Article
Multidisciplinary Sciences
Evan Mercier, Xiaolin Wang, Manisankar Maiti, Wolfgang Wintermeyer, Marina Rodnina
Summary: The study reveals that during the synthesis of membrane proteins, the lateral gate fluctuations are highly dynamic, continuously sampling between open and closed states even without ligands. Ribosome binding and transmembrane segment insertion do not stop the gate fluctuations but tend to increase sampling of the open state. Binding of YidC facilitates substantial opening of the gate, aiding in the folding of YidC-dependent polytopic membrane proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Karina T. Shirakawaa, Fernanda Angelica Salaa, Mayara M. Miyachiroc, Viviana Jobc, Daniel Maragno Trindadea, Andrea Dessena, Christoph Mayer, Eberhard Karls
Summary: The biosynthesis of peptidoglycan (PG) in bacteria involves a multimembered complex of Mur enzymes. Genomic analysis of over 140 bacterial genomes revealed various forms of Mur enzyme fusions among different species, with Proteobacteria carrying the highest number. The crystal structure of the MurE-MurF chimera from Bordetella pertussis showed a head-to-tail elongated architecture, supported by an interconnecting hydrophobic patch. Fluorescence polarization assays demonstrated the interaction of MurE-MurF with other Mur ligases, supporting the existence of a Mur complex in the cytoplasm.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Physics, Multidisciplinary
Igor S. Aranson
Summary: Bacteria, as one of the oldest and most abundant species on Earth, play a significant role in various ecological cycles and can cause infectious diseases. Bacterial suspensions, as examples of active matter, exhibit complex collective behavior. This study provides a critical assessment of the progress in bacterial active matter from a physics perspective, covering experimental results and theoretical approaches.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Article
Computer Science, Software Engineering
Suiyun Zhang, Zhizhong Han, Yu-Kun Lai, Matthias Zwicker, Hui Zhang
Summary: This article introduces an interactive framework based on active learning to help users create customized small object arrangements. By learning prior knowledge through probability mining and propagating user preferences using a novel active learning approach, the framework enables users to effectively create customized arrangements with minimal effort.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Biochemistry & Molecular Biology
Oleg V. Batishchev, Maksim A. Kalutskii, Ekaterina A. Varlamova, Anna N. Konstantinova, Kirill I. Makrinsky, Yury A. Ermakov, Ivan N. Meshkov, Valerij S. Sokolov, Yulia G. Gorbunova
Summary: A comprehensive tool was developed to predict and assess the photodynamic efficacy of photosensitizers in antibacterial photodynamic therapy. A new photosensitizer molecule with a high potential antimicrobial activity was discovered, showing higher minimum inhibitory concentration values for E. coli and A. baumannii compared to common antibiotics.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Microbiology
Emma Kundracik, Josephine Trichka, Jose Diaz Aponte, Alicia Roistacher, Arne Rietsch
Summary: In this study, we identified the involvement of the needle tip protein in the assembly of the translocation pore in the type III secretion system. This finding expands our understanding of the important protein-protein interactions among translocator proteins.
Article
Chemistry, Multidisciplinary
Xu Zhao, Xiangyang Li, Lulu An, Lirong Zheng, Jinlong Yang, Deli Wang
Summary: In this study, the valence-electron arrangement of Ni active centers was controlled by using Ni-vacancy-enriched Ni3N. The Ni vacancies promoted the valence-electron delocalization of OH-adsorption centers and weakened the binding of H-adsorption centers, leading to a 15-fold enhancement in mass activity compared to Ni3N without vacancies. This research demonstrates the potential of finely tuning the valence-electron arrangement for designing efficient catalysts.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Yaohui Li, Rongzhen Zhang, Chi Wang, Farhad Forouhar, Oliver B. Clarke, Sergey Vorobiev, Shikha Singh, Gaetano T. Montelione, Thomas Szyperski, Yan Xu, John F. Hunt
Summary: The evolutionary benefit of oligomeric structures in proteins lacking evidence of intersubunit cooperativity is unclear. In this study, a conserved tetramer interface is shown to maintain the active-site structure in a certain class of proteins, the SDR superfamily. Oligomerization reduces the metabolic cost of enzyme biosynthesis and increases tolerance to destabilizing mutations, enhancing evolutionary fitness.
Review
Biochemistry & Molecular Biology
Lea Daverkausen-Fischer, Margarethe Draga, Felicitas Proels
Summary: The endoplasmic reticulum (ER) plays a central role in protein folding and secretion. BiP and ERdj proteins are important chaperones in the ER, assisting in the folding process and regulating protein synthesis, translocation, and degradation. Dysfunction of these proteins can lead to the accumulation of unfolded proteins and the development of metabolic diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Materials Science, Biomaterials
Hui Xie, Wanshan Hu, Fei Zhang, Changbo Zhao, Tingting Peng, Caizhen Zhu, Jian Xu
Summary: This study improved the antibacterial effect and dye decomposition efficiency of new material platforms for wastewater treatment by synthesizing and studying photosensitizers with aggregation-induced emission (AIE) fluorescent units. It provides theoretical and experimental guidance for designing new photosensitizers for wastewater treatment.
JOURNAL OF MATERIALS CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Konstantin M. Boyko, Mariya V. Kryukova, Lada E. Petrovskaya, Elena A. Kryukova, Alena Y. Nikolaeva, Dmitry A. Korzhenevsky, Galina Yu. Lomakina, Ksenia A. Novototskaya-Vlasova, Elizaveta M. Rivkina, Dmitry A. Dolgikh, Mikhail P. Kirpichnikov, Vladimir O. Popov
Summary: The novel cold-active esterase PMGL3, belonging to the HSL family, forms a unique tetrameric structure with significant impact on stability and catalysis demonstrated by mutant analysis.
Article
Biochemistry & Molecular Biology
Tess R. Malcolm, Matthew J. Belousoff, Hariprasad Venugopal, Natalie A. Borg, Nyssa Drinkwater, Sarah C. Atkinson, Sheena McGowan
Summary: M17 leucyl aminopeptidases rely on oligomerization for functional diversification, with metal ions playing a crucial role in mediating the formation of active hexamers. The dynamic equilibrium between active hexameric species and smaller inactive species of PfA-M17 and Pv-M17 can be controlled by manipulating the identity and concentration of available metals. Structural studies reveal that Pv-M17 forms active hexamers more readily and processes substrates faster than PfA-M17, suggesting a sophisticated metal-dependent equilibrium that may apply to other M17 aminopeptidases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Paul Whitley, Brayan Grau, James C. Gumbart, Luis Martinez-Gil, Ismael Mingarro
Summary: The endoplasmic reticulum (ER) plays a crucial role in eukaryotic cells by facilitating the entry and distribution of newly synthesized proteins. Membrane-integrated amino acids are typically non-polar/hydrophobic and form alpha-helical transmembrane (TM) helices for survival in the ER's non-aqueous environment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Song Liu, Suraj Shankar, M. Cristina Marchetti, Yilin Wu
Summary: Active matter is composed of units that generate mechanical work by consuming energy, such as living systems and biopolymers. The goal is to understand and control the self-organization in space and time. Most active systems exhibit spatial order or temporal synchronization, while simultaneous control of spatial and temporal organization requires complex interactions.
Article
Biochemistry & Molecular Biology
Alex A. Meier, Hee-Jung Moon, Sinan Sabuncu, Priya Singh, Trey A. Ronnebaum, Siyu Ou, Justin T. Douglas, Timothy A. Jackson, Pierre Moenne-Loccoz, Minae Mure
Summary: This study investigates the spatial arrangement of LTQ and the active site Cu2+ in mature LOXL2. The results suggest that LTQ resides within 2.9 angstrom of the active site of Cu2+, and both LTQ and Cu2+ are solvent-exposed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
William J. Allen, Robin A. Corey, Daniel W. Watkins, A. Sofia F. Oliveira, Kiel Hards, Gregory M. Cook, Ian Collinson
Summary: Transport of proteins across and into membranes is a fundamental process in biology. Recent studies have shown that the diffusion of arginine residues limits pre-protein transport, while lysine can be transported across membranes in its neutral form. These findings have implications for understanding the mechanism of protein secretion and suggest a potential role of proton-motive force in aiding transport.
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
Biology
Bob Schiffrin, Jonathan M. Machin, Theodoros K. Karamanos, Anastasia Zhuravleva, David J. Brockwell, Sheena E. Radford, Antonio N. Calabrese
Summary: This study reveals the crucial interaction between the OMP chaperone SurA and the OMP folding catalyst BAM, and proposes a model for OMP biogenesis.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Chalmers Chau, Fabio Marcuccio, Dimitrios Soulias, Martin Andrew Edwards, Andrew Tuplin, Sheena E. Radford, Eric Hewitt, Paolo Actis
Summary: This study presents a polymer-electrolyte solid-state nanopore system for analyzing biomolecular conformation under physiological conditions. By using specific salts, the system's performance is enhanced, allowing for the analysis of Chikungunya virus RNA conformation.
Article
Biochemistry & Molecular Biology
Roberto Maya-Martinez, Yong Xu, Nicolas Guthertz, Martin Walko, Theodoros K. Karamanos, Frank Sobott, Alexander L. Breeze, Sheena E. Radford
Summary: This study utilized NMR methods combined with photo-induced crosslinking to detect and structurally characterize transient dimers of D76N-112m. The results showed that these crosslinked dimers have different structures from previously characterized dimers and possess potent inhibitory effects on amyloid formation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Lucy Troman, Sara Alvira, Bertram Daum, Vicki A. M. Gold, Ian Collinson
Summary: Gram-negative bacteria have a protein-rich envelope crucial for various functions like energy production and protection against environmental challenges. Proteins are transported through the envelope by molecular chaperones like SurA. The interaction between SurA and the Sec-machinery helps prevent protein aggregation and degradation, ensuring safe passage of proteins to the periplasm and outer-membrane.
BIOCHEMICAL JOURNAL
(2023)
Article
Pharmacology & Pharmacy
Nokomis Ramos-Gonzalez, Sam Groom, Katy J. Sutcliffe, Sukhvinder Bancroft, Chris P. Bailey, Richard B. Sessions, Graeme Henderson, Eamonn Kelly
Summary: The illicit use of fentanyl-like drugs and the resulting overdose deaths is a major problem. This study compared the efficacy and signaling bias of different fentanyls, and found that carfentanil is biased towards beta-arrestin.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Cell Biology
Natalia Jimenez-Moreno, Madhu Kollareddy, Petros Stathakos, Joanna J. Moss, Zurine Anton, Deborah K. Shoemark, Richard B. Sessions, Ralph Witzgall, Maeve Caldwell, Jon D. Lane
Summary: LMX1A and LMX1B are essential for dopaminergic neuronal differentiation and survival, and they also act as transcription factors for cellular stress protection through autophagy. Their suppression impairs autophagy response and mitochondrial function, while their inducible overexpression protects against rotenone toxicity in vitro.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Cell Biology
Hope I. Needs, Kevin A. Wilkinson, Jeremy M. Henley, Ian Collinson
Summary: Mitochondrial protein import is essential for organellar biogenesis and ATP supply. This study reveals that the aggregation-prone Tau variant reduces the levels of components of the import machinery, but does not affect protein import or respiratory function. Instead, it induces the formation of tunnelling nanotubes (TNTs) potentially for the recruitment or disposal of mitochondria. These findings suggest a link between Tau aggregation and defective mitochondrial import relevant to disease.
JOURNAL OF CELL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Sophie McCammon, Kirils Makarovs, Susan Banducci, Vicki Gold
Summary: The antimicrobial resistance crisis is leading to a world where previously treatable infections can be deadly. Phage therapy, which uses viruses to kill bacteria, is being explored as an alternative to antibiotics. However, little attention has been paid to the social challenges that may hinder the development and implementation of phage therapy. This study assesses the UK public's awareness, acceptance, preferences, and opinions regarding phage therapy through a survey. The results show that the public's acceptance of phage therapy is moderate and can be increased through priming participants to think about novel medicines and antibiotic resistance. Factors such as success rate, side effect rate, treatment duration, and approval for use affect participants' treatment preferences. Framing phage therapy without using harsh words leads to higher acceptance rates.
Article
Multidisciplinary Sciences
Rebecca Conners, Rayen Ignacia Leon-Quezada, Mathew McLaren, Nicholas J. Bennett, Bertram Daum, Jasna Rakonjac, Vicki A. M. Gold
Summary: Phages, viruses that infect bacteria, are prevalent in every ecosystem on Earth and have various applications in molecular biology and biotechnology. The structure and mechanisms of infection and assembly of filamentous phages, particularly the Ff phages, have been largely unknown. In this study, the researchers used cryo-electron microscopy and a highly efficient system to produce short Ff-derived nanorods, successfully determining the structure of a filamentous virus including the tips. By combining the structure with mutagenesis, they identified important phage domains involved in bacterial attack and release of new viral progeny, leading to the proposal of new models for the phage lifecycle.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
William J. Allen, Ian Collinson
Summary: Encapsulation and compartmentalization in cellular life require specialized machines called translocons to partition proteins across impermeable barriers. Recent technical innovations in structural biology, biophysics, and biochemistry have led to a largely complete understanding of the bacterial version of the core Sec machinery. This knowledge will have immense value for studying other translocons in biological membranes and potentially altering their functions for pharmaceutical or biotechnological purposes.
Article
Microbiology
Mathew McLaren, Rebecca Conners, Michail N. Isupov, Patricia Gil-Diez, Lavinia Gambelli, Vicki A. M. Gold, Andreas Walter, Sean R. Connell, Bryony Williams, Bertram Daum
Summary: This study investigates the hibernating ribosomes in microsporidian parasites and demonstrates that they are locked in a dimeric state, ready to be activated once the host cell is invaded. The study also provides structural evidence for the mechanism of ribosomal hibernation in microsporidia, suggesting that eukaryotes utilize this mechanism in translational control.
NATURE MICROBIOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Fabio Marcuccio, Dimitrios Soulias, Chalmers C. C. Chau, Sheena E. Radford, Eric Hewitt, Paolo Actis, Martin Andrew Edwards
Summary: In this study, the addition of poly(ethylene) glycol (PEG) to the external solution is shown to enhance the detection of biomolecules using solid-state nanopores. The researchers demonstrate that this addition creates an imbalance in the transport properties of cations and anions, which significantly affects the current response of the nanopore. The findings suggest that tuning the diffusion coefficients of ions could enhance the sensitivity of nanopore sensing.
ACS NANOSCIENCE AU
(2023)
