystal structure of CYP154C5, researchers were able to alter the regioselectivity of the enzyme in steroid hydroxylation. This change in selectivity was attributed to an alternative binding mode of the steroid in the active site of the mutant enzyme. Additionally, molecular dynamics simulations indicated that higher uncoupling in the mutant enzyme may have been caused by the entrance of water to the active site.
Article
Biochemistry & Molecular Biology
Siyu Di, Shengxian Fan, Fengjie Jiang, Zhiqi Cong
Summary: This article summarizes the importance of the design, mechanism, evolution, application, and perspective of these novel non-natural P450 peroxygenases for the oxidation of non-native substrates.
Article
Biochemistry & Molecular Biology
Justin C. Miller, Mary A. Schuler
Summary: This study identified key residues that toggle SLS and SLAS selectivity in two CYP72A subfamily enzymes from Camptotheca acuminata. The mutations in substrate recognition sequence 1 (SRS1) determine the selectivity, and changes in other regions can also affect enzyme activity towards different substrates. Understanding the determinants of selectivity in these enzymes provides opportunities for more tailored heterologous production of TIAs.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Zhan Song, Meijing Wei, Yinghao Fang, Fuping Lu, Minze Jia, Hui-Min Qin, Shuhong Mao
Summary: Custom exogenous ferredoxin (Fdx) was employed to enhance the conversion rate of 4-androstene-3,17-dione (AD) by facilitating electron transfer between reductase and oxygenase through a newly created conduit. The specific amino acid residues in the multienzyme complex responsible for direct electron transfer (DET) pathways were analyzed and some unique residues from the reductase or ferredoxin domains were identified. The electrostatic interactions in mutant MT2 (Y110R in KshA, T85D in DmFdx2) were strengthened using an iterative saturation mutagenesis (ISM) strategy. Moreover, Fdx was proposed as a scaffold for immobilization and self-assembly of the multi-enzyme complex, leading to increased AD conversion rates.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Jie Chen, Sheng Dong, Wenhan Fang, Yiping Jiang, Zhifeng Chen, Xiangquan Qin, Cong Wang, Haifeng Zhou, Longyi Jin, Yingang Feng, Binju Wang, Zhiqi Cong
Summary: We report the selective hydroxylation of alkylbenzenes using an engineered P450 peroxygenase driven by a dual-functional small molecule (DFSM). By combining different P450BM3 variants with DFSMs, more than half of all possible hydroxylated products were obtained from each substrate with high regioselectivity (>99%), enantioselectivity (>99% ee), and high total turnover numbers (up to 80963). Synergistic effects between exogenous DFSMs and the protein environment controlled the regio- and enantioselectivity, as revealed by crystal structure analysis, molecular dynamic simulations, and theoretical calculations. This work has implications for exogenous-molecule-modulated enzymatic regiodivergent and enantioselective hydroxylation with potential applications in synthetic chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Rosa Espinoza, Mark A. Maskeri, Aneta Turlik, Anjanay Nangia, Yogan Khatri, John Montgomery, K. N. Houk, David H. Sherman
Summary: This study reports the ability of bacterial P450 TamI L295A to switch between different oxidizing species in the synthesis of new tirandamycin antibiotics. By providing experimental evidence and theoretical calculations, new insights into the active oxidant species used by P450 TamI are revealed, providing new understanding of the oxidative decorations of tirandamycin.
Article
Biochemistry & Molecular Biology
Peter D. Giang, Luke R. Churchman, Jeanette E. Stok, Rochelle M. Soo, James J. De Voss
Summary: A study found that Rhodococcus globerulus (R. globerulus) isolated from soil beneath Eucalyptus sp. can thrive on mono-terpenes such as 1,8-cineole, p-cymene and (R)- and (S)-limonene as its sole sources of carbon and energy. The research revealed a novel cytochrome P450 (CYP108N12) in R. globerulus which may be responsible for initiating the biodegradation of structurally similar monoterpene compounds. This finding suggests that CYP108N12 has potential as a biocatalyst with specific hydroxylation capabilities.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Chemistry, Physical
Chun-Chi Chen, Meng Dai, Lilan Zhang, Jing Zhao, Wei Zeng, Min Shi, Jian-Wen Huang, Weidong Liu, Rey-Ting Guo, Aitao Li
Summary: We investigated the mechanism of the P450tol enzyme from Rhodococcus coprophilus TC-2, which can hydroxylate toluene at the benzylic site. We solved the crystal structures of P450tol and its complex with the substrate, revealing how P450tol restricts the binding position of toluene and enables precise hydroxylation at the benzylic site. Additionally, we found that P450tol can also hydroxylate larger substrates and synthesized a self-sufficient chimeric enzyme with improved activity and stability. These findings highlight the potential of P450tol in biotechnological and pharmaceutical applications.
Article
Chemistry, Physical
Shinya Ariyasu, Kai Yonemura, Chie Kasai, Yuichiro Aiba, Hiroki Onoda, Yuma Shisaka, Hiroshi Sugimoto, Takehiko Tosha, Minoru Kubo, Takashi Kamachi, Kazunari Yoshizawa, Osami Shoji
Summary: This study reports the catalytic oxidation of methane to methanol by wild-type P450BM3 without mutagenesis. The findings have significant implications for the development of biological methane oxidation technology.
Review
Chemistry, Multidisciplinary
Thomas C. Pochapsky, Susan Sondej Pochapsky
ACCOUNTS OF CHEMICAL RESEARCH
(2019)
Article
Microbiology
Brian Shing, Seema Singh, Larissa M. Podust, James H. McKerrow, Anjan Debnath
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2020)
Article
Cell Biology
Xiaochao Tan, Priyam Banerjee, Edward A. Pham, Florentine U. N. Rutaganira, Kaustabh Basu, Neus Bota-Rabassedas, Hou-Fu Guo, Caitlin L. Grzeskowiak, Xin Liu, Jiang Yu, Lei Shi, David H. Peng, B. Leticia Rodriguez, Jiaqi Zhang, Veronica Zheng, Dzifa Y. Duose, Luisa M. Solis, Barbara Mino, Maria Gabriela Raso, Carmen Behrens, Ignacio I. Wistuba, Kenneth L. Scott, Mark Smith, Khanh Nguyen, Grace Lam, Ingrid Choong, Abhijit Mazumdar, Jamal L. Hill, Don L. Gibbons, Powel H. Brown, William K. Russell, Kevan Shokat, Chad J. Creighton, Jeffrey S. Glenn, Jonathan M. Kurie
SCIENCE TRANSLATIONAL MEDICINE
(2020)
Meeting Abstract
Biochemistry & Molecular Biology
Vandna Sharma, Brian Shing, Anjan Debnath, Larissa Podust
Editorial Material
Biochemistry & Molecular Biology
Christina M. Termini, Melanie R. McReynolds, Florentine U. N. Rutaganira, ReAnna S. Roby, Antentor O. Hinton Jr, Calvin S. Carter, Sunny C. Huang, Zer Vue, Denise Martinez, Haysetta D. Shuler, Brittany L. Taylor
Summary: The success of scientific endeavors heavily relies on mentorship, which has traditionally been conducted through in-person interactions. The COVID-19 pandemic has caused disruptions in the research environment, prompting mentors to adapt their methods to support trainee growth and development in uncertain times.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Review
Biochemical Research Methods
Thomas C. Pochapsky
Summary: Many economically important biosyntheses require regiospecific and stereospecific oxidations at unactivated carbons, which are commonly catalyzed by cytochrome P450 monooxygenases. High-resolution solution nuclear magnetic resonance (NMR) provides insights into the dynamic processes and conformational changes needed by P450 enzymes to achieve the specificity and efficiency necessary for these reactions.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Christina M. Termini, Florentine U. N. Rutaganira, Caroline B. Palavicino-Maggio, Chelsey C. Spriggs, Chantell S. Evans, Melanie R. McReynolds
Summary: Virtual interviewing is now common in the academic job market, and it is important for candidates and departments to consider best practices when using this method. Virtual interviews can be leveraged and adapted for hybrid academic job searches combining virtual and in-person activities in a post-pandemic world.
Article
Chemistry, Multidisciplinary
Daniel Leichnitz, Chia-Chi Peng, Luka Raguz, Florentine U. N. Rutaganira, Theresa Jautzus, Lars Regestein, Nicole King, Christine Beemelmanns
Summary: In this study, bacterial sulfonosphingolipids, including rosette-inducing factors (RIFs), were analyzed in seven bacterial prey strains using high-resolution tandem mass spectrometry and molecular networking. Six RIF-like compounds were isolated and their structures elucidated, with two RIF-2 diastereomers and one congener being successfully synthesized for the first time. Bioactivity studies revealed that the rosette inducing activity of RIFs is specifically inhibited by co-occurring sulfonosphingolipids in choanoflagellate Salpingoeca rosetta.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Microbiology
Jingwei Xu, Charles F. Ericson, Yun-Wei Lien, Florentine U. N. Rutaganira, Fabian Eisenstein, Miki Feldmueller, Nicole King, Martin Pilhofer
Summary: The characterization of an extracellular contractile injection system (eCIS) from the marine bacterium Algoriphagus machipongonensis (AlgoCIS) reveals structural features linked to the assembly and function of this nanomachine. The study shows that the eCIS system has unique features, including a 'cap adaptor', a 'plug', and a 'cage', which are conserved in other CISs. These elements play important roles in assembly, cargo loading, and function.
NATURE MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Luka Raguz, Chia-Chi Peng, Florentine U. N. Rutaganira, Thomas Kruger, Aleksa Stanisic, Theresa Jautzus, Hajo Kries, Olaf Kniemeyer, Axel A. Brakhage, Nicole King, Christine Beemelmanns
Summary: The study developed a synthetic compound IOR-1A that inhibits rosette formation in S.rosetta and demonstrated the biochemical basis of cell differentiation processes within S.rosetta through the synthesis of derivatives and evaluation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Guadalupe Alvarez, Thu Le, Nathan Wong, Julian Echave, Thomas C. Pochapsky, Eliana K. Asciutto
Summary: This study investigates the effects of mutations near the active site on the catalytic activity of Cytochrome P450(cam) in the oxidation reaction. Computational experiments and in vitro site-directed mutations were used to examine the reaction products and enzyme activity. The results show that all mutant enzymes retained the same regio- and stereospecificity as the wild type enzyme, but with varying degrees of efficiency, indicating that large portions of the enzyme have evolved to achieve efficient oxidation reaction.
Editorial Material
Biochemistry & Molecular Biology
Alfred Mays, Angela Byars-Winston, Antentor Hinton Jr, Andrea G. Marshall, Annet Kirabo, Avery August, Bianca J. Marlin, Blake Riggs, Blanton Tolbert, Celestine Wanjalla, Chad Womack, Chantell S. Evans, Christopher Barnes, Chrystal Starbird, Clintoria Williams, Corey Reynolds, Cornelius Taabazuing, Craig E. Cameron, Debra D. Murray, Derek Applewhite, Derrick J. Morton, Dexter Lee, Dionna W. Williams, Donald Lynch, Donita Brady, Erin Lynch, Florentine U. N. Rutaganira, Gustavo M. Silva, Haysetta Shuler, Ishmail Abdus Saboor, Jamaine Davis, Kafui Dzirasa, Latanya Hammonds-Odie, Loretta Reyes, Mariya T. Sweetwyne, Melanie R. McReynolds, Michael D. L. Johnson, Nathan A. Smith, Nikea Pittman, Olujimi A. Ajijola, Quinton Smith, Rena A. S. Robinson, Samantha C. Lewis, Sandra A. Murray, Sherilynn Black, Sonya E. Neal, Stanley Andrisse, Steven Townsend, Steven M. Damo, Theanne N. Griffith, W. Marcus Lambert, William M. Clemons Jr
Summary: We, 52 Black scientists, address the significance of Juneteenth in the field of STEMM and shed light on the challenges, hardships, and lack of acknowledgement faced by Black scientists. We examine the historical presence of racism in scientific practices and propose institutional-level solutions to alleviate the burdens on Black scientists.
Article
Biochemistry & Molecular Biology
Xinyue Liu, Abigail Garber, Julia Ryan, Aditi Deshpande, Dagmar Ringe, Thomas C. Pochapsky
Meeting Abstract
Chemistry, Multidisciplinary
Joshua Corpuz, Larissa Podust, Matt Jaremko, Tony Davis, Michael Burkart
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Review
Chemistry, Inorganic & Nuclear
Xinyue Liu, Thomas C. Pochapsky