Article
Chemistry, Multidisciplinary
Qiang Li, Marko Trajkovski, Chaochao Fan, Jialiang Chen, Yifei Zhou, Kuan Lu, Hongjun Li, Xuncheng Su, Zhen Xi, Janez Plavec, Chuanzheng Zhou
Summary: Fluorinated nucleotides are crucial for F-19 NMR studies of nucleic acid structure and function. The synthesized 4'-SCF3-thymidine exhibits high adaptability and sensitivity, making it valuable for distinguishing diverse DNA structures with single-nucleotide resolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Xi Wang, Harry M. Greenblatt, Lavi S. Bigman, Binhan Yu, Channing C. Pletka, Yaakov Levy, Junji Iwahara
Summary: This study investigates how D/E repeats cause autoinhibition of HMGB1 and its specific binding to cisplatin-modified DNA. By varying ionic strength, the conformational equilibrium between autoinhibited and uninhibited states can be shifted, revealing fuzzy interactions of D/E repeats with other intrinsically disordered regions. Mutations mimicking post-translational modifications relevant to nuclear export of HMGB1 can moderately modulate DNA-binding affinity, possibly by impacting the autoinhibition.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hamida Laroussi, Ariadna B. Juarez-Martinez, Aline Le Roy, Elisabetta Boeri Erba, Frank Gabel, Bernard de Massy, Jan Kadlec
Summary: Meiotic recombination in mice is initiated by DNA double-strand breaks (DSBs), catalyzed by the TOPOVIL complex. This complex's activity is regulated by meiotic factors such as REC114, MEI4, and IHO1, but the mechanism is not well understood. This study reveals the molecular details of these factors and their interactions, including REC114 forming homodimers, associating with MEI4 as a heterotrimer, and IHO1 forming tetramers. The study also shows that IHO1 directly interacts with REC114 and shares a binding surface with TOPOVIBL and another meiotic factor ANKRD31. These findings suggest the existence of a ternary IHO1-REC114-MEI4 complex and highlight the potential regulatory role of REC114 in mediating interactions with multiple partners.
Review
Microbiology
Eugen Pfeifer, Jorge M. Sousa, Marie Touchon, Eduardo P. C. Rocha
Summary: Interactions between viruses, cells, and other genetic elements play a crucial role in the success of infections. These interactions can involve antagonism, competition, cooperation, or parasitism. Rapid evolution through genetic exchanges and functional diversification shapes multilayered networks of interactions that determine the outcome of viral infections.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Cell Biology
Dima Daccache, Emma De Jonge, Pascaline Liloku, Karen Mechleb, Marita Haddad, Sam Corthaut, Yann G. -J. Sterckx, Alexander N. N. Volkov, Corentin Claeys Bouuaert
Summary: In this study, the authors describe the structural and functional properties of the meiotic DNA double-strand break complex. They show that the Rec114-Mei4 and Mer2 proteins are important for complex condensation and that their architectures are evolutionarily conserved. The study presents models of the Rec114-Mei4 and Mer2 complexes supported by various techniques, and reveals their DNA-binding properties.
GENES & DEVELOPMENT
(2023)
Review
Biochemistry & Molecular Biology
Kevin H. Mayo
Summary: Extra- and intra-cellular activity occurs under the direction of inter-molecular interactions. Galectins and chemokines are small protein effector molecules that mediate various cellular functions. Previous research has neglected the importance of their interactions in the same cellular environment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Belen Chaves-Arquero, Cecilia Persson, Nekane Merino, Julen Tomas-Cortazar, Adriana L. Rojas, Juan Anguita, Francisco J. Blanco
Summary: Salp15 is a protein found in the saliva of the tick Ixodes scapularis. It interferes with the cellular immune response of the mammalian host by inhibiting the activation of CD4(+) T-lymphocytes. This protein has potential therapeutic applications in immune system disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Masayuki Takahashi, Bengt Norden
Summary: Linear dichroism (LD) is a polarized light absorption spectroscopy used for studying filamentous molecules. LD can measure signals in a solution by aligning the sample using flow-induced shear force or a strong electric field. LD can assess the orientation of chromophores and distinguish different ligands. It can provide information about the structures of protein-DNA complexes in real time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Manon Julien, Rania Ghouil, Ambre Petitalot, Sandrine M. Caputo, Aura Carreira, Sophie Zinn-Justin
Summary: BRCA2 protein plays essential roles in DNA repair, replication protection, and cell division. Pathogenic variants in BRCA2 can lead to genome instability and are associated with breast and/or ovarian cancers. The disordered regions in BRCA2 are predicted to mediate important interactions during DNA repair, mitosis, and meiosis.
Article
Biochemistry & Molecular Biology
Min Kyung Shinn, Alexander G. Kozlov, Timothy M. Lohman
Summary: Escherichia coli RecO is a recombination mediator protein that interacts with RecR to play a crucial role in homologous recombination. Analytical ultracentrifugation studies reveal a pH-dependent dimer-tetramer equilibrium for RecR and positive cooperativity between RecO and RecR resulting in the formation of RecR(4)O and RecR(4)O(2) complexes. Binding of RecO to SSB-Ct peptides induces an allosteric effect, shifting the equilibrium towards RecR(4)O complex formation. These findings suggest a mechanism for how SSB binding influences the distribution of RecOR complexes to facilitate homologous recombination initiation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Jiri Wald, Dirk Fahrenkamp, Nikolaus Goessweiner-Mohr, Wolfgang Lugmayr, Luciano Ciccarelli, Oliver Vesper, Thomas C. Marlovits
Summary: This study provides insights into the structure and mechanism of the ATP-hydrolysing RuvAB complex during the assembly and processing of the Holliday junction. The findings reveal the spatiotemporal relationship between ATP hydrolysis, nucleotide exchange, and conformational changes, and elucidate the mechanistic basis for DNA recombination.
Article
Chemistry, Multidisciplinary
Rongfu Zhang, Timothy A. Cross, Xinhua Peng, Riqiang Fu
Summary: Understanding the dynamics and structure of water is crucial in biological systems. Directly probing the interfacial water in hydrated phospholipids is challenging, but a novel solid-state NMR technique was developed to successfully observe two distinct water species in the headgroup region of hydrated lipid bilayers. These findings provide an opportunity to study water dynamics on a millisecond or slower timescale in biomacromolecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Genetics & Heredity
Jennifer Redington, Jaigeeth Deveryshetty, Lakshmi Kanikkannan, Ian Miller, Sergey Korolev
Summary: PALB2 plays a crucial role in genome stability, homologous recombination, and DNA repair, with its interaction with MRG15 being essential for its localization in transcriptionally active genes. The binding of PALB2 to the MRG surface is mutually exclusive with other protein interactions, indicating a strong affinity. Mutations in PALB2 may cause minor attenuation of the binding affinity with MRG15.
Article
Biochemistry & Molecular Biology
Theodore J. Litberg, Rajesh Kumar Reddy Sannapureddi, Zijue Huang, Ahyun Son, Bharathwaj Sathyamoorthy, Scott Horowitz
Summary: Maintaining a healthy protein folding environment is essential for cellular function. Recently, nucleic acids, especially G-quadruplexes, were found to be effective chaperones for preventing protein aggregation. Through structure-function and NMR analyses, several factors that affect the ability of G-quadruplexes to prevent protein aggregation, such as structural topology, accessibility and dynamics of G-quadruplexes, and their oligomerization state, were identified. Understanding these factors will help elucidate the possible roles of G-quadruplexes in neurodegenerative disease.
Article
Biochemistry & Molecular Biology
Eathen O. Ryan, Zhoumai Jiang, Hoa Nguyen, Xu Wang
Summary: This study investigated the interaction between PTN and heparin hexasaccharide using NMR and found that PTN's arginines, lysines, and tryptophans have strong interactions with the 2-O-sulfated uronate protons in heparin hexasaccharide.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)