Article
Multidisciplinary Sciences
Joseph L. Watson, Estere Seinkmane, Christine T. Styles, Andrei Mihut, Lara K. Kruger, Kerrie E. Mcnally, Vicente Jose Planelles-Herrero, Michal Dudek, Patrick M. Mccall, Silvia Barbiero, Michael Vanden Oever, Sew Yeu Peak-Chew, Benjamin T. Porebski, Aiwei Zeng, Nina M. Rzechorzek, David C. S. Wong, Andrew D. Beale, Alessandra Stangherlin, Margot Riggi, Janet Iwasa, Jorg Morf, Christos Miliotis, Alina Guna, Alison J. Inglis, Jan Brugues, Rebecca M. Voorhees, Joseph E. Chambers, Qing-Jun Meng, John S. O'Neill, Rachel S. Edgar, Emmanuel Derivery
Summary: The availability of water is crucial for optimum protein function and biochemical activity. In concentrated macromolecular solutions, modest changes in temperature have a significant impact on water potential, but this effect is counteracted by changes in osmotic strength. This duality of temperature and osmotic strength allows for simple manipulation of solvent thermodynamics to prevent cell death under extreme cold or heat shock. Water potential-driven changes in macromolecular assembly, particularly biomolecular condensation, rapidly compensate for osmotic and thermal fluctuations in the cytoplasm, ensuring water availability.
Article
Biology
Bronwyn A. Lucas, Benjamin A. Himes, Liang Xue, Timothy Grant, Julia Mahamid, Nikolaus Grigorieff
Summary: The study emphasizes the importance of understanding molecular mechanisms within the broader context of the cell and introduces a 2D template matching method to address technical limitations. By implementing GPU acceleration in the cisTEM software, the approach becomes more scalable and accessible. Experimental results demonstrate that 2D template matching is a versatile tool for in situ visual proteomics and in situ structure determination, showcasing its precision and sensitivity in identifying molecular complexes.
Article
Chemistry, Analytical
Kevin Jeanne Dit Fouque, Alyssa Garabedian, Fenfei Leng, Yuk-Ching Tse-Dinh, Mark E. Ridgeway, Melvin A. Park, Francisco Fernandez-Lima
Summary: The study introduces a new generation trapped ion mobility spectrometer (TIMS) that is capable of trapping high-molecular-weight macromolecular assemblies with high mobility resolution and measurement of ion-neutral collision cross-section.
ANALYTICAL CHEMISTRY
(2021)
Review
Biotechnology & Applied Microbiology
Brooke A. Jackson Hoffman, Elizabeth A. Pumford, Amaka I. Enueme, Kirsten L. Fetah, Olivia M. Friedl, Andrea M. Kasko
Summary: This review summarizes recent research and clinically available macromolecular or polymeric Toll-like receptor (TLR) agonists and inhibitors. These agents interact with TLR, a class of innate immune receptors that recognize macromolecular ligands characteristic of pathogens. The review also discusses synthetic materials that interface with TLR and investigates the use of these materials to improve ligand stability or efficacy. Strategies for modifying or enhancing current agents and future prospects for the development of these agents are also addressed.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Polymer Science
Andres Cardil, Miguel Palenzuela, Juan F. Vega, Marta E. G. Mosquera
Summary: A recent study has successfully produced nano-sized macromolecular assemblies through a combined polymerization process of glycidyl methacrylate mediated by aluminum complexes. The morphological features and rheological properties of these novel nanoassemblies were investigated. The study revealed that the nanoparticles exhibited a thin disk shape on a flat surface, and their rheological behavior resembled that of un-entangled polymers.
Article
Agriculture, Dairy & Animal Science
Lea Middendorf, Marion Schmicke, Kristian Duengelhoef, Erwin Sieverding, Heinrich Windhaus, Dieter Mischok, Dimitri Radko, Christian Visscher
Summary: Hepatic lipidosis (HL) in fattening turkeys is a well-known disease, but the exact cause and pathogenesis remain unclear. A recent study found high levels of iron in liver tissue of turkeys with HL, suggesting potential malnutrition/starvation and severe liver damage.
JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION
(2021)
Review
Pharmacology & Pharmacy
Sergi Ferre, Francisco Ciruela, Carmen W. Dessauer, Javier Gonzalez-Maeso, Terence E. Hebert, Ralf Jockers, Diomedes E. Logothetis, Leonardo Pardo
Summary: The study proposes the concept of GPCR-effect assemblies (GEMMAs), which are pre-assembled before receptor activation and allow more efficient interactions between specific signaling components. This offers an alternative model to the conventional collision coupling model and explains the differential properties of GPCRs in different cellular environments.
PHARMACOLOGY & THERAPEUTICS
(2022)
Article
Materials Science, Biomaterials
Yue Zhang, Xin Tian, Xinming Li
Summary: In this study, self-assembling peptides composed of histidine and other amino acids were designed and synthesized. These peptides can form self-assembled nanotubes with hydrolase activities under physiological conditions. By incorporating transition metal ions, such as Cu2+, the catalytic functions of these peptides can be modulated, leading to the formation of hybrid nanomaterials with altered morphologies and peroxidase-like activities.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Cell Biology
Fei Chen, Bihui Han, Yanxiu Meng, Yu Han, Bing Liu, Bo Zhang, Yanzhong Chang, Pengxiu Cao, Yumei Fan, Ke Tan
Summary: The decreased expression of ceruloplasmin in breast-invasive carcinoma is associated with a favorable prognosis and tumor immune cell infiltration, suggesting its potential as a therapeutic target and predictor of immunotherapy efficacy.
Article
Neurosciences
V. T. Cheli, M. Sekhar, D. A. Santiago Gonzalez, C. G. Angeliu, G. E. Denaroso, Z. Smith, C. Wang, P. M. Paez
Summary: Ceruloplasmin (Cp) is crucial for cell iron efflux and its absence leads to neurodegeneration and brain iron accumulation. This study found that astrocytes express high levels of Cp and its iron efflux is essential for oligodendrocyte maturation and myelination. Deletion of astrocytic Cp during early postnatal stages resulted in hypomyelination, delayed oligodendrocyte maturation, and increased oxidative stress. Deletion of astrocytic Cp in older mice led to iron accumulation, neurodegeneration, myelin loss, and abnormal behavioral profiles. The study highlights the importance of astrocytic Cp in brain development, aging, and myelin integrity.
Article
Chemistry, Multidisciplinary
Daichi Sawada, Kouichi Asakura, Taisuke Banno
Summary: The study explores the induction of multistep phase transitions using cationic amphiphiles in molecular crystals, with insights into the phase transitions mechanism revealed through H-1 NMR and fluorescence anisotropy measurements. The findings suggest that multiple pathway-dependent phase transitions of supramolecular self-assemblies can offer a methodology for the development of new stimuli-responsive materials.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Jennifer K. Lee, Jung-Heun Ha, James F. Collins
Summary: Physiologically relevant iron-copper interactions have been frequently documented, with excess enteral iron inhibiting copper absorption and leading to copper depletion in pregnant and lactating dams and their pups. This highlights the importance of considering the impact of excess iron supplementation on copper absorption and homeostasis.
Article
Biochemistry & Molecular Biology
Anne-Elisabeth Molza, Yvonne Westermaier, Magali Moutte, Pierre Ducrot, Claudia Danilowicz, Veronica Godoy-Carter, Mara Prentiss, Charles H. Robert, Marc Baaden, Chantal Prevost
Summary: Recent advances in structural biophysics and integrative modelling methods have allowed us to understand the structures of large macromolecular assemblies, leading to new insights into biological processes. We have developed a modelling pipeline that combines experimental and theoretical knowledge with state-of-the-art modelling tools, enabling the study of complex biological systems and mechanisms.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Chemistry, Multidisciplinary
Yao-Hua Liu, Ying-Ming Zhang, Hua-Jiang Yu, Yu Liu
Summary: The use of cucurbiturils (CBs) in biomacromolecular assemblies has made significant progress in various applications, including biosensors, biochemical reaction regulation, and disease treatment. CBs have also shown the ability to promote subcellular bioimaging in different organelles, demonstrating diverse applications in the field of supramolecular chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Pattaraporn Thepsuwan, Asmita Bhattacharya, Zhenfeng Song, Stephen Hippleheuser, Shaobin Feng, Xiaoqiong Wei, Nupur K. Das, Mariana Sierra, Juncheng Wei, Deyu Fang, Yu-Ming M. Huang, Kezhong Zhang, Yatrik M. Shah, Shengyi Sun
Summary: The SEL1L-HRD1 protein complex of endoplasmic reticulum-associated degradation (ERAD) in hepatocytes controls systemic iron homeostasis through regulating ceruloplasmin (CP), a ferroxidase involved in iron distribution. The absence of ERAD leads to accumulation of CP in the ER and increased secretion, affecting iron distribution and oxidation status.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Daria S. Morozova, Alexey A. Martyanov, Sergei Obydennyi, Julia-Jessica D. Korobkin, Alexey Sokolov, Ekaterina Shamova, Irina Gorudko, Anna L. Khoreva, Anna Shcherbina, Mikhail A. Panteleev, Anastasia N. Sveshnikova
Summary: In this study, an ex vivo experimental model for observation of granulocyte activity in thrombus formation was developed. Results showed that granulocytes from patients with WAS had reduced motility compared to healthy donors. The study suggests that WASP deficiency disrupts granulocyte behavior in thromboinflammatory conditions.
Article
Biochemical Research Methods
Vitaly G. Grigorenko, Tatiana E. Petrova, Ciaran Carolan, Maya Yu Rubtsova, Igor Uporov, Joana Pereira, Grzegorz Chojnowski, Valeriya R. Samygina, Victor S. Lamzin, Alexey M. Egorov
Summary: This study presents novel crystal structures of the native beta-lactamase TEM-171 and its complexes with the inhibitor tazobactam. The results provide valuable insights for the rational design of new beta-lactamase inhibitors.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
A. Sokolov, I. N. Isakova-Sivak, D. A. Mezhenskaya, V. A. Kostevich, N. P. Gorbunov, A. Yu Elizarova, V. A. Matyushenko, Yu M. Berson, N. A. Grudinina, N. N. Kolmakov, Y. A. Zabrodskaya, A. S. Komlev, I. Semak, A. Budevich, L. G. Rudenko, V. B. Vasilyev
Summary: The pathogenesis of SARS-CoV-2 infection involves dysregulations of iron metabolism. Spike protein competes with transferrin receptor 1 (TfR1) ligands and shows cross-reactivity with lactoferrin (Lf) and transferrin (Tf). Apo-Lf and holo-Lf can inhibit SARS-CoV-2 replication and protect against COVID-19-induced pathogenesis.
Article
Biophysics
I. S. Vaskan, A. T. Prikhodko, M. V. Petoukhov, E. V. Shtykova, N. V. Bovin, A. B. Tuzikov, V. A. Oleinikov, A. V. Zalygin
Summary: The detailed analysis of the surface structure of nanoparticles is essential for the rational design of drug delivery systems. However, characterizing the surface structure under physiological conditions is challenging. In this study, the combination of SAXS contrast variation and ab initio bead modeling was used to investigate nanoparticle surface structure. By gradually increasing the solvent electron density, the shell coating thickness and uniformity around the nanoparticle core were assessed.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Biochemistry & Molecular Biology
Iain M. Hay, Maria Shamin, Eve R. Caroe, Ahmed S. A. Mohanned, Dmitri I. Svergun, Cy M. Jeffries, Stephen C. Graham, Hayley J. Sharpe, Janet E. Deane
Summary: Type IIB receptor protein tyrosine phosphatases mediate cell adhesion and signaling through their extracellular and cytoplasmic domains, respectively. The crystal structure of PTPRK has revealed an intermembrane adhesion mode consistent with other family members. Comparison with PTPRM structure suggests that conformational differences between the domains may contribute to homophilic specificity. Analysis of the full-length PTPRM and PTPRK proteins using small-angle X-ray scattering reveals rigid extended conformations and one residue difference at the interaction interface that affects dimer formation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Goksin Liu, Erhan Ekmen, Farzaneh Jalalypour, Haydyn D. T. Mertens, Cy M. Jeffries, Dmitri Svergun, Ali Rana Atilgan, Canan Atilgan, Zehra Sayers
Summary: This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations and populations of a pH/ionic strength (IS) sensitive protein. The protein studied is the periplasmic ferric binding protein A (FbpA) involved in iron capture from higher organisms by bacteria. The study reveals the detectable changes in conformational distribution of FbpA under different conditions, but detection of conformational changes due to point mutation D52A and changes in ionic strength has been challenging.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Gabriela Guedez, Gabriele Loers, Cy M. Jeffries, Sandra Kozak, Rob Meijers, Dmitri I. Svergun, Melitta Schachner, Christian Loew
Summary: The cell adhesion molecule L1 plays crucial roles in neural development, regeneration, synaptic plasticity, and tumor cell migration. L1 is a member of the immunoglobulin superfamily and consists of Ig-like domains and fibronectin type III homologous repeats. The second Ig-like domain is involved in cell binding, and the fibronectin type III homologous repeats contribute to signal transduction.
Article
Biochemistry & Molecular Biology
Eva-Maria Krammer, Clarisse Bridot, Sonia Serna, Begona Echeverria, Shubham Semwal, Benoit Roubinet, Kim van Noort, Ruud H. P. Wilbers, Gleb Bourenkov, Jerome de Ruyck, Ludovic Landemarre, Niels Reichardt, Julie Bouckaert
Summary: The FimH type-1 fimbrial adhesin allows pathogenic Escherichia coli to adhere to glycoproteins in human bladder and intestinal tract linings. Oligomannose-3 and oligomannose-5 have the highest affinity for FimH. Our findings provide important structural insights for the design of multivalent FimH antagonists that bind with positive cooperativity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Instruments & Instrumentation
Tilman Donath, Dubravka Sisak Jung, Max Burian, Valeria Radicci, Pietro Zambon, Andrew N. Fitch, Catherine Dejoie, Bingbing Zhang, Marie Ruat, Michael Hanfland, Cameron M. Kewish, Grant A. van Riessen, Denys Naumenko, Heinz Amenitsch, Gleb Bourenkov, Gerard Bricogne, Ashwin Chari, Clemens Schulze-Briese
Summary: This paper facilitates the optimal use of EIGER2 detectors by providing theory and practical advice on their design, technical specifications, operating modes, and new acquisition features. It also presents examples of their implementation and application at several synchrotron sources, demonstrating their advantages in high-throughput data collection, X-ray diffraction, and optical experiments.
JOURNAL OF SYNCHROTRON RADIATION
(2023)
Article
Biochemical Research Methods
Masakazu Fukuda, Melissa A. Graewert, Cy M. Jeffries, Dmitri I. Svergun, Tadao Yamazaki, Akiko Koga, Yuji Yamanaka
Summary: This study investigates the acidic variants of therapeutic monoclonal antibodies (mAbs) using a refolding approach. The results showed that these acidic variants are conformational variants with minor and localized conformational changes.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Elena V. Mikhalchik, Liliya N. Maltseva, Roxalana K. Firova, Marina A. Murina, Irina V. Gorudko, Daria V. Grigorieva, Viktor A. Ivanov, Ekaterina A. Obraztsova, Dmitry V. Klinov, Ekaterina V. Shmeleva, Sergey A. Gusev, Oleg M. Panasenko, Alexey V. Sokolov, Nikolay P. Gorbunov, Lyubov Y. Filatova, Nadezhda G. Balabushevich
Summary: This study investigated the effect of incorporating pectin into vaterite microparticles on cytotoxicity and mucin-dependent neutrophil activation. The results showed that the inclusion of pectin did not cause damage to neutrophils and did not have direct pro- or antioxidant effects. However, when neutrophils were activated by mucin-treated microparticles, the incorporation of pectin into vaterite microspheres enabled an antioxidant effect to be reached, presumably via exposed ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Stefano Da Vela, Giovanni Saudino, Francesca Lucarelli, Lucia Banci, Dmitri I. Svergun, Simone Ciofi-Baffoni
Summary: In humans, the biosynthesis and trafficking of mitochondrial [4Fe-4S]2+ clusters is a highly coordinated process that requires a complex protein machinery. Two [2Fe-2S]2+ clusters are converted into a [4Fe-4S]2+ cluster on an ISCA1-ISCA2 complex. NFU1 is the accessory protein that first receives the [4Fe-4S]2+ cluster from the ISCA1-ISCA2 complex.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kirill Kovalev, Fedor Tsybrov, Alexey Alekseev, Vitaly Shevchenko, Dmytro Soloviov, Sergey Siletsky, Gleb Bourenkov, Michael Agthe, Marina Nikolova, David von Stetten, Roman Astashkin, Sergey Bukhdruker, Igor Chizhov, Antoine Royant, Alexander Kuzmin, Ivan Gushchin, Riccardo Rosselli, Francisco Rodriguez-Valera, Nikolay Ilyinskiy, Andrey Rogachev, Valentin Borshchevskiy, Thomas R. Schneider, Ernst Bamberg, Valentin Gordeliy
Summary: By studying a bacterial inward proton-pumping rhodopsin, researchers have uncovered its molecular mechanism and revealed how proton wires mediate ion selectivity and proton transport through cell membrane. Proton transport is essential for cell life and understanding the mechanisms behind it is a challenge. The study presents a comprehensive function-structure analysis of a light-driven bacterial inward proton pump, providing insights into proton translocation and the use of synchrotron source for rhodopsin studies. The results also have implications for optogenetics.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Microbiology
Eleonora A. Starikova, Jennet T. Mammedova, Arina Ozhiganova, Tatiana A. Leveshko, Aleksandra M. Lebedeva, Alexey V. Sokolov, Dmitry V. Isakov, Alena B. Karaseva, Larissa A. Burova, Igor V. Kudryavtsev
Summary: In this study, the impact and mechanism of streptococcal arginine deiminase (ADI) on the function of human peripheral blood T lymphocytes were investigated. The results showed that ADI decreased arginine concentration, suppressed immune cell activity and altered cell differentiation state, as well as inhibited autophagy processes.
Article
Biochemistry & Molecular Biology
Alexander L. L. Ksenofontov, Maxim V. V. Petoukhov, Vladimir V. V. Matveev, Natalia V. V. Fedorova, Pavel I. I. Semenyuk, Alexander M. M. Arutyunyan, Tatiana I. I. Manukhova, Ekaterina A. A. Evtushenko, Nikolai A. A. Nikitin, Olga K. V. Karpova, Eleonora V. V. Shtykova
Summary: The amino acid sequences of the coat proteins (CPs) of PVX and AltMV share about 40% identity. The N-terminal domains of these proteins differ in sequence and the presence of an N-terminal fragment in PVX CP. The N-terminal domain of PVX CP contributes to the higher thermal stability and ordered structure of PVX virions compared to AltMV.
BIOCHEMISTRY-MOSCOW
(2023)