Article
Multidisciplinary Sciences
Lin Mei, Matthew J. Reynolds, Damien Garbett, Rui Gong, Tobias Meyer, Gregory M. Alushin
Summary: This study focuses on the role of T-plastin in constructing actin networks. By using a machine-learning-enabled cryo-electron microscopy technique, the researchers uncover a sequential bundling mechanism that allows T-plastin to bridge and link parallel and antiparallel actin filaments. This bridging mechanism is essential for adapting to different actin network structures and functions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Shakiba Nikfarjam, Rebecca Gibbons, Faraz Burni, Srinivasa R. Raghavan, Mikhail A. Anisimov, Taylor J. Woehl
Summary: Cells can assemble dynamic protein-based nanostructures through dissipative assembly. In this study, we demonstrated the dissipative cross-linking of transient protein hydrogels using a redox cycle, which exhibited protein unfolding-dependent lifetimes and mechanical properties. The results indicate that the protein secondary structure mediated the transient hydrogel's lifetime and mechanical properties by mediating the redox reactions.
Article
Biochemistry & Molecular Biology
Christopher Tsiros, Emily Punch, Emily Schaffter, Sabrina Apel, Matthew J. Gage
Summary: Titin, the largest muscle protein, plays a crucial role in muscle tension, sarcomeric integrity, and cell signaling. This study demonstrates that the N2A region of Titin binds to F-actin through specific domains, and this binding is length-dependent and calcium-dependent.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Takayuki Yasunaga, Johannes Wiegel, Max D. Bergen, Martin Helmstaedter, Daniel Epting, Andrea Paolini, Oezgun Cicek, Gerald Radziwill, Christina Engel, Thomas Brox, Olaf Ronneberger, Peter Walentek, Maximilian H. Ulbrich, Gerd Walz
Summary: Motile cilia of Xenopus epidermis are anchored to microridge-like membrane protrusions to maintain their directionality. The actin cytoskeleton is dynamic during the early development of multiciliated cells, and subapical actin filaments are anchored to microridge-like structures. These observations identify microridge-like structures as an essential component of basal body rootlet anchoring in MCCs.
NATURE COMMUNICATIONS
(2022)
Article
Polymer Science
Isamu Kawarazaki, Mikihiro Hayashi, Akitsugu Shibata, Michihiro Kaai
Summary: This study investigates the effects of domain cross-linking on tensile properties of ABA triblock copolymers, highlighting improvements in stress and recovery properties. The research provides essential insights for understanding the mechanical properties of block copolymer-based materials and suggests potential modifications for enhancing their physical properties.
Article
Immunology
Utpal Kumar Adhikari, Elif Sakiz, Xian Zhou, Umma Habiba, Sachin Kumar, Meena Mikhael, Matteo Senesi, Chun Guang Li, Gilles J. Guillemin, Lezanne Ooi, Monique Antoinette David, Steven Collins, Tim Karl, Mourad Tayebi
Summary: This study demonstrated that cross-linking PrP(C) with anti-PrP antibodies triggers a neuronal hypersensitivity response and emphasizes the crucial role of microglia in initiating an IgG-mediated neuronal hypersensitivity response. Furthermore, it suggests the importance of including allergenic evaluation of therapeutic antibodies for neurodegenerative disorders to develop safe and targeted biotherapeutics.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Zhuoyuan Zhang, Jianwei Lin, Zheng Liu, Gaofei Tian, Xiao-Meng Li, Yihang Jing, Xin Li, Xiang David Li
Summary: This article reviews recent advances in using photo-crosslinking strategies to investigate the epigenetic interactome, focused on the protein-protein interactions mediated by epigenetic marks in histone tails. The future directions include developing photo-crosslinking-based tools and methods for studying binding events in nucleosomal/chromatinic contexts, and for capturing the epigenetic interactome in live cells or even organisms.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Jasjot Singh, Hadeer Elhabashy, Pathma Muthukottiappan, Markus Stepath, Martin Eisenacher, Oliver Kohlbacher, Volkmar Gieselmann, Dominic Winter
Summary: Lysosomes are crucial organelles for degradation and metabolism regulation. Protein complexes play a decisive role in lysosomal function. This study investigates lysosomes and early endosomes using cross-linking mass spectrometry, revealing protein interactions, structures, and cargo of flotillin-mediated endocytosis.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Ulrike Doering, Dmitry Grigoriev, Tino Riske, Andreas Fery, Alexander Boeker
Summary: The mechanical properties of proteinaceous and composite microcapsules loaded with oil were measured using SFM and evaluated with the Reissner model. The results showed significantly higher Young's moduli in protein capsules due to intermolecular crosslinking, while conformational restrictions in composite microcapsules led to reduced elasticity.
Review
Cell Biology
Franziska Lehne, Sven Bogdan
Summary: The actin cytoskeleton is a dynamic filament system that provides structure and forces for cellular processes. It is regulated by conserved proteins, including calcium-binding EF-hand-containing actin cross-linking proteins. Previous studies have shown that cytoplasmic calcium plays a role in relaying information to the actin cytoskeleton, but the mechanisms are still unclear. This mini-review summarizes new perspectives on how calcium fluxes are transduced to the actin cytoskeleton in a physiological context, focusing on three specific calcium-binding proteins and their effects on actin reorganization during cell migration and wound closure.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Optics
V Stancalie
Summary: In this study, a close-coupling calculation using the Breit Pauli R-matrix approach was conducted for the photoionization process of ground and excited states of a Ne-like Mo XXXIII ion. The results indicate variations in the behavior of photoionization cross sections of different excited states due to model differences and correlation effects.
JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER
(2021)
Article
Chemistry, Multidisciplinary
Zaiqiang Ma, Kangren Kong, Yu Yin, Zhengxi Guo, Xiaoming Ma, Qingyun Lin, Jie Wang, Yinlin Shen, Xingyu Lu, Xurong Xu, Xueqian Kong, Zhaoming Liu, Ruikang Tang
Summary: In this study, a group of compounds resembling alloy-like minerals were synthesized by cross-linking ionic oligomers, and their mechanical properties could be adjusted by tailoring their chemical compositions. This strategy expands the chemical scope of inorganic materials and holds promise for preparing high-performance minerals.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Analytical
Julius Fuersch, Carsten Voormann, Kai-Michael Kammer, Florian Stengel
Summary: Small heat-shock proteins (sHSPs) play important roles in the cellular stress response across all species, primarily by binding early unfolding states of proteins to prevent aggregation. Research on yeast Hsp26 using cross-linking mass spectrometry (XL-MS) has provided detailed structural information on sHSP activation and client binding, revealing the significance of the middle domain in client-independent interaction and potential client specificity through additional binding sites within its alpha-crystallin domain and C-terminal extension.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Helisa H. Wippel, Juan D. Chavez, Andrew D. Keller, James E. Bruce
Summary: The XL-MS technique provides insight into protein conformations and interactions within their cellular environment, while the iqPIR strategy allows for comparative interactome studies using isotope encoded chemical cross-linkers. Multiplexed iqPIR enables quantitative interactome analysis of up to six biological samples in a single LC-MS acquisition, revealing specific protein conformational and interaction changes in response to different inhibitors.
ANALYTICAL CHEMISTRY
(2022)
Article
Materials Science, Multidisciplinary
Yongan Niu, Shanhong Zhao, Bolun Song, Chao Wang, Xianqi Cao, Xin Zhang
Summary: In this study, aluminum phosphate framework (APF)/bismaleimide (BMI) hybrid composites with the double cross-linking hybrid (DCH) structures were successfully fabricated. The three-dimensional (3D) structures of APF played a critical role in enhancing the mechanical properties. The lamellar aluminum phosphate (LAP) particles were chosen to strengthen the APF/BMI composites, and it was found that they could enhance the mechanical properties and decrease the dielectric constant. This study provides helpful insights for designing higher performance inorganic/organic hybrid composites and expanding their applications.
MATERIALS & DESIGN
(2023)
Correction
Crystallography
M. A. Marchenkova, P. V. Konarev, A. S. Boikova, K. B. Ilina, Yu. V. Pisarevsky, M. V. Kovalchuk
CRYSTALLOGRAPHY REPORTS
(2022)
Article
Crystallography
Yuliya Kordonskaya, Vladimir Timofeev, Margarita A. Marchenkova, Petr Konarev
Summary: This study simulated the possible types of precursor clusters in proteinase K solution using molecular dynamics technique. By stability analysis, the most probable type of dimer formed before crystallization was identified. SAXS data modeling supported the results and abnormal stability increase of thermophilic proteinase K at higher temperature was observed.
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
Francesca Paoletti, Sonia Covaceuszach, Alberto Cassetta, Antonio N. N. Calabrese, Urban Novak, Petr Konarev, Joze Grdadolnik, Doriano Lamba, Simona Golic Grdadolnik
Summary: Nerve growth factor (NGF) and its precursor, proNGF, play different roles in neuronal maintenance and apoptosis. The binding of NGF or proNGF to receptors triggers intracellular signaling pathways, which can be modulated by small-molecule ligands. ATP binds to the pro-peptide of proNGF with a micromolar dissociation constant, and this interaction is modulated by Mg2+. The binding of ATP induces a conformational rearrangement of the flexible pro-peptide domain, suggesting its role as an allosteric modulator of proNGF conformation.
Article
Biophysics
Joerg Ehrit, Tobias W. Graewert, Hendrik Goeddeke, Petr Konarev, Dmitri I. Svergun, Norbert Nagel
Summary: This study investigated the structural organization of polysorbate micelles, both alone and in the presence of myristic acid. The results showed that the micelles were polydisperse ellipsoidal structures containing about 22-35 molecules per micelle. Addition of myristic acid had minimal effects on the scattering data at low concentrations, but increased the average size of the micelles at high concentrations, indicating penetration of myristic acid into the surfactant micelles. These findings provide insights into the role of polysorbate in preventing or delaying fatty acid particle formation.
BIOPHYSICAL JOURNAL
(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
Timur N. Bozin, Igor M. Berdyshev, Ksenia N. Chukhontseva, Maria A. Karaseva, Petr V. Konarev, Anna M. Varizhuk, Dmitry M. Lesovoy, Alexander S. Arseniev, Sergey V. Kostrov, Eduard V. Bocharov, Ilya V. Demidyuk
Summary: A new protein inhibitor called M4in was discovered in the bacterium Serratia proteamaculans and its mechanism of action is still unknown. This inhibitor may play a role in regulating bacterial pathogenesis by controlling the activity of a protease called protealysin-like proteases (PLPs). The researchers determined the 3D structure of M4in using NMR spectroscopy and proposed a molecular mechanism for the inhibitor based on their model analysis and site-directed mutagenesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Anna S. Kichkailo, Andrey A. Narodov, Maria A. Komarova, Tatiana N. Zamay, Galina S. Zamay, Olga S. Kolovskaya, Evgeniy E. Erakhtin, Yury E. Glazyrin, Dmitry V. Veprintsev, Roman Moryachkov, Vladimir V. Zabluda, Irina Shchugoreva, Polina Artyushenko, Vladimir A. Mironov, Dmitry I. Morozov, Vladimir A. Khorzhevskii, Anton Gorbushin, Anastasia A. Koshmanova, Elena D. Nikolaeva, Igor P. Grinev, Ivan I. Voronkovskii, Daniil S. Grek, Kirill Belugin, Alexander A. Volzhentsev, Oleg N. Badmaev, Natalia A. Luzan, Kirill A. Lukyanenko, Georgy Peters, Ivan N. Lapin, Andrey K. Kirichenko, Petr Konarev, Evgeny Morozov, Gleb G. Mironov, Ana Gargaun, Darija Muharemagic, Sergey S. Zamay, Elena Kochkina, Maya A. Dymova, Tatiana E. Smolyarova, Alexey E. Sokolov, Andrey A. Modestov, Nikolay A. Tokarev, Nikolay Shepelevich, Anastasia Ozerskaya, Natalia G. Chanchikova, Alexey Krat, Ruslan A. Zukov, Varvara I. Bakhtina, Pavel G. Shnyakin, Pavel A. Shesternya, Valery A. Svetlichnyi, Marina M. Petrova, Ivan P. Artyukhov, Felix N. Tomilin, Maxim Berezovski
Summary: We developed DNA aptamers that specifically bind to glial tumor cells for visualization diagnostics of central nervous system tumors. These aptamers were selected to bind to postoperative human glial primary tumors and not to healthy brain cells and meningioma. The study involved sequencing and analyzing ssDNA pools, determining three-dimensional structures, isolating and identifying molecular target proteins, and verifying binding sites and post-translational modifications. The aptamers were successfully used for detection, staining, and visualization of brain tumors.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Crystallography
Felix N. Chukhovskii, Petr V. Konarev, Vladimir V. Volkov
Summary: The central point of validity in computer X-ray diffraction micro tomography is to enhance the digital contrast and spatial resolution of 3D-recovered nano-scaled objects in crystals. To tackle this issue, denoising of 2D image patterns data involved in the 3D high-resolution recovery processing is addressed. The effectiveness of the statistical average hypothesis is demonstrated through the recovery of nano-scaled crystal structures and the validation using the peak signal-to-noise ratio (PSNR) criterion.
Article
Crystallography
Margarita A. A. Marchenkova, Sergei V. V. Chapek, Petr V. V. Konarev, Ksenia B. B. Ilina, Georgy S. S. Peters, Yury V. V. Pisarevsky, Vladimir A. A. Shishkov, Alexander V. V. Soldatov, Mikhail V. V. Kovalchuk
Summary: A multichannel microfluidic cell(MFC)obtained using 3D printing was used to study the structure of complex solutions by small-angle X-ray scattering(SAXS)at the BioMUR beamline of the Kurchatov synchrotron. A comparative analysis of SAXS signal showed that MFC has significant advantages over the standard capillary. The dynamics of SAXS scattering curves for lysozyme solutions were investigated, and the obtained data were consistent with known data.
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
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
M. A. Marchenkova, A. S. Boikova, K. B. Ilina, P. V. Konarev, Yu. V. Pisarevsky, Yu. A. Dyakova, M. V. Kovalchuk
Summary: A model for the transition from disordered liquid state to the solid phase has been proposed based on the correlation between precursor clusters and solid phase formation. The model was experimentally validated by studying the oligomeric structure of lysozyme protein solutions and the peculiarities of solid phase formation. The results showed that the presence of octamers is necessary for solid phase formation, with perfect monocrystals forming at low octamer concentrations, mass crystallization occurring at higher supersaturation, and an amorphous phase forming at high octamer concentrations.
Article
Chemistry, Multidisciplinary
Ivan Reznik, Mikhail A. Baranov, Sergei A. Cherevkov, Petr V. Konarev, Vladimir V. Volkov, Stanislav Moshkalev, Daria B. Trushina
Summary: This study addresses the challenge of continuous CaCO3 particle synthesis using microfluidic technology. CaCO3 nanoparticles in vaterite form were successfully synthesized using a custom microfluidic chip. The two-phase synthesis method inside emulsion microreactors demonstrated superior performance in terms of size control compared with the one-phase approach. The ability to obtain CaCO3 nanoparticles in the desired polymorph form with the possibility of scaling up the synthesis opens up opportunities for various industrial applications of the developed two-phase microfluidic method.