Review
Biochemistry & Molecular Biology
Jun-Tao Guo, Fareeha Malik
Summary: Single-stranded DNA binding proteins (SSBs) play critical roles in maintaining genome stability and transcriptional regulation, and machine learning-based approaches have been developed for predicting SSBs from double-stranded DNA binding proteins (DSBs).
Article
Chemistry, Inorganic & Nuclear
Monalisa Mohanty, Gurunath Sahu, Atanu Banerjee, Sudhir Lima, Sushree Aradhana Patra, Aurelien Crochet, Giuseppe Sciortino, Daniele Sanna, Valeria Ugone, Eugenio Garribba, Rupam Dinda
Summary: The transport and cytotoxicity of molybdenum-based drugs have been explained with the concept of chemical transformation. The structures and transformations of four molybdenum complexes were studied, and their binding affinity with DNA and cytotoxicity were evaluated. The results showed that the complexes can interact with DNA through non-covalent interactions and induce apoptotic death of cancer cells.
INORGANIC CHEMISTRY
(2022)
Article
Biochemical Research Methods
Fengjiao Zhao, Yang Du, Zhong Zheng, Meng Cui, Zhiqiang Liu
Summary: The study characterized the interactions between ginsenosides and myglobin using native ESI-MS and molecular docking, revealing the underlying mechanisms involved. This approach provides a new method and insights for investigating the interactions between natural drugs and proteins in various diseases.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Duong T. Bui, Zhixiong Li, Pavel I. Kitov, Ling Han, Elena N. Kitova, Marlene Fortier, Camille Fuselier, Philippine Granger Joly de Boissel, David Chatenet, Nicolas Doucet, Stephen M. Tompkins, Yves St-Pierre, Lara K. Mahal, John S. Klassen
Summary: Electrospray ionization mass spectrometry (ESI-MS) is a powerful label-free assay for detecting noncovalent biomolecular complexes and quantifying binding thermochemistry. However, the assumption that the ion signals of free and bound species in ESI-MS measurements can quantitatively reflect their relative concentrations is only valid when their response factors are similar.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemical Research Methods
Jian Zhang, Sina Ghadermarzi, Akila Katuwawala, Lukasz Kurgan
Summary: Efforts to elucidate protein-DNA interactions at the molecular level rely on accurate predictions of DNA-binding residues in protein sequences. DNAgenie, a new predictor utilizing a custom-designed machine learning architecture, outperforms current methods in predicting residue-level interactions with A-DNA, B-DNA, and single-stranded DNA, reducing cross-predictions and generating promising leads for potential DNA-binding proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Valentina Milasinovic, Kresimir Molcanov
Summary: The structural analysis of six new co-crystals revealed the presence of sandwich-like I-quinone-I- structures, with the competition between this motif and halogen bonding being described for the first time. The black color of the crystals indicates charge transfer from iodide to the quinoid ring, interpreted as n -> pi*. Intermolecular interactions were analyzed using Hirshfeld surfaces and Voronoi-Dirichlet polyhedra.
Article
Chemistry, Multidisciplinary
Yang Jiao, Haochuan Mao, Yunyan Qiu, Guangcheng Wu, Hongliang Chen, Long Zhang, Han Han, Xuesong Li, Xingang Zhao, Chun Tang, Xiao-Yang Chen, Yuanning Feng, Charlotte L. Stern, J. Fraser Stoddart, Michael R. Wasielewski
Summary: Molecular recognition based on noncovalent bonding is important in directing supramolecular phenomena. Weakly associated recognition motifs are challenging to identify and investigate. This study synthesized a [2]catenane compound to enhance weak interactions and reduce system complexity. By using this compound as a model, three possible binding modes between CBPQT and BIPY were discovered and characterized. These findings have potential applications in self-assembled materials and supramolecular catalysis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Deepika Kagra, Raman Jangra, Purshotam Sharma
Summary: A nonredundant dataset of around 300 high-resolution X-ray structures of RNA:protein complexes was analyzed for hydrogen bonds, identifying 17100 contacts that were classified based on various criteria. Comparison with DNA:protein complexes revealed differences in hydrogen bonding due to the absence of 2'-OH group in DNA. The search for stable base:amino acid pairs yielded 37 unique pairs that may act as well-defined RNA:protein interaction motifs.
Article
Biochemistry & Molecular Biology
Lei Tian, Keli Zhu, Yuanyuan Chen, Xiaowei Zheng, Heng Zhang, Zhi Geng, Wenqian Li, Niannian Ding, Jingyu Chen, Yuhui Dong, Peng Cao, Yong Gong, Zhenfeng Zhang
Summary: The KTSC domain containing proteins are widely distributed in different organisms, but their function is still uncertain. This study characterizes Mvu8s protein from Methanolobus vulcani and shows its specific binding to single-stranded DNA. The crystal structure of Mvu8s reveals its homo-tetramer arrangement and the mechanism of single-stranded DNA wrapping.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Chemistry, Multidisciplinary
Kamran T. Mahmudov, Fatali E. Huseynov, Vusala A. Aliyeva, M. Fatima C. Guedes da Silva, Armando J. L. Pombeiro
Summary: Lanthanide complexes have diverse structures and properties, and the design of the secondary coordination sphere is crucial for their development as functional materials. Various interactions, such as hydrogen bonds, halogen bonds, and pi interactions, are used to decorate the secondary coordination sphere of lanthanide complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Inorganic & Nuclear
Asma Nahaei, Zeinab Mandegani, Samira Chamyani, Masood Fereidoonnezhad, Hamid R. Shahsavari, Nikolai Yu Kuznetsov, S. Masoud Nabavizadeh
Summary: A class of cyclometalated Rh-III complexes with thiolate ligands were synthesized and characterized. These complexes demonstrated selective cytotoxicity against cancer cells in vitro. Complex 5 exhibited effective inhibition of tumor growth in an in vivo xenograft mouse model with negligible toxicity to major organs. Mechanistic studies revealed high binding affinity between the Rh-thiolate complexes and DNA as well as moderate binding affinity with BSA.
INORGANIC CHEMISTRY
(2022)
Article
Crystallography
Alexander S. Novikov
Summary: CCDC and PDB offer resources for exploring chemical and biochemical compound structures, while the IsoStar program suite aids chemists in analyzing noncovalent interactions between chemical functional groups.
Article
Biochemistry & Molecular Biology
Simone Pelliciari, Mei-Jing Dong, Feng Gao, Heath Murray
Summary: Genome replication is essential for cell proliferation, and a basal mechanism for opening bacterial chromosome origins has been proposed recently. Core elements of this mechanism are predicted to be present in the majority of bacterial chromosome origins, indicating functional conservation and a potential ancestral system for opening bacterial chromosome origins.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Huixin Luo, Wei Tang, Hongyu Liu, Xiangmei Zeng, William Shu Ching Ngai, Rui Gao, Heyun Li, Ran Li, Huangtao Zheng, Jianting Guo, Fangfei Qin, Gang Wang, Kexin Li, Xinyuan Fan, Peng Zou, Peng R. Chen
Summary: The interactions between RNA and proteins are crucial for cellular processes. This study developed a photocatalytic crosslinking strategy combined with mass spectrometry and RNA sequencing to study the composition and dynamics of protein-RNA interactions. The approach identified numerous RNA binding proteins in human cells and investigated the dynamic changes of RBPs in macrophage cells and their interactions with SARS-CoV-2 RNA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Inorganic & Nuclear
Asma Nahaei, Zeinab Mandegani, Samira Chamyani, Masood Fereidoonnezhad, Hamid R. Shahsavari, Nikolai Yu Kuznetsov, S. Masoud Nabavizadeh
Summary: A class of cyclometalated Rh-III complexes bearing thiolate ligands were produced and evaluated for their cytotoxicity in cancer cells and normal cells, showing selectivity towards cancer cells. Complex 5 exhibited effective tumor growth inhibition in a mouse model, with minimal toxicity to major organs. Molecular docking and spectroscopic techniques shed light on the mechanisms of anticancer activities of these complexes, highlighting their potential as promising leads for DNA-targeted anticancer drugs.
INORGANIC CHEMISTRY
(2022)