Article
Nanoscience & Nanotechnology
Arjun Rana, Chen-Ting Liao, Ezio Iacocca, Ji Zou, Minh Pham, Xingyuan Lu, Emma-Elizabeth Cating Subramanian, Yuan Hung Lo, Sinead A. Ryan, Charles S. Bevis, Robert M. M. Karl Jr, Andrew J. Glaid, Jeffrey Rable, Pratibha Mahale, Joel Hirst, Thomas Ostler, William Liu, Colum M. O'Leary, Young-Sang Yu, Karen Bustillo, Hendrik Ohldag, David A. Shapiro, Sadegh Yazdi, Thomas E. Mallouk, Stanley J. Osher, Henry C. Kapteyn, Vincent H. Crespi, John V. Badding, Yaroslav Tserkovnyak, Margaret M. Murnane, Jianwei Miao
Summary: The researchers successfully created 138 stable magnetic monopoles on a ferromagnetic meta-lattice and used soft X-ray vector ptycho-tomography to determine their magnetization vector and emergent magnetic field. The study found that the distances between monopole-anti-monopole pairs, monopole-monopole pairs, and anti-monopole-anti-monopole pairs were 18.3 +/- 1.6 nm, 36.1 +/- 2.4 nm, and 43.1 +/- 2.0 nm, respectively. This work demonstrates the potential of ferromagnetic meta-lattices as a platform for studying the interactions and dynamics of magnetic monopoles, and the broad application of soft X-ray vector ptycho-tomography for quantitatively imaging 3D vector fields in magnetic and anisotropic materials at the nanoscale.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Abigail R. Orun, Ethan T. Shields, Sara Dmytriw, Ananya Vajapayajula, Caroline K. Slaughter, Christopher D. Snow
Summary: Researchers have designed isoreticular cocrystals as scaffolds for DNA-binding molecules. These cocrystals have tunable DNA-DNA junctions and can accommodate different guest molecules during crystallization. The design principles can be applied to existing cocrystals to develop programmable scaffolds for DNA-binding molecules.
Article
Biochemistry & Molecular Biology
Ying Yu, Junsong Guo, Zhengjun Cai, Yingchen Ju, Jun Xu, Qiong Gu, Huihao Zhou
Summary: This study utilized fragment screening and X-ray crystallography to identify new building blocks and binding mechanisms for the discovery of new GyrB inhibitors. Some chemical fragments were found to affect enzyme activity, providing new insights for the design of GyrB inhibitors.
BIOORGANIC CHEMISTRY
(2021)
Review
Chemistry, Inorganic & Nuclear
Roberta Cargnelutti, Ricardo F. Schumacher, Andrei L. Belladona, Jean C. Kazmierczak
Summary: This review provides an overview of pyridyl-selenium compounds and their metal complexes in the fields of pharmacology, material science, and technology, covering coordination chemistry, synthetic methodologies, and structural characterization. Relevant direct applications in nanomaterial preparation, organic synthesis catalysis, photocatalytic hydrogen production, and oxygen activation are also discussed.
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Davide Michieletto, Yair A. G. Fosado, Elias Melas, Marco Baiesi, Luca Tubiana, Enzo Orlandini
Summary: This study explores how type 2 Topoisomerase (TopoII) proteins enhance the relaxation of DNA molecules by speeding up the topological search and optimizing the sampling of the topological space. The findings suggest that the time scale of topological relaxation is independent of the substrate length. These results are significant for understanding the role of DNA topological simplification in vitro and in vivo.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Inorganic & Nuclear
Samuel J. Edwards, Daniel T. Bowron, Robert J. Baker
Summary: The solution structure of 1.0 M Uranyl Chloride has been determined, showing an equilibrium between [UO2(H2O)(5)](2+) and [UO2Cl(H2O)(4)](+) with a stability constant of 0.23 +/- 0.03 mol(-1) dm(-3). A smaller fraction of [UO2Cl2(H2O)(3)] ion is also observed in the solution. The data reveal that the uranyl ion is a poor hydrogen bond acceptor in solution, while the coordinated waters exhibit enhanced hydrogen bond ability compared to bulk water.
DALTON TRANSACTIONS
(2022)
Article
Polymer Science
Aleksandra Radko, Sebastian Lalik, Aleksandra Deptuch, Teresa Jaworska-Golab, Robert Ekiert, Natalia Gorska, Katarzyna Makyla-Juzak, Jacek Niziol, Monika Marzec
Summary: The study investigated DNA complexes with different surfactants using Fourier transform middle infrared spectroscopy, X-ray diffraction and dielectric spectroscopy methods, confirming electrostatic interactions in complex formation. A packing model for the complex molecules, depending on the type of surfactant, was proposed based on SAXS results. The dielectric process in low frequency range was interpreted as oscillation of surfactant ions, similar to ions in pure DNA solutions.
Article
Biochemistry & Molecular Biology
Vaitea Opuu, Giuliano Nigro, Christine Lazennec-Schurdevin, Yves Mechulam, Emmanuelle Schmitt, Thomas Simonson
Summary: Amino acids with noncanonical backbones are important for protein engineering, but optimizing their properties is challenging. In this study, a computational protein design method was used to redesign an aminoacyl-tRNA synthetase and improve its activity towards noncanonical amino acids.
Article
Crystallography
Hristina Sbirkova-Dimitrova, Rusi Rusew, Nikola Kuvandjiev, Annie Heroux, Tzanko Doukov, Boris L. Shivachev
Summary: Understanding DNA-ligand binding interactions require ligand screening, crystallization, and structure determination. In this study, single crystals of two DNA sequences were grown in the presence of Thioflavin T (ThT) or its analog XRB, and their structures were solved. The binding of XRB to DNA was found to slightly change the DNA's buckle parameters at the CpG regions.
Article
Biochemistry & Molecular Biology
Mustafa Bal, Aysegul Kose, Seyit Ali Gungor
Summary: This study synthesized benzimidazole compounds containing benzophenone group according to the literature and investigated their DNA binding properties using UV-vis and photoluminescence spectroscopy. The structures of the compounds were determined using methods such as FT-IR, H-1, C-13 NMR, UV-vis, photoluminescence spectroscopy, and X-ray crystallography. Information about the binding types, binding mode, and binding energies of the compounds with DNA were collected using UV-vis, photoluminescence spectroscopy, and viscosity tests. Binding interactions were also investigated using molecular docking. The calculated binding constants (Kb) for substances A, B, and C were found to be 3.0 x 10(4), 7.0 x 10(4), and 3.0 x 10(4) M-1, respectively. Compound B showed the best DNA binding activity in in vitro studies. It is believed that these synthesized compounds may have potential in cancer drug research as DNA binding agents.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
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, Inorganic & Nuclear
Sarah L. McDarmont, Meredith H. Jones, Colin D. McMillen, Everett Clinton Smith, Jared A. Pienkos, Evan E. Joslin
Summary: Studies have shown the potential for metallodrugs as bioactive therapeutics in the past few decades. Six new ruthenium(II) complexes with specific structures were synthesized and characterized. The results indicate that coordination to ruthenium(II) centers does not significantly increase the toxicity of bioactive ligands.
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)
Review
Chemistry, Applied
Qurat Ul Ain, Rekha Sharma
Summary: This review provides a comprehensive overview of the synthesis, characterization, and biological applications of bisthiosemicarbazone ligands and their metal complexes reported until 2022. The coordination chemistry of these complexes with p and d block elements, determined by single crystal X-ray crystallography, is explored. Various spectroscopic techniques such as IR, UV-Vis, ESR, and NMR are discussed for the characterization of ligands and their complexes. The structure and bonding aspects of the complexes are discussed separately, and their geometries include square planar, square pyramidal, octahedral, and pentagonal pyramidal. Structure-activity relationship and the influence of co-ligands on biological activity are also examined.
APPLIED ORGANOMETALLIC CHEMISTRY
(2023)
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
Microbiology
Martijn Fenaux, Xiaodong Lin, Fumiaki Yokokawa, Zachary Sweeney, Oliver Saunders, Lili Xie, Siew Pheng Lim, Marianne Uteng, Kyoko Uehara, Robert Warne, Wang Gang, Christopher Jones, Satya Yendluri, Helen Gu, Keith Mansfield, Julie Boisclair, Tycho Heimbach, Alexandre Catoire, Kathryn Bracken, Margaret Weaver, Heinz Moser, Weidong Zhong
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2016)
Article
Biochemical Research Methods
Dennis A. Veselkov, Ivan Laponogov, Xiao-Su Pan, Jogitha Selvarajah, Galyna B. Skamrova, Arthur Branstrom, Jana Narasimhan, Josyula V. N. Vara Prasad, L. Mark Fisher, Mark R. Sanderson
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2016)
Article
Chemistry, Medicinal
Folkert Reck, Alun Bermingham, Johanne Blais, Vladimir Capka, Taryn Cariaga, Anthony Casarez, Richard Colvin, Charles R. Dean, Alex Fekete, Wanben Gong, Ellie Growcott, Hongqiu Guo, Adriana K. Jones, Cindy Li, Fengxia Li, Xiaodong Lin, Mika Lindvall, Sara Lopez, David McKenney, Louis Metzger, Heinz E. Moser, Ramadevi Prathapam, Dita Rasper, Patrick Rudewicz, Vijay Sethuraman, Xiaoyu Shen, Jacob Shaul, Robert L. Simmons, Kyuto Tashiro, Dazhi Tang, Meiliana Tjandra, Nancy Turner, Tsuyoshi Uehara, Charles Vitt, Steven Whitebread, Aregahegn Yifru, Xu Zang, Qingming Zhu
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2018)
Article
Multidisciplinary Sciences
Ivan Laponogov, Xiao-Su Pan, Dennis A. Veselkov, Galyna B. Skamrova, Trishant R. Umrekar, L. Mark Fisher, Mark R. Sanderson
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Medicinal
Johanna M. Jansen, Gianfranco De Pascale, Susan Fong, Mika Lindvall, Heinz E. Moser, Keith Pfister, Bob Warne, Charles Wartchow
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Article
Chemistry, Medicinal
Frederick Cohen, James B. Aggen, Logan D. Andrews, Zahra Assar, Jen Boggs, Taylor Choi, Paola Dozzo, Ashton N. Easterday, Cat M. Haglund, Darin J. Hildebrandt, Melissa C. Holt, Kristin Joly, Adrian Jubb, Zeeshan Kamal, Timothy R. Kane, Andrei W. Konradi, Kevin M. Krause, Martin S. Linsell, Timothy D. Machajewski, Olga Miroshnikova, Heinz E. Moser, Vincent Nieto, Thu Phan, Craig Plato, Alisa W. Serio, Julie Seroogy, Anton Shakhmin, Adam J. Stein, Alex D. Sun, Serguei Sviridov, Zhan Wang, Kenneth Wlasichuk, Wen Yang, Xiaoming Zhou, Hai Zhu, Ryan T. Cirz
Article
Chemistry, Medicinal
Fiorella Ruggiu, Shengtian Yang, Robert L. Simmons, Anthony Casarez, Adriana K. Jones, Cindy Li, Johanna M. Jansen, Heinz E. Moser, Charles R. Dean, Folkert Reck, Mika Lindvall
ACS INFECTIOUS DISEASES
(2019)
Article
Chemistry, Medicinal
Colin K. Skepper, Duncan Armstrong, Carl J. Balibar, Daniel Bauer, Cornelia Bellamacina, Bret M. Benton, Dirksen Bussiere, Gianfranco De Pascale, Javier De Vicente, Charles R. Dean, Bhavesh Dhumale, L. Mark Fisher, John Fuller, Mangesh Fulsunder, Lauren M. Holder, Cheng Hu, Bhavin Kantariya, Guillaume Lapointe, Jennifer A. Leeds, Xiaolin Li, Peichao Lu, Anatoli Lvov, Sylvia Ma, Shravanthi Madhavan, Swapnil Malekar, David McKenney, Wosenu Mergo, Louis Metzger, Heinz E. Moser, Daniel Mutnick, Jonas Noeske, Colin Osborne, Ashish Patel, Darshit Patel, Tushar Patel, Krunal Prajapati, Katherine R. Prosen, Folkert Reck, Daryl L. Richie, Alice Rico, Mark R. Sanderson, Shailesh Satasia, William S. Sawyer, Jogitha Selvarajah, Nirav Shah, Kartik Shanghavi, Wei Shu, Katherine Thompson, Martin Traebert, Anand Vala, Lakhan Vala, Dennis A. Veselkov, Jason Vo, Michael Wang, Marcella Widya, Sarah L. Williams, Yongjin Xu, Qin Yue, Richard Zang, Bo Zhou, Alexey Rivkin
JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Chemistry, Medicinal
Guillaume Lapointe, Colin K. Skepper, Lauren M. Holder, Duncan Armstrong, Cornelia Bellamacina, Johanne Blais, Dirksen Bussiere, Jianwei Bian, Cody Cepura, Helen Chan, Charles R. Dean, Gianfranco De Pascale, Bhavesh Dhumale, L. Mark Fisher, Mangesh Fulsunder, Bhavin Kantariya, Julie Kim, Sean King, Lauren Kossy, Upendra Kulkarni, Jay Lakshman, Jennifer A. Leeds, Xiaolan Ling, Anatoli Lvov, Sylvia Ma, Swapnil Malekar, David McKenney, Wosenu Mergo, Louis Metzger, Keshav Mhaske, Heinz E. Moser, Mina Mostafavi, Sunil Namballa, Jonas Noeske, Colin Osborne, Ashish Patel, Darshit Patel, Tushar Patel, Philippe Piechon, Valery Polyakov, Krunal Prajapati, Katherine R. Prosen, Folkert Reck, Daryl L. Richie, Mark R. Sanderson, Shailesh Satasia, Bhautik Savani, Jogitha Selvarajah, Vijay Sethuraman, Wei Shu, Kyuto Tashiro, Katherine Thompson, Krishniah Vaarla, Lakhan Vala, Dennis A. Veselkov, Jason Vo, Bhavesh Vora, Trixie Wagner, Laura Wedel, Sarah L. Williams, Satya Yendluri, Qin Yue, Aregahegn Yifru, Yong Zhang, Alexey Rivkin
Summary: This study describes the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV by binding to and stabilizing DNA cleavage complexes. Compound 25, identified through optimization of this series, shows potent activity against Gram-positive bacteria, favorable in vitro safety profile, and excellent in vivo pharmacokinetic properties. The X-ray crystal structure of the ternary complex formed by topoisomerase IV, compound 25, and cleaved DNA suggests a structural basis for the reduced impact of QRDR mutations on the antibacterial activity of 25 compared to fluoroquinolones.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Allan S. Wagman, Ryan Cirz, Glenn McEnroe, James Aggen, Martin S. Linsell, Adam A. Goldblum, Sara Lopez, Marcela Gomez, George Miller, Lloyd J. Simons, Thomas R. Belliotti, Christina R. Harris, Toni-Jo Poel, Michael J. Melnick, Ricky D. Gaston, Heinz E. Moser
Review
Chemistry, Organic
Folkert Reck, Johanna M. Jansen, Heinz E. Moser