Article
Microbiology
Sabine Schmidt, Jan Stephan Wichers-Misterek, Hannah Michaela Behrens, Jakob Birnbaum, Isabelle G. Henshall, Jana Droege, Ernst Jonscher, Sven Flemming, Carolina Castro-Pena, Paolo Mesen-Ramirez, Tobias Spielmann
Summary: This study identified novel proteins involved in endocytosis and at the K13 compartment in malaria parasites. It also provided insights into the highly adaptive nature of endocytosis in these parasites.
Article
Multidisciplinary Sciences
Tommi Kotila, Hugo Wioland, Muniyandi Selvaraj, Konstantin Kogan, Lina Antenucci, Antoine Jegou, Juha T. Huiskonen, Guillaume Romet-Lemonne, Pekka Lappalainen
Summary: The authors report the structure and function analysis of highly divergent actin from Leishmania parasite. The study reveals the rapid dynamics and molecular basis of parasite actin, providing insight into the evolution of the actin cytoskeleton. The findings show how divergent parasites achieve rapid actin dynamics using a simple set of actin-binding proteins, elucidating the evolution of the actin cytoskeleton.
NATURE COMMUNICATIONS
(2022)
Article
Pharmacology & Pharmacy
Santimoy Sen, Sheetal Lagas, Abhishek Roy, Hemant Kumar
Summary: Cells rely on a balanced cytoskeleton to maintain cellular integrity and regulate signaling pathways. Dysregulation of the cytoskeleton can lead to various pathological conditions, and targeting cytoskeletal dynamics may provide new therapeutic approaches for these diseases.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Hiroki Sakuta, Naoki Nakatani, Takayuki Torisawa, Yutaka Sumino, Kanta Tsumoto, Kazuhiro Oiwa, Kenichi Yoshikawa
Summary: Water phase separation in cells can lead to mechanical motion by entrapping protein motors and generating vortex flow inside cell-sized droplets. This study reveals that the water phase separation interface can drive translational motion of droplets by spontaneously entrapping kinesins and microtubules and generating vortex flow. The findings highlight the importance of water phase separation in both chemical and mechanical processes.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Plant Sciences
Luigi Parrotta, Claudia Faleri, Cecilia Del Casino, Lavinia Mareri, Iris Aloisi, Gea Guerriero, Jean-Francois Hausman, Stefano Del Duca, Giampiero Cai
Summary: This article investigates the association between callose synthase and cytoskeleton in the pollen tube. The study confirms this association and demonstrates colocalization using immunogold labeling. The results suggest that callose synthase interacts with microtubules and exerts its activity in cooperation with the microtubular cytoskeleton.
PLANT CELL REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Walter Alvarado, Joshua Moller, Andrew L. Ferguson, Juan J. de Pablo
Summary: The study identifies and characterizes two metastable states, the alpha-tetrahedron and the beta-rhombus, in short chromatin segments, which play important roles in DNA accessibility and local chromatin condensation or elongation. Increases in nucleosome repeat length result in more pronounced structural irregularity and flexibility.
ACS CENTRAL SCIENCE
(2021)
Article
Biology
Erumbi S. S. Rangarajan, Emmanuel W. W. Smith, Tina Izard
Summary: Cell attachment is crucial and mediated by cadherin receptors binding and alpha-catenin interaction. Alpha-catenin modulates cell migration and adhesion by linking junctions and plasma membrane to actin cytoskeleton. CryoEM structures provide mechanistic insights into alpha-catenin function and its role in cell adhesion and disease.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Peter Nietmann, Kevin Kaub, Andrejus Suchenko, Susanne Stenz, Claas Warnecke, Mohan K. Balasubramanian, Andreas Janshoff
Summary: This study investigates the implications of different actins expressed in epithelial cells for network mechanics and dynamics. The authors find that gamma-actin forms stiffer networks compared to beta-actin, attributed to selective interactions with Mg2+-ions. They also observe that beta-actin networks show more small contraction foci, while gamma-actin networks have fewer but larger foci, indicative of a stronger interaction with myosin motors.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yashar Bashirzadeh, Hossein Moghimianavval, Allen P. Liu
Summary: Cell shape changes during locomotion and cytokinesis are primarily driven by myosin-induced remodeling of cortical actin patterns. The architecture of actin networks, which largely determines the shape of the membrane, is influenced by passive crosslinkers such as alpha-actinin and fascin, as well as the actin nucleator Arp2/3 complex. By reconstituting actomyosin networks in cell-sized lipid bilayer vesicles, the study shows that the size of the vesicle and the concentrations of alpha-actinin and fascin can lead to the assembly of different actomyosin patterns, such as rings and aster-like structures.
Review
Cell Biology
Hui Yi Grace Lim, Nicolas Plachta
Summary: The cytoskeleton plays crucial roles in regulating cell function and behavior during early mammalian embryogenesis. The early mouse embryo provides a valuable model for studying cytoskeletal dynamics and interactions in vivo. Through genetic manipulations and live-imaging approaches, researchers are able to uncover novel cytoskeletal structures and mechanisms controlling key developmental processes.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hiroaki Ishida, Andrew G. Woodman, Naoya Kitada, Tomoyasu Aizawa, Hans J. Vogel
Summary: This study investigated the properties of the headpiece regions of plastins from different organisms and found that the amoeba protein possesses calcium binding properties and a regulatory 'switch helix', which is absent in plastins from plants, yeast, and other nonmotile systems.
SCIENTIFIC REPORTS
(2023)
Article
Physics, Fluids & Plasmas
Matteo Paoluzzi, Luca Angelani, Giorgio Gosti, M. Cristina Marchetti, Ignacio Pagonabarraga, Giancarlo Ruocco
Summary: Experimental evidence suggests a feedback relationship between cell shape and motion. Investigating the effect of aligning cell crawling direction with cell elongation in a biological tissue model, researchers found that this alignment led to nematic patterns in the fluid phase which eventually transitioned into a quasihexagonal solid. However, highly asymmetric cells did not undergo this phase transition, exhibiting characteristics of glassy systems in their dynamics.
Article
Cell Biology
Olivia R. Buonarati, Adam P. Miller, Steven J. Coultrap, K. Ulrich Bayer, Steve L. Reichow
Summary: By utilizing single-particle electron microscopy, a comparative analysis of neuronal CaMKII holoenzymes' alpha and beta isoforms was conducted, revealing different assembly states in the basal condition. The study also suggests that the beta isoform of CaMKII adopts a larger extended state, allowing for direct resolution of intra-holoenzyme kinase domain dimers.
Article
Chemistry, Multidisciplinary
Thomas C. Nicholas, Adam Edward Stones, Adam Patel, F. Marc Michel, Richard J. Reeder, Dirk G. A. L. Aarts, Volker L. Deringer, Andrew L. Goodwin
Summary: Researchers have used advanced atomistic models to reveal that the structure of amorphous calcium carbonate is determined by the bridging modes of calcium ions, and have discovered that the geometrically frustrated effective interactions between calcium ions are the key factors responsible for its complex structure and resistance to crystallization.
Article
Microbiology
Anika Steffen, Bjoern Reusch, Nadine Gruteser, Daniela Mainz, Renza Roncarati, Arnd Baumann, Theresia E. B. Stradal, Dagmar Knebel-Moersdorf
Summary: Virus-induced changes of the host cell cytoskeleton play a pivotal role in the pathogenesis of viral infections. The viral protein Arif-1 manipulates the actin cytoskeleton of host insect cells and may be involved in systemic virus spread. Recent studies have shown the formation of invadosome-like structures induced by Arif-1, suggesting a function in virus dissemination.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Marco Rusnati, Giulia Paiardi, Chiara Tobia, Chiara Urbinati, Alessio Lodola, Pasqualina D'Ursi, Miriam Corrado, Riccardo Castelli, Rebecca C. Wade, Massimiliano Tognolini, Paola Chiodelli
Summary: UniPR1331, a derivative of 3 beta-hydroxy-Delta(5)-cholenic acid, has been shown to inhibit Eph-ephrin interaction and VEGFR2 activation, leading to the suppression of tumor cell-driven angiogenesis. These findings highlight the potential of Delta(5)-cholenic acid as a promising molecular scaffold for the development of multitarget antiangiogenic compounds.
CANCER GENE THERAPY
(2022)
Correction
Biotechnology & Applied Microbiology
Marco Rusnati, Giulia Paiardi, Chiara Tobia, Chiara Urbinati, Alessio Lodola, Pasqualina D'Ursi, Miriam Corrado, Riccardo Castelli, Rebecca C. Wade, Massimiliano Tognolini, Paola Chiodelli
CANCER GENE THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Giulia Paiardi, Stefan Richter, Pasqua Oreste, Chiara Urbinati, Marco Rusnati, Rebecca C. Wade
Summary: Heparin has been found to have antiviral activity against SARS-CoV-2 by inhibiting viral binding to host cells, competing with binding to host heparan sulfate proteoglycan coreceptors, and preventing spike cleavage. These findings provide insights into potential strategies for SARS-CoV-2 antiviral therapy.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Microbiology
Philip Eisenberg, Leon Albert, Jonathan Teuffel, Eric Zitzow, Claudia Michaelis, Jane Jarick, Clemens Sehlke, Lisa Grosse, Nicole Bader, Ariane Nunes-Alves, Bernd Kreikemeyer, Hermann Schindelin, Rebecca C. Wade, Tomas Fiedler
Summary: The study reveals the importance of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN in Streptococcus pyogenes and its potential as a target for antimicrobial substances that selectively kill S. pyogenes and other streptococci.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni
Summary: This study used simulation tools to uncover the molecular and subcellular mechanisms of AC function, with a focus on the AC5 isoform. The research revealed an inactive state of the enzyme in the presence of an inhibitory G alpha subunit, regardless of the presence of a stimulatory G alpha. The binding of G alpha subunits reshaped the free-energy landscape of the AC5 enzyme.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Hanno Schmidt, Katharina Mauer, Manuel Glaser, Bahram Sayyaf Dezfuli, Soren Lukas Hellmann, Ana Lucia Silva Gomes, Falk Butter, Rebecca C. Wade, Thomas Hankeln, Holger Herlyn
Summary: This study presents a bioinformatics workflow for the identification of candidate target proteins in parasites. The workflow combines genomics, transcriptomics, and proteomics to reduce the time and cost in the development of new strategies against parasites. The results demonstrate the effectiveness of the workflow in identifying highly specific candidate targets in Acanthocephala (thorny-headed worms). Virtual ligand screening also identified promising compounds for the control of these parasites.
Review
Pharmacology & Pharmacy
Joanna Panecka-Hofman, Ina Poehner, Rebecca C. Wade
Summary: This article reviews the application of structure-based drug design approaches in discovering anti-Trypanosomatid compounds. Although some progress has been made, our incomplete understanding of parasite biology and biochemistry is currently hindering the discovery of selective anti-parasitic drugs.
EXPERT OPINION ON DRUG DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Hirdesh Kumar, John R. Jimah, Santosh A. Misal, Nichole D. Salinas, Michal Fried, Paul H. Schlesinger, Niraj H. Tolia
Summary: The cell-traversal protein CelTOS plays a critical role in apicomplexan parasites and malaria vaccine development. Through studying different protein regions, researchers have identified the mechanism of pore formation and critical regions in CelTOS. These findings are important for understanding the escape mechanism of malaria and other apicomplexan parasites, as well as studying the function of other pore-forming proteins.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Debabrata Dey, Ariane Nunes-Alves, Rebecca C. Wade, Gideon Schreiber
Summary: Protein crowders have been found to significantly affect the diffusion rates of small molecules, primarily by influencing self-aggregation, interactions with proteins, and surface adsorption.
Review
Chemistry, Multidisciplinary
Abraham Muniz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade
Summary: Brownian dynamics (BD) is a computational method used to simulate molecular diffusion processes, and recent developments have improved its accuracy and expanded its applications. In biological research, BD is used to study the diffusive behavior of molecules under various conditions and to compute rate constants for molecular association and examine transport properties. The development of software packages for BD simulations has provided new features and expanded the range of questions that can be addressed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biology
Luca Costantino, Stefania Ferrari, Matteo Santucci, Outi M. H. Salo-Ahen, Emanuele Carosati, Silvia Franchini, Angela Lauriola, Cecilia Pozzi, Matteo Trande, Gaia Gozzi, Puneet Saxena, Giuseppe Cannazza, Lorena Losi, Daniela Cardinale, Alberto Venturelli, Antonio Quotadamo, Pasquale Linciano, Lorenzo Tagliazucchi, Maria Gaetana Moschella, Remo Guerrini, Salvatore Pacifico, Rosaria Luciani, Filippo Genovese, Stefan Henrich, Silvia Alboni, Nuno Santarem, Anabela da Silva Cordeiro, Elisa Giovannetti, Godefridus J. Peters, Paolo Pinton, Alessandro Rimessi, Gabriele Cruciani, Robert M. Stroud, Rebecca C. Wade, Stefano Mangani, Gaetano Marverti, Domenico D'Arca, Glauco Ponterini, Maria Paola Costi
Summary: A new drug strategy that inhibits the activity of hTS protein and provides a new approach to fight drug-resistant cancers has been discovered.
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Ina Poehner, Antonio Quotadamo, Joanna Panecka-Hofman, Rosaria Luciani, Matteo Santucci, Pasquale Linciano, Giacomo Landi, Flavio Di Pisa, Lucia Dello Iacono, Cecilia Pozzi, Stefano Mangani, Sheraz Gul, Gesa Witt, Bernhard Ellinger, Maria Kuzikov, Nuno Santarem, Anabela Cordeiro-da-Silva, Maria P. Costi, Alberto Venturelli, Rebecca C. Wade
Summary: In this study, a systematic and multidisciplinary approach was used to develop selective antiparasitic compounds. Through computational fragment-based design and crystallographic structure determination, compounds with activity against multiple targets were obtained. Additionally, the combination of polypharmacology design and parasite-specific optimization led to the discovery of compounds effective against T. brucei brucei.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
A. Toral-Lopez, D. B. Kokh, E. G. Marin, R. C. Wade, A. Godoy
Summary: Biological Field-Effect Transistors (BioFETs) have shown great potential for detecting small amounts of ions and molecules. The use of two-dimensional (2D) materials can enhance their performance and enable new applications, which is particularly relevant in the current pandemic where fast, reliable, and affordable detection methods are needed. However, there is a lack of comprehensive computational approaches to understand the mechanisms underlying sensor behavior. In this study, a multiscale platform is proposed that combines atomic models of molecules with mesoscopic device-level simulations, providing a detailed description of the sensor behavior.
NANOSCALE ADVANCES
(2022)
Meeting Abstract
Biophysics
Madhura De, Mehmet A. Oeztuerk, Sebastian Isbaner, Martin Wuertz, Gabriele Mueller, Katalin Toth, Rebecca C. Wade
BIOPHYSICAL JOURNAL
(2022)