Review
Biochemistry & Molecular Biology
Anna Kocyla, Jozef Ba Tran, Artur Krezel
Summary: Zinc ions play a crucial role in modulating protein-protein interactions at interfaces, affecting cellular processes and communication. However, understanding the formation, dissociation, stability, and reactivity of ZPPIs in a zinc interactome is hindered by experimental challenges.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Aleix Tarres-Sole, Federica Battistini, Joachim M. Gerhold, Olivier Pietrement, Belen Martinez-Garcia, Elena Ruiz-Lopez, Sebastien Lyonnais, Pau Bernado, Joaquim Roca, Modesto Orozco, Eric Le Cam, Juhan Sedman, Maria Sola
Summary: A new mechanism of mitochondrial DNA compaction was discovered, in which the Gcf1p protein in Candida albicans utilizes its multiple domains to connect co-aligned DNA segments without altering DNA topology.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Seongjin Park, Karine Prevost, Emily M. Heideman, Marie-Claude Carrier, Muhammad S. Azam, Matthew A. Reyer, Wei Liu, Eric Masse, Jingyi Fei
Summary: RNA-binding protein Hfq plays a crucial role in post-transcriptional gene regulation in bacteria, with widespread mRNA-binding activity. Short RNAs can either form a ternary complex with mRNA on Hfq or displace mRNA from Hfq in a binding face-dependent manner. Hfq binding to certain mRNAs through its distal face can recruit RNase E to promote mRNA turnover.
Article
Biochemistry & Molecular Biology
Archit Gupta, Ashish Joshi, Kanika Arora, Samrat Mukhopadhyay, Purnananda Guptasarma
Summary: The bacterial chromosome, known as its nucleoid, is an amorphous assemblage of globular nucleoprotein domains that exist as an irregularly-shaped, membrane-less, intracellular compartment separated from the cell's cytoplasm. Two abundant nucleoid-associated proteins, HU and Dps, undergo spontaneous complex coacervation with different forms of DNA/RNA, causing condensation and compaction of nucleic acids into liquid-liquid phase separated condensates in vitro. These complex coacervation modes may serve as models for understanding the in vivo relationships among nucleoid-associated proteins, explaining the presence of multiple isoforms of HU and the roles of HU and Dps in E. coli growth.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Engineering, Electrical & Electronic
M. Mohanbabu, P. N. Sathishkumar, N. S. P. Bhuvanesh, R. Karvembu, K. Saravanan, E. Vinoth, S. Aravindhan
Summary: The structural investigation and characterization of twin chiral carboxamide compounds synthesized by slow-evaporation method were described. The chirality of the compounds was confirmed, and the intermolecular connections were analyzed. The chemical electronic characteristics and binding affinities were characterized using computational methods.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2023)
Article
Multidisciplinary Sciences
Sarah A. Mosure, Timothy S. Strutzenberg, Jinsai Shang, Paola Munoz-Tello, Laura A. Solt, Patrick R. Griffin, Douglas J. Kojetin
Summary: Heme is an endogenous ligand for REV-ERB nuclear receptors, regulating their activity by binding with corepressor NCoR and influencing the thermodynamic interaction profile between NCoR and REV-ERBβ. This finding sheds light on the mechanism of heme-dependent REV-ERB activity.
Article
Multidisciplinary Sciences
Yiwei Chen, Kai Xu, Luca Piccoli, Mathilde Foglierini, Joshua Tan, Wenjie Jin, Jason Gorman, Yaroslav Tsybovsky, Baoshan Zhang, Boubacar Traore, Chiara Silacci-Fregni, Claudia Daubenberger, Peter D. Crompton, Roger Geiger, Federica Sallusto, Peter D. Kwong, Antonio Lanzavecchia
Summary: This study demonstrates that Plasmodium falciparum RIFINs can bind to LILRB1 through D3, and inserting receptor domains into the VH-CH1 elbow can generate novel antibodies, as shown by a naturally selected example.
Article
Biochemistry & Molecular Biology
Peng Wang, Jing Zhao, Seyedmehdi Hossaini Nasr, Sarah A. Otieno, Fuming Zhang, Wei Qiang, Robert J. Linhardt, Xuefei Huang
Summary: The highly sulfated HS oligosaccharides show the strongest binding affinity with A beta and can reduce cellular toxicities induced by A beta. Elongating the glycan length significantly enhances A beta affinity. This study provides new insights into HS/A beta interactions.
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
Nikita Y. Shmelev, Tesfu H. Okubazghi, Pavel A. Abramov, Vladislav Y. Komarov, Mariana I. Rakhmanova, Alexander S. Novikov, Artem L. Gushchin
Summary: Treating [(PPh3)AuCl] complex with silver triflate in dichloromethane leads to synthesis of dinuclear gold(I) complexes with high yields. Crystal structures show linear gold ions with twisted bipyridine ligands allowing aurophilic interactions. Photoluminescence in solid state with different emission colors and phosphorescent lifetimes is observed when excited at 300 nm.
DALTON TRANSACTIONS
(2021)
Article
Multidisciplinary Sciences
Shukun Luo, Bruna G. Coutinho, Prikshat Dadhwal, Yasuhiro Oda, Jiahong Ren, Amy L. Schaefer, E. Peter Greenberg, Caroline S. Harwood, Liang Tong
Summary: Some plant-associated proteobacteria have LuxR family transcription factors known as PipR subfamily members that play important roles in interactions with plant hosts and bacterial virulence of plants. The ethanolamine derivative, HEHEAA, was identified as an effective effector of PipR-mediated gene regulation in the plant endophyte Pseudomonas GM79. Crystallization of a HEHEAA-responsive SBP revealed the molecular basis of PipR system responses to plant factors, showing that different PipR-associated SBPs bind different effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Sohyoung Lee, Sean Inzerillo, Gi Young Lee, Erick M. Bosire, Saroj K. Mahato, Jeongmin Song
Summary: Glycans play a crucial role in bacterial pathogenesis and host responses against pathogens. Interactions between bacterial and host glycans can benefit the pathogen, host, or both. Technological advances in glycoscience have accelerated research and offer valuable insights into antibacterial strategies to combat drug-resistant pathogens on a global scale.
TRENDS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Kai Walstein, Arsen Petrovic, Dongqing Pan, Birte Hagemeier, Dorothee Vogt, Ingrid R. Vetter, Andrea Musacchio
Summary: By reconstituting the human kinetochore component CENP-C, researchers have discovered a new structure and function, indicating that human kinetochores are formed by clustering multiple copies of a fundamental module, which may have important implications for transgenerational inheritance.
Article
Multidisciplinary Sciences
Federico Cerullo, Sebastian Filbeck, Pratik Rajendra Patil, Hao-Chih Hung, Haifei Xu, Julia Vornberger, Florian W. Hofer, Jaro Schmitt, Guenter Kramer, Bernd Bukau, Kay Hofmann, Stefan Pfeffer, Claudio A. P. Joazeiro
Summary: This study uncovers the function of Bacillus subtilis MutS2, a member of the conserved MutS family, in translational quality control. MutS2 acts as a ribosome-binding protein and functions in sensing collisions between stalled and translating ribosomes. It promotes ribosomal subunit dissociation, ribosome recycling, and initiation of ribosome-associated protein quality control. These findings demonstrate the conserved role of ribosome collisions in mounting a complex response to translation interruption.
Article
Biology
Amit K. Gandhi, Zhen-Yu J. Sun, Walter M. Kim, Yu-Hwa Huang, Yasuyuki Kondo, Daniel A. Bonsor, Eric J. Sundberg, Gerhard Wagner, Vijay K. Kuchroo, Gregory A. Petsko, Richard S. Blumberg
Summary: Investigating the transitions of hCEACAM1 between monomeric and dimeric states is crucial for understanding its activity. By mutating residues within the hCEACAM1 IgV GFCC face and using various techniques, the study reveals the structural information and conformational behavior of hCEACAM1 in solution, highlighting the importance of the flexibility of the GFCC' face in governing the formation of hCEACAM1 dimers and selective heterodimers.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Xuan Xie, Xia Sun, Yuheng Wang, Ben Lehner, Xianghua Li
Summary: This article discusses how mutations interact to alter phenotypes and concludes that non-additive interactions (epistasis and dominance) are frequent, context-dependent, and challenging to predict even in the simplest biological systems.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Silvia Hormeno, Oliver J. Wilkinson, Clara Aicart-Ramos, Sahiti Kuppa, Edwin Antony, Mark S. Dillingham, Fernando Moreno-Herrero
Summary: Human DNA helicase B (HELB) plays important regulatory roles in DNA replication and recombination. It interacts with Replication Protein A (RPA) and RPA-single-stranded DNA (ssDNA) filaments to exhibit ATP hydrolysis translocation and helicase activities, and its ability to clear RPA from ssDNA allows other proteins to access these intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Emily J. Stevens, Daniel J. Morse, Dora Bonini, Seana Duggan, Tarcisio Brignoli, Mario Recker, John A. Lees, Nicholas J. Croucher, Stephen Bentley, Daniel J. Wilson, Sarah G. Earle, Robert Dixon, Angela Nobbs, Howard Jenkinson, Tim van Opijnen, Derek Thibault, Oliver J. Wilkinson, Mark S. Dillingham, Simon Carlile, Rachel M. McLoughlin, Ruth C. Massey
Summary: Streptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia, and meningitis. The haemolytic toxin pneumolysin (Ply) is identified as a primary virulence factor for this bacterium, and a novel modular protein, ZomB, is found to regulate Ply activity and potentially influence bacterial colonization in the respiratory tract and lungs in mice. Additionally, the antibiotic resistance gene acquired on the ICE ICESp23FST81 is shown to play a role in controlling the expression of a major virulence factor, suggesting its importance in the success of S. pneumoniae lineages that acquire it.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Francesco Aulicino, Martin Pelosse, Christine Toelzer, Julien Capin, Erwin Ilegems, Parisa Meysami, Ruth Rollarson, Per-Olof Berggren, Mark Simon Dillingham, Christiane Schaffitzel, Moin A. Saleem, Gavin Welsh, Imre Berger
Summary: This article addresses the challenge of delivering multiple components into living cells for precise gene-editing. The researchers utilize baculovirus, which has a high cargo capacity, to successfully replace multiple exons and restore protein expression in cells derived from patients with nephrotic syndrome. The study also demonstrates the efficient search and replace of DNA without detectable indels.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Holly C. Ford, William J. Allen, Goncalo C. Pereira, Xia Liu, Mark Simon Dillingham, Ian Collinson
Summary: This article describes the import process of mitochondrial proteins and the research progress in understanding its mechanisms. Using a newly developed assay based on split NanoLuc luciferase, researchers found that the size and net charge of pre-sequences influence the import process, which is driven by the transmembrane potential and ATP hydrolysis. The study also revealed the functional differences between the two membranes involved in the import process.
Article
Chemistry, Multidisciplinary
Andrew J. J. Devine, Alice E. E. Parnell, Catherine R. R. Back, Nicholas R. R. Lees, Samuel T. T. Johns, Ainul Z. Z. Zulkepli, Rob Barringer, Katja Zorn, James E. M. Stach, Matthew P. P. Crump, Martin A. A. Hayes, Marc W. W. van der Kamp, Paul R. R. Race, Christine L. L. Willis
Summary: This study reveals the key epoxidation reaction in the synthesis of Abyssomicin C and the structure of the enzyme AbyV involved in this reaction. The combination of selective carbon-13 labeling with NMR spectroscopy proves to be an important tool in studying enzyme-catalyzed reactions in vitro.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Charles Winterhalter, Daniel Stevens, Stepan Fenyk, Simone Pelliciari, Elie Marchand, Panos Soultanas, Aravindan Ilangovan, Heath Murray
Summary: This study reports both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. By characterizing the initiation protein DnaD, distinct protein interfaces required for helicase loading were identified. The role of the repressor protein SirA in inhibiting helicase recruitment was also discovered, advancing our understanding of DNA replication initiation in B. subtilis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Javier Coloma, Nayim Gonzalez-Rodriguez, Francisco A. Balaguer, Karolina Gmurczyk, Clara Aicart-Ramos, oscar M. Nuero, Juan Roman Luque-Ortega, Kimberly Calugaru, Neal F. Lue, Fernando Moreno-Herrero, Oscar Llorca
Summary: Cdc13 plays a crucial role in telomere replication and stability by forming dimers and higher-order complexes, which regulate binding and structure of DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Sara De Braganc, Clara Aicart-Ramos, Raquel Arribas-Bosacoma, Angel Rivera-Calzada, Juan Pablo Unfried, Laura Prats-Mari, Mikel Marin-Baquero, Puri Fortes, Oscar Llorca, Fernando Moreno-Herrero
Summary: The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). In this study, the contributions of core NHEJ proteins and accessory factors APLF and lncRNA NIHCOLE to DNA synapsis were investigated using magnetic tweezers. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF, and this effect is enhanced by a small structured RNA domain within NIHCOLE. A model is proposed where Ku70-Ku80 can bind DNA, APLF, and structured RNAs simultaneously to promote stable DNA end joining.
Article
Biochemical Research Methods
Ganesh Agam, Christian Gebhardt, Milana Popara, Rebecca Maechtel, Julian Folz, Benjamin Ambrose, Neharika Chamachi, Sang Yoon Chung, Timothy D. Craggs, Marijn de Boer, Dina Grohmann, Taekjip Ha, Andreas Hartmann, Jelle Hendrix, Verena Hirschfeld, Christian G. Huebner, Thorsten Hugel, Dominik Kammerer, Hyun-Seo Kang, Achillefs N. Kapanidis, Georg Krainer, Kevin Kramm, Edward A. Lemke, Eitan Lerner, Emmanuel Margeat, Kirsten Martens, Jens Michaelis, Jaba Mitra, Gabriel G. Moya Munoz, Robert B. Quast, Nicole C. Robb, Michael Sattler, Michael Schlierf, Jonathan Schneider, Tim Schroeder, Anna Sefer, Piau Siong Tan, Johann Thurn, Philip Tinnefeld, John van Noort, Shimon Weiss, Nicolas Wendler, Niels Zijlstra, Anders Barth, Claus A. M. Seidel, Don C. Lamb, Thorben Cordes
Summary: Single-molecule Forster-resonance energy transfer (smFRET) experiments are valuable for studying biomolecular structure and dynamics. An international blind study involving 19 laboratories demonstrates the reproducibility and accuracy of smFRET measurements for proteins. The study highlights the importance of smFRET in integrative structural biology and its promise for dynamic structural studies.
Article
Biochemistry & Molecular Biology
Charles Winterhalter, Simone Pelliciari, Daniel Stevens, Stepan Fenyk, Elie Marchand, Nora B. Cronin, Panos Soultanas, Tiago R. D. Costa, Aravindan Ilangovan, Heath Murray
Summary: This study investigated the DNA replication initiation protein DnaD in Bacillus subtilis and identified a new single-stranded DNA motif called DnaD Recognition Element (DRE) in oriC. Through cryo-electron microscopy imaging, it was proposed that the location of DRE orchestrates the strand-specific recruitment of helicase during DNA replication initiation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
George H. Hutchins, Claire E. M. Noble, H. Adrian Bunzel, Christopher Williams, Paulina Dubiel, Sathish K. N. Yadav, Paul M. Molinaro, Rob Barringer, Hector Blackburn, Benjamin J. Hardy, Alice E. Parnell, Charles Landau, Paul R. Race, Thomas A. A. Oliver, Ronald L. Koder, Matthew P. Crump, Christiane Schaffitzel, A. Sofia F. Oliveira, Adrian J. Mulholland, J. L. Ross Anderson
Summary: The electron-conducting circuitry of life is a valuable, yet untapped resource in nanoscale biomolecular engineering. Researchers have characterized and analyzed a new diheme maquette protein, 4D2, and used it to create a modular platform for heme protein design. They redesigned a monoheme variant and validated its properties through experimental electrostatic redox potential calculations. 4D2 was then extended into a tetraheme helical bundle, demonstrating its potential as a molecular wire. This platform presents opportunities for redox protein design and the development of artificial electron-conducting circuitry in the future.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Genetics & Heredity
Sara De Braganca, Mark S. Dillingham, Fernando Moreno-Herrero
Summary: Genome integrity and maintenance are crucial for the survival of all organisms. Double-strand breaks (DSBs) are highly toxic DNA lesions, and two major pathways, homologous recombination (HR) and non-homologous end joining (NHEJ), are responsible for repairing DSBs. Single-molecule techniques provide insights into the mechanisms of HR and NHEJ repair.
TRENDS IN GENETICS
(2023)
Meeting Abstract
Biophysics
Timothy D. Craggs
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Victoria E. Hill, Agnes Noy, Timothy D. Craggs
BIOPHYSICAL JOURNAL
(2023)
