Article
Chemistry, Multidisciplinary
Golam Moula, Ayaka Nagasaki, Tsuyoshi Matsumoto, Matthias E. Miehlich, Karsten Meyer, Roger E. Cramer, Kazuyuki Tatsumi
Summary: The construction of synthetic models of the nitrogenase P-N-cluster has been a long-standing challenge, and the closest mimic constructed to date is the optimal nitrogenase P-N-cluster model represented by cluster 2. The model has been characterized by X-ray crystallography and relevant physico-chemical methods, revealing its magnetic and Mossbauer spectrum properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Christian Trncik, Tanja Mueller, Philipp Franke, Oliver Einsle
Summary: This study presents the crystal structure of the ADP-bound reductase component AnfH of the iron-only nitrogenase and compares it with other iron protein homologs. The results show that all three iron proteins adopt the same conformation. Cross-reactivity assays reveal that AnfH is compatible with iron-only nitrogenase and to a lesser degree with the vanadium-containing enzyme, but not with molybdenum nitrogenase.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Kresimir Rupnik, Lee Rettberg, Kazuki Tanifuji, Johannes G. Rebelein, Markus W. Ribbe, Yilin Hu, Brian J. Hales
Summary: NifB, a radical SAM enzyme, is involved in the biosynthesis of the L cluster and contains the characteristic motifs associated with SAM binding. The study of NifB reveals the mechanism of L cluster biosynthesis through interaction with SAM.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Valerie Waser, Manjistha Mukherjee, Nico V. Igareta, Ryo V. Tachibana, Thomas R. R. Ward
Summary: Researchers designed and assembled an artificial [Fe4S4]-containing Fischer-Tropsch catalyst using biotin-streptavidin technology. They synthesized a stable bis-biotinylated [Fe4S4] cofactor and incorporated it in streptavidin. The effect of the protein environment on catalytic activity was investigated, and the catalyst exhibited up to 14 turnovers for the reduction of CO2 to hydrocarbons.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Biochemistry & Molecular Biology
Markus W. Ribbe, Kamil Gorecki, Mario Grosch, Joseph B. Solomon, Robert Quechol, Yiling A. Liu, Chi Chung Lee, Yilin Hu
Summary: This review provides an overview of the properties and functions of the Fe protein, highlighting its relevance to areas related to catalysis, biosynthesis, and applications in the nitrogenase system.
Article
Chemistry, Inorganic & Nuclear
Alexandra C. Brown, Daniel L. M. Suess
Summary: Reported in this paper are alkyne and alkene adducts of synthetic [Fe4S4]+ clusters that mimic intermediates and inhibitorbound states in enzymes involved in isoprenoid biosynthesis. Spectroscopic analysis shows that both clusters have similar properties to the related species in isoprenoid biosynthetic enzymes. This study contributes to the understanding of the reaction mechanism of enzymes that interact with pi-acidic molecules.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Youngsuk Kim, Arun Sridharan, Daniel L. M. Suess
Summary: This study reports the synthesis of a three-member series of isostructural mononitrosylated [Fe4S4] clusters and reveals the significance of mononitrosylated intermediates in NO sensing/signaling.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
News Item
Biochemistry & Molecular Biology
Alexander Leitner
Summary: Chemical probes are valuable tools for identifying ligand-binding and drug-target sites on proteins, and a new software has been developed to evaluate their performance in chemoproteomic applications.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daniel S. Trettel, William Resager, Beatrix M. Ueberheide, Conor C. Jenkins, Wade C. Winkler
Summary: Bacterial microcompartments (BMCs) are structures found in bacteria that are used for various metabolic purposes. By using chemical probes, the structure of a native BMC was observed, revealing that the shell layer is more dynamic than previously thought. Analysis of cross-linking chemical probes showed a complex multivalent network among cargo proteins, supporting the idea that biomolecular condensation drives interactions between cargo and shell proteins before encapsulation.
Article
Microbiology
Ana Perez-Gonzalez, Emilio Jimenez-Vicente, Jakob Gies-Elterlein, Alvaro Salinero-Lanzarote, Zhi-Yong Yang, Oliver Einsle, Lance C. Seefeldt, Dennis R. Dean
Summary: Azotobacter vinelandii can produce three genetically distinct components for nitrogen fixation, with metal-specific assembly scaffolds required for Mo-dependent and V-dependent components but not for the Fe-only component. The FeFe-cofactor associated with the Fe-only component does not require intermediate assembly sites, highlighting its simplicity and potential for transferring nitrogen fixation into plants.
Article
Chemistry, Multidisciplinary
Congli Wang, Zhenghan Di, Zhichu Xiang, Jian Zhao, Lele Li
Summary: This study introduces an extremely simple approach for co-delivery of proteins and nucleic acids into cancer cells by one-step, coordination-driven self-assembly, resulting in significant inhibition of tumor growth in vivo. The platform offers efficient co-encapsulation of the two macromolecular components with high loading content and tunable ratios, showing great potential for personalized medicine.
Article
Chemistry, Multidisciplinary
Dor Zaguri, Manuela R. Zimmermann, Georg Meisl, Aviad Levin, Sigal Rencus-Lazar, Tuomas P. J. Knowles, Ehud Gazit
Summary: The study found that the aggregation propensity of three phenylalanine-containing molecules increases significantly with size, with triphenylalanine being the most aggregation-prone species under experimental conditions. In the context of classical nucleation theory, this increase in aggregation propensity is attributed to the larger free energy decrease upon aggregation of larger peptides, and not to the presence/absence of a peptide bond per se. This work provides insights into the aggregation processes of chemically simple systems and suggests that both backbone-containing peptides and backbone-lacking amino acids assemble through a similar mechanism, supporting the classification of amino acids in the continuum of amyloid-forming building blocks.
Article
Biochemistry & Molecular Biology
Dorothy E. D. P. Hawkins, Oliver W. Bayfield, Herman K. H. Fung, Daniel N. Grba, Alexis Huet, James F. Conway, Alfred A. Antson
Summary: Double-stranded DNA viruses utilize terminase proteins to package viral DNA into the capsid. In this study, the first structural data for a cos virus DNA packaging motor was presented, showing the assembly of terminase proteins, procapsids with the portal protein, and DNA with a cos site. The cryo-EM structure revealed the termination state of packaging and the asymmetry induced by the binding of large terminase/DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Chengpin Liang, Jielin Chen, Mingqiang Li, Zhilei Ge, Chunhai Fan, Jianlei Shen
Summary: This study utilized the thermal hysteresis method to investigate the self-assembly process of amphiphilic DNA nanostructures. It was found that under different ionic strengths, amphiphilic DNA strands initially formed metastable micelles through an entropy-driven process, which then transformed into amphiphilic tetrahedral DNA frameworks.
CHEMICAL COMMUNICATIONS
(2022)
Article
Microbiology
Amrit Koirala, Volker S. Brozel
Summary: The study analyzed the phylogeny of diazotrophs using both structural and cofactor assembly proteins of nitrogenase, revealing wide distribution of these genes across different bacterial phyla and archaeal phyla, validating the co-evolution of assembly proteins and showing undocumented horizontal gene transfers across phyla.
Article
Biochemistry & Molecular Biology
Kresimir Rupnik, Kazuki Tanifuji, Lee Rettberg, Markus W. Ribbe, Yilin Hu, Brian J. Hales
Review
Chemistry, Multidisciplinary
Kazuki Tanifuji, Yasuhiro Ohki
Article
Multidisciplinary Sciences
Lee A. Rettberg, Jarett Wilcoxen, Andrew J. Jasniewski, Chi Chung Lee, Kazuki Tanifuji, Yilin Hu, R. David Britt, Markus W. Ribbe
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Wonchull Kang, Lee A. Rettberg, Martin T. Stiebritz, Andrew J. Jasniewski, Kazuki Tanifuji, Chi Chung Lee, Markus W. Ribbe, Yilin Hu
Summary: NifB is a crucial radical SAM enzyme for nitrogenase cofactor assembly, and the X-ray crystal structures of MtNifB reveal insights into the mechanism of cofactor biosynthesis. The coordinated binding of SAM in holo MtNifB suggests important pathways for SAM cleavage and cofactor core formation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Jasper Liedtke, Chi Chung Lee, Kazuki Tanifuji, Andrew J. Jasniewski, Markus W. Ribbe, Yilin Hu
Summary: This study presents a biochemical and spectroscopic characterization of a Mo-nitrogenase variant with a citrate-substituted cofactor analogue, revealing the impact of citrate substitution on CO and N2 reduction pathways. The results suggest a crucial role of homocitrate in substrate reduction by nitrogenase and the potential to modulate product profiles of nitrogenase reactions through organic ligand substitution.
Article
Biochemistry & Molecular Biology
Kresimir Rupnik, Lee Rettberg, Kazuki Tanifuji, Johannes G. Rebelein, Markus W. Ribbe, Yilin Hu, Brian J. Hales
Summary: NifB, a radical SAM enzyme, is involved in the biosynthesis of the L cluster and contains the characteristic motifs associated with SAM binding. The study of NifB reveals the mechanism of L cluster biosynthesis through interaction with SAM.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shahid Shahid, Mahbbat Ali, Desiree Legaspi-Humiston, Jarett Wilcoxen, A. Andrew Pacheco
Summary: The decaheme enzyme cytochrome c nitrite reductase facilitates the reduction of nitrite to ammonium with different kinetics of intermediate formation when strong or weak reductants are used, indicating its complex mechanism influenced by the catalyst.
Article
Chemistry, Multidisciplinary
Kazuki Tanifuji, Andrew J. Jasniewski, David Villarreal, Martin T. Stiebritz, Chi Chung Lee, Jarett Wilcoxen, Yasuhiro Okhi, Ruchira Chatterjee, Isabel Bogacz, Junko Yano, Jan Kern, Britt Hedman, Keith O. Hodgson, R. David Britt, Yilin Hu, Markus W. Ribbe
Summary: The study investigates the insertion of the 'ninth sulfur' in the biosynthesis of cofactors, revealing its role in cluster transfer and the incorporation of Se2- and Te2- species into the cluster. The research also proposes a mechanism involving the reduction of SO32- to S2- for labeling the catalytically important belt region for nitrogenase mechanistic investigations.
Article
Chemistry, Physical
Chi Chung Lee, Wonchull Kang, Andrew J. Jasniewski, Martin T. Stiebritz, Kazuki Tanifuji, Markus W. Ribbe, Yilin Hu
Summary: This study provides direct evidence that N2 is captured on the M-cluster via electron and sulfur depletion, and the N2-captured state is catalytically active in generating NH3. The study also reveals the conditions for product release and the dynamic changes of belt-sulfurs during catalysis. These findings highlight the crucial role of the mobilization of cofactor belt-sulfurs in the nitrogenase reaction.
Review
Biotechnology & Applied Microbiology
Jonathan Tellechea-Luzardo, Martin T. Stiebritz, Pablo Carbonell
Summary: Advances in synthetic biology and genetic engineering have led to the development of transcription factor (TF)-based biosensors, which are promising tools for detecting chemical compounds and eliciting specific responses. However, widespread use of these biosensors is hindered by challenges that can be addressed by increasing knowledge of metabolite-activated transcription factors, identifying new transcription factors, and improving the design workflow for biosensor circuits. These improvements are especially important in the bioproduction field, where better biosensor-based approaches are needed for screening and regulation. This work summarizes the current understanding of TF-based biosensors, discusses recent experimental and computational approaches for modification and improvement, and suggests future research directions for bioproduction screening and genetic circuit regulation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Joseph B. Solomon, Mahtab F. Rasekh, Caleb J. Hiller, Chi Chung Lee, Kazuki Tanifuji, Markus W. Ribbe, Yilin Hu
Summary: The Fe proteins MaNifH and MaVnfH from Methanosarcina acetivorans exhibit different reactivities towards C1 substrates in the all-ferrous state, with MaVnfH showing weaker reactivity due to adopting the all-ferrous state at a more positive reduction potential. This suggests the possibility of MaVnfH accessing the all-ferrous state under physiological conditions, which has implications for the reaction mechanism of nitrogenase.
