Article
Chemistry, Multidisciplinary
Benedikt Prasser, Lisa Schoner, Lin Zhang, Oliver Einsle
Summary: The final step of denitrification involves the reduction of nitrous oxide to N-2 by Cu-dependent nitrous oxide reductase (N2OR). The assembly of N2OR is mediated by a metallochaperone encoded by the nos gene cluster, with Cu-A and Cu-Z metal centers. While only Cu-I is delivered to the enzyme, the presence of Zn-II is crucial for the functionality and structural integrity of the chaperone.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Alex J. Plajer, Andrew D. Bond, Dominic S. Wright
Summary: Phosph(III)azanes with the heterocyclobutane P2N2 ring have been established as building blocks in main-group coordination and supramolecular compounds. The incorporation of electron-withdrawing groups and transition metal coordination to the ring P atoms can modulate proton acidity and anion binding constants. Chelation of metal atoms to the P atoms of certain compounds can significantly enhance anion binding constants, surpassing those of traditional organic receptors like squaramides and ureas.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Physics, Applied
Jong Woo Kim, Mathew J. Cherukara, Ashish Tripathi, Zhang Jiang, Jin Wang
Summary: Coherent surface scattering imaging requires a mathematical conversion to visualize specimen structures, which can now be predicted using a deep learning neural network model to instantly obtain results from scattering patterns. This is highly beneficial for both experimental effectiveness and data analysis.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Cen Chen, Ziyuan Fang, Zhen Huang
Summary: Crystallization phasing and obtaining high-quality crystals are major challenges for X-ray crystallographic analysis of nucleic acids. In this study, the authors addressed these challenges by incorporating selenium atoms into DNA duplexes, which resulted in larger and higher quality crystals compared to standard DNA crystals. These findings provide a simple strategy to overcome crystallization challenges in nucleic acid crystallography.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Multidisciplinary Sciences
Akimitsu Higuchi, Wataru Shihoya, Masae Konno, Tatsuya Ikuta, Hideki Kandori, Keiichi Inoue, Osamu Nureki
Summary: SzRs, a newly identified rhodopsin family in Asgard archaea, exhibit unique kinetic behaviors in inward H+ release compared to other H+ pumps. The crystal structure of SzR AM_5_00977 revealed that key residues and structural features are different from other microbial rhodopsins, suggesting a distinct mechanism for inward H+ release.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Hai Li, Chia-Ying Huang, Elena G. Govorunova, Oleg A. Sineshchekov, Adrian Yi, Kenneth J. Rothschild, Meitian Wang, Lei Zheng, John L. Spudich
Summary: The crystal structure of bromide-bound GtACR1 reveals structural changes that relax the constrictions of the channel and involve a novel salt-bridge switch mechanism. These findings suggest that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark, facilitating channel opening.
Article
Chemistry, Inorganic & Nuclear
Li Zeng-Hui, He Liang, Guo Yu-Jun, Luo Ming-Bu, Lin Qi-Pu
Summary: A new 3D luminescent metal-organic framework with good water stability was synthesized under solvothermal conditions, showing potential as a luminescence sensing material. The compound exhibited an emission peak at 455 nm upon excitation at 370 nm, with a slight redshift compared to the free ligand Py(2)TTz.
CHINESE JOURNAL OF STRUCTURAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Sunbin Deng, Jiaxi Cai, Stephen C. Harrison, Huilin Zhou, Stephen M. Hinshaw
Summary: Successful mitosis relies on the correct attachment of chromosomes to microtubules. The kinetochore plays a crucial role in this process by recognizing specific chromatin and ensuring the formation of only one kinetochore per chromatid at the correct location. The crystal structure of the Cse4 peptide bound to the inner kinetochore Okp1-Ame1 complex provides insights into centromere recognition and the organization of the inner kinetochore.
Article
Biochemistry & Molecular Biology
Supeshala Nawarathnage, Sara Soleimani, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramirez, Parag Gajjar, Derick R. Bunn, Cameron Stewart, Tobin Smith, Maria J. Pedroza Romo, Seth Brown, Tzanko Doukov, James D. Moody
Summary: The study found that TELSAM-target protein fusions crystallize more rapidly and at lower protein concentrations compared to the target protein alone. TELSAM polymers do not need direct contact to form well-diffracting crystals. Fusion to TELSAM polymers can stabilize weak inter-target protein crystal contacts and adjust the helical rise of TELSAM polymers.
Article
Chemistry, Multidisciplinary
Jiali Yang, Takahiro Mori, Xingxing Wei, Yudai Matsuda, Ikuro Abe
Summary: The novel isomerase NsrQ from Aspergillus novofumigatus plays a key role in the biosynthesis of fungal tetrahydroxanthones by catalyzing a two-step isomerization reaction. Through biochemical and structural characterizations, it was found that NsrQ and its homologue Dcr3 utilize Glu and His residues as acid-base catalysts and important hydrophobic residues for shaping the active site pocket for substrate binding. The crystal structures of NsrQ and Dcr3 revealed their cone-shaped alpha + beta barrel fold and similarities to the nuclear transport factor 2-like superfamily enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Oliver F. Harder, Sarah V. Barrass, Marcel Drabbels, Ulrich J. Lorenz
Summary: Microsecond time-resolved cryo-EM allows for observation of fast protein dynamics, as demonstrated by the contraction of the CCMV capsid induced by a pH jump.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Filip Topic, Joseph M. Marrett, Tristan H. Borchers, Hatem M. Titi, Christopher J. Barrett, Tomislav Friscic
Summary: This study presents the first X-ray single crystal structures of hypochlorite and hypobromite salts, shedding light on the solid-state geometry and supramolecular chemistry of hypohalite ions through variable-temperature Raman spectroscopy and periodic density-functional theory calculations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Molly J. McBride, Sarah R. Pope, Kai Hu, C. Denise Okafor, Emily P. Balskus, J. Martin Bollinger, Amie K. Boal
Summary: The study identified the crucial role of SznF in the biosynthesis of streptozotocin, revealing the binding of two iron cofactors and addressing previous uncertainties about the cofactors. During the cofactor (dis)assembly process, dynamic changes in the core helix were observed, and an unexpected glutamate ligand was found to be involved.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Christo N. Nanev, Emmanuel Saridakis, Naomi E. Chayen
Summary: X-ray crystallography is currently the dominant method for determining the structure of proteins and biomolecules. However, it faces challenges in obtaining high-resolution data from small protein crystals. Serial crystallography using XFELs is a promising alternative method that can produce excellent structural data from weakly diffracting objects. In this study, the authors calculate the mean crystal size and growth time needed for batch crystallization, which is the main method for preparing microcrystalline slurries. They also consider the impact of impurities on the growth of microcrystals. Experimental results with lysozyme support the theoretical predictions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Raheel Ahmad, Alexei M. Tyryshkin, Lingjun Xie, William. A. Hansen, Brahm J. Yachnin, Ashraf Mashrai, Sagar D. Khare, Spencer Knapp
Summary: Precise metal-protein coordination by design is challenging. A new method involving the irreversible attachment of bis(1-methylimidazol-2-yl)ethene (BMIE) to cysteine has been developed. This method allows for compact imidazole-based metal-coordinating ligands. The utility of this method has been confirmed through the modification of a model protein, carboxypeptidase G2 (CPG2).
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Madhu Nagaraj, Zahra Najarzadeh, Jonathan Pansieri, Henrik Biverstal, Greta Musteikyte, Vytautas Smirnovas, Steve Matthews, Cecilia Emanuelsson, Janne Johansson, Joel N. Buxbaum, Ludmilla Morozova-Roche, Daniel E. Otzen
Summary: The study analyzes the impact of four different human chaperones on the aggregation process of functional amyloids in bacterial biofilms, showing that they primarily target primary nucleation during fibrillation rather than elongation or secondary nucleation, and the inhibition efficiency is correlated with their affinity for monomeric CsgA and FapC.
Article
Crystallography
Amit Kumar, Xu Zhang, Oscar Vadas, Fisentzos A. Stylianou, Nicolas Dos Santos Pacheco, Sarah L. Rouse, Marc L. Morgan, Dominique Soldati-Favre, Steve Matthews
Summary: A model for parasitic motility has been proposed, suggesting that parasite actin is connected to surface adhesins through a glideosome-associated connector protein (GAC). GAC is responsible for transmitting force to surface adhesins, rather than generating force. Proper connection between actin and adhesins is crucial for motility and invasion.
Article
Biochemistry & Molecular Biology
Ian R. Kelsall, Elisha H. McCrory, Yingqi Xu, Cheryl L. Scudamore, Sambit K. Nanda, Paula Mancebo-Gamella, Nicola T. Wood, Axel Knebel, Stephen J. Matthews, Philip Cohen
Summary: The E3 ligase activity of HOIL-1 is essential for preventing the accumulation of toxic polysaccharide deposits, as it ubiquitylates serine and threonine residues in proteins. HOIL-1 can monoubiquitylate glycogen and alpha 1:4-linked maltoheptaose, facilitating their removal from cells and preventing the formation of polyglucosan.
Article
Multidisciplinary Sciences
Peipei Zhang, Xiaohui Zhao, Yawen Wang, Ke Du, Zhihao Wang, Jianfeng Yu, Gang Chang, Steve Matthews, Hongliang Wang, Bing Liu
Summary: The HU protein is crucial for bacterial cell viability and serves as an antibiotic target. This study reveals that Gp46 from bacteriophage SPO1 can inhibit HU, leading to growth defects in bacteria. Through structural analysis, it is found that Gp46 occupies the DNA binding site of HU, thus preventing DNA binding. This discovery provides valuable insights into developing antibacterial and anti-malaria drugs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Zeus Saldana-Ahuactzi, Jorge Soria-Bustos, Veronica I. Martinez-Santos, Jorge A. Yanez-Santos, Ygnacio Martinez-Laguna, Maria Lilia Cedillo-Ramirez, Jose L. Puente, Jorge A. Giron
Summary: This study investigated the role of virulence and global regulators in the regulation of the fimS switch in the human enteropathogenic E. coli (EPEC) strain E2348/69. The results demonstrated that Fis is a negative regulator of type 1 pili (T1P) expression and is likely required for the inversion of the fimS switch.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Fabiola Avelino-Flores, Jorge Soria-Bustos, Zeus Saldana-Ahuactzi, Ygnacio Martinez-Laguna, Jorge A. Yanez-Santos, Maria L. Cedillo-Ramirez, Jorge A. Giron
Summary: The study investigated the influence of various environmental and nutritional signals on the expression of the flagellin gene in EPEC, finding that specific conditions can significantly enhance fliC transcription. When EPEC encounters certain signals in the intestinal niche, it may activate fliC expression to promote growth and colonization in the host.
Article
Cell Biology
Edgardo Madrid-Paulino, Dulce Mata-Espinosa, Juan Carlos Leon-Contreras, Isela Serrano-Fujarte, Sol de Diaz de Leon-Guerrero, Tomas Villasenor, Lucero Ramon-Luing, Jose L. Puente, Leslie Chavez-Galan, Rogelio Hernandez-Pando, Leonor Perez-Martinez, Gustavo Pedraza-Alva
Summary: The transcription factor Klf10 plays a critical role in the survival and infection of Mycobacterium tuberculosis by negatively modulating IFN-gamma levels. Klf10 prevents the reprogramming of macrophages from phagocytosis to macropinocytosis, enhancing bacterial engulfment and bactericidal activity.
JOURNAL OF LEUKOCYTE BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zeus Saldana-Ahuactzi, Leigh A. Knodler
Summary: FoxR is identified as a new member of the AraC/XylS family which regulates xenosiderophore-mediated iron uptake in S. Typhimurium and likely other Enterobacteriaceae members. Under iron-limiting conditions, FoxR acts as a transcriptional activator of foxA, promoting iron uptake by the bacteria.
MOLECULAR MICROBIOLOGY
(2022)
Article
Cell Biology
Kaining Zhang, Shanshan Li, Yawen Wang, Zhihao Wang, Nancy Mulvenna, Hang Yang, Peipei Zhang, Huan Chen, Yan Li, Hongliang Wang, Yongxiang Gao, Sivaramesh Wigneshweraraj, Steve Matthews, Kaiming Zhang, Bing Liu
Summary: In this study, we report a phage-encoded enolase inhibitor protein, Gp60, which can inhibit bacterial growth and peptidoglycan synthesis by disrupting the structure of enolase. This phage-inspired disassembly of enolase represents an alternative strategy for the development of antimicrobial drugs.
Article
Multidisciplinary Sciences
Georg Meisl, Catherine K. Xu, Jonathan D. Taylor, Thomas C. T. Michaels, Aviad Levin, Daniel Otzen, David Klenerman, Steve Matthews, Sara Linse, Maria Andreasen, Tuomas P. J. Knowles
Summary: The study reveals that both disease-related proteins and proteins with functional roles in biology are capable of self-replication. However, the rate of self-replication is insignificant on the biologically relevant time scale for proteins fulfilling structural roles, while disease-related proteins can self-replicate quickly within the associated disease's time scale.
Article
Biochemistry & Molecular Biology
Xeni Miliara, Takashi Tatsuta, Akinori Eiyama, Thomas Langer, Sarah L. Rouse, Steve Matthews
Summary: The PRELID-TRIAP1 family is responsible for lipid transfer in mitochondria. The lipid binding is mediated by an extended, water-mediated hydrogen bonding network. Disruption of this network by mutation R53E results in lipid release from the protein.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
Rajesh Mondal, Zeus Saldana-Ahuactzi, Jorge Soria-Bustos, Andrew Schultz, Jorge A. Yanez-Santos, Ygnacio Martinez Laguna, Maria L. Cedillo-Ramirez, Jorge A. Giron
Summary: The study suggests that EPEC attaches to host intestinal epithelial cells through the tip adhesin protein EcpD and binds to host ECM glycoproteins and mucins. The findings highlight the versatility of EPEC in binding to different host proteins and indicate that the interaction between ECP and the host's ECM glycoproteins may facilitate colonization of the intestinal mucosal epithelium.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Cristina Lara-Ochoa, Alejandro Huerta-Saquero, Abraham Medrano-Lopez, Wanyin Deng, B. Brett Finlay, Ygnacio Martinez-Laguna, Jose L. Puente
Summary: This study investigates the regulatory mechanism of attaching and effacing (A/E) lesions formed by EPEC, EHEC, and CR. The results suggest that the interaction between GrlR and GrlA plays an important role in the regulation of LEE genes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Karina Espinosa-Mazariego, Zeus Saldana-Ahuactzi, Sara A. A. Ochoa, Bertha Gonzalez-Pedrajo, Miguel A. A. Cevallos, Ricardo Rodriguez-Martinez, Mariana Romo-Castillo, Rigoberto Hernandez-Castro, Ariadnna Cruz-Cordova, Juan Xicohtencatl-Cortes
Summary: This study aimed to determine whether E. coli BL21 (ECBL) transformed with lng operon lacking lngA gene (pE9034A Delta lngA) and complemented in trans with lngA variants of ETEC clinical strains, as well as point substitutions, exhibited modified adherence to HT-29 cells.