Article
Instruments & Instrumentation
Andrey Yu Gruzinov, Martin A. Schroer, Karen Manalastas-Cantos, Alexey G. Kikhney, Nelly R. Hajizadeh, Florian Schulz, Daniel Franke, Dmitri Svergun, Clement E. Blanchet
Summary: Small-angle X-ray scattering (SAXS) is a method for studying nanostructured systems and biological macromolecules, while anomalous X-ray scattering (ASAXS) utilizes changes in scattering properties of atoms to obtain element-specific information. ASAXS measurements on biological macromolecules are challenging due to weak anomalous effects, but recent developments at the P12 beamline have allowed for successful ASAXS experiments on model systems.
JOURNAL OF SYNCHROTRON RADIATION
(2021)
Article
Biochemistry & Molecular Biology
Alexander W. Mauney, Uma M. Muthurajan, Karolin Luger, Lois Pollack
Summary: Nucleosomes in eukaryotic cells are organized into higher order structures for genome compaction, and understanding their organization is crucial in studying DNA storage efficiency. Arrays of linked nucleosomes serve as models for understanding how DNA and protein properties affect their arrangement, while important questions remain regarding the effects of histone proteins and other chromatin-associated protein partners on nucleosome spacing.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Instruments & Instrumentation
Oskar Berntsson, Ann E. Terry, Tomas S. Plivelic
Summary: The function of biomolecules is closely related to their structure and changes therein. Time-resolved X-ray solution scattering and laser-induced temperature jumps are powerful techniques for studying structural changes in biomolecules.
JOURNAL OF SYNCHROTRON RADIATION
(2022)
Article
Physics, Particles & Fields
Iris Abt, Chris Gooch, Felix Hagemann, Lukas Hauertmann, David Hervas Aguilar, Xiang Liu, Oliver Schulz, Martin Schuster, Anna Julia J. Zsigmond
Summary: This paper describes the construction and operation of a novel Compton scanner setup for pulse shape studies in high-purity germanium detectors. It also discusses the reconstruction of interaction points in the detector and the testing of simulation inputs and models using the Compton scanner.
EUROPEAN PHYSICAL JOURNAL C
(2022)
Article
Chemistry, Multidisciplinary
Andreas Josef Schmid, Lars Wiehemeier, Sebastian Jaksch, Harald Schneider, Arno Hiess, Torsten Bogershausen, Tobias Widmann, Julija Reitenbach, Lucas P. Kreuzer, Matthias Kuehnhammer, Oliver Lohmann, Georg Brandl, Henrich Frielinghaus, Peter Mueller-Buschbaum, Regine von Klitzing, Thomas Hellweg
Summary: In order to exploit the potential of the new European Spallation Source in Lund, researchers have developed plug and play sample environments for different soft matter samples using a general carrier platform and unified connectors for software integration and control. This allows for reduced downtimes of instruments related to changing sample environments.
APPLIED SCIENCES-BASEL
(2021)
Article
Chemistry, Physical
Abigail Barclay, Birthe B. Kragelund, Lise Arleth, Martin Cramer Pedersen
Summary: Recent advances in protein expression protocols have allowed for the investigation of structurally complex and disordered biomolecules using small-angle scattering experiments. A modeling scheme has been developed that combines classical form factor based modeling with spherical harmonics-based formulation to accurately calculate scattering profiles from these complex samples. The scheme can account for flexible domains and other structurally elaborate components, and we demonstrate its utility through a case study on a growth hormone receptor membrane protein. We also explore how the scattering profiles vary under different contrasts and discuss the implications for data modeling.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Instruments & Instrumentation
Peng Pan, Jaafar Najafi Rad, Philippe Roncin
Summary: This article describes a UHV setup for grazing incidence fast atom diffraction (GIFAD) experiments, which has a similar geometry to reflection high energy electron diffraction experiments used for surface growth monitoring. The article presents several custom instrumental developments and carefully analyzes the difficulties associated with accurately measuring small scattering angles and the related calibration.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Biochemistry & Molecular Biology
Dmitry S. Molodenskiy, Dmitri Svergun, Alexey G. Kikhney
Summary: This article introduces a method based on artificial neural networks for analyzing small-angle X-ray scattering data, which can reliably predict the size and shape information of dissolved particles.
Article
Chemistry, Multidisciplinary
Florian A. Jung, Maximilian Schart, Lukas Buehrend, Elisabeth Meidinger, Jia-Jhen Kang, Bart-Jan Niebuur, Sina Ariaee, Dmitry S. Molodenskiy, Dorthe Posselt, Heinz Amenitsch, Constantinos Tsitsilianis, Christine M. Papadakis
Summary: Multiblock copolymers with charged blocks exhibit different self-assembly behavior in solutions and thin films, depending on the degree of ionization of the blocks. In solutions, the solubility of the P2VP block and the flexibility of the PDMAEMA block influence structure formation; while in thin films, the segregation strength is crucial for structure formation.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Chemistry, Physical
Dominika Zakutna, Kevin Graef, Dominique Dresen, Lionel Porcar, Dirk Honecker, Sabrina Disch
Summary: The magnetorheological sample environment allows for simultaneous control of magnetic field and shear flow during measurements, enabling the study of structural and magnetic changes in ferrofluids.
COLLOID AND POLYMER SCIENCE
(2021)
Article
Chemistry, Physical
Azzaya Khasbaatar, Andrew Cheng, Austin L. Jones, Justin J. Kwok, Sang Kyu Park, Jessica K. Komar, Oliver Lin, Nicholas E. Jackson, Qian Chen, Dean M. DeLongchamp, John R. Reynolds, Ying Diao
Summary: The aggregation of conjugated polymers in solution is crucial for the morphology and performance of bulk heterojunction organic solar cells (OSCs). However, the specific structures of polymer aggregates in solution and their effects on OSC morphology and performance have not been extensively studied. In this study, we investigate the impact of polymer aggregate structures on the morphology and processing resilience of OSCs using a benzodithiophene-based donor polymer (PM7) and its ester-functionalized derivatives (PM7 D1 and D2). Our results show that PM7 solution forms a combination of semi-crystalline fiber aggregates and amorphous polymer chain network aggregates, while PM7 D1 and D2 solutions primarily form amorphous network aggregates through sidechain associations. Interestingly, the fiber aggregates of PM7 break down at elevated solution temperatures, while the polymer network aggregates remain stable. This temperature-dependent behavior leads to highly processing temperature-sensitive performance in blade-coated devices fabricated from PM7 and ITIC-4F, whereas PM7 D1 and D2 polymers exhibit improved processing temperature resiliency. Furthermore, we find that amorphous, network-like aggregates contribute to superior device performance in blade-coated OSCs due to the formation of blend films with short pi-pi stacking distance, small domain spacing, and face-on preferred molecular orientation. Conversely, fiber-like aggregates result in large pi-pi stacking distance, large domain spacing, and isotropic molecular orientation, which degrade device performance.
CHEMISTRY OF MATERIALS
(2023)
Article
Multidisciplinary Sciences
J. S. Park, J. D. Almer, K. C. James, L. J. Natanson, S. R. Stock
Summary: Members of subclass Elasmobranchii possess bioapatite mineralization in their cartilage skeletons, which has similar crystallography to bone but exhibits some differences. The mineral phase in shark centra has larger nanocrystallite sizes and is associated with less microstrain compared to bone.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biochemistry & Molecular Biology
Staelle Makamte, Aurelien Thureau, Amira Jabrani, Annick Paquelin, Anne Plessis, Matthieu Sanial, Olga Rudenko, Francesco Oteri, Marc Baaden, Valerie Biou
Summary: The inhibition of the Hedgehog pathway by SuFu is crucial for vertebrate development, but has little effect in drosophila. Crystal structures of SuFu in human and drosophila show differences, and our study reveals that the solution structures of SuFu in drosophila and vertebrates are also different. The highly conserved IDR2 region in vertebrates allows for partner interactions and post-translational modifications, while insects have a shorter and less mobile IDR2 region.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Polymer Science
Apisit Banpean, Hideaki Takagi, Nobutaka Shimizu, Noriyuki Igarashi, Shinichi Sakurai
Summary: The study focused on the confined crystallization of PEG in PLLA spherulite in a PLLA/PEG blend specimen using SAXS/WAXS measurements. The results showed suppression of PEG lamellae growth in the thickness direction due to space confinement by preformed PLLA lamellae, while also observing more regular stacking in the blend specimen.
Article
Chemistry, Physical
Christina Efthymiou, L. Magnus Bergstrom, Jannik Nedergaard Pedersen, Jan Skov Pedersen, Per Hansson
Summary: Through experiments, it was found that common amphiphilic drug molecules form small micelles during self-assembly, with micelle size reaching a maximum at a certain concentration and slightly decreasing at higher concentrations. An increase in drug concentration and decrease in pH lead to an increase in micelle charge, and the aggregation behavior of all studied drugs resembles that of conventional surfactants.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
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
Joao P. L. Guerra, Clement E. Blanchet, Bruno J. C. Vieira, Joao C. Waerenborgh, Nykola C. Jones, Soren Vronning Hoffmann, Alice S. Pereira, Pedro Tavares
Summary: DNA-binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes as a bacterial defense mechanism. They protect bacterial DNA from damage by binding directly or removing precursors of reactive oxygen species. The conformation of the N-terminal tails of Dps proteins is altered upon metal binding in a reversible and specific manner, indicating a potential regulatory process for their DNA-binding properties through metal binding to their N- and/or C-terminal extensions.
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.
Article
Multidisciplinary Sciences
Melissa A. Graewert, Christoph Wilhelmy, Tijana Bacic, Jens Schumacher, Clement Blanchet, Florian Meier, Roland Drexel, Roland Welz, Bastian Kolb, Kim Bartels, Thomas Nawroth, Thorsten Klein, Dmitri Svergun, Peter Langguth, Heinrich Haas
Summary: This study presents a generic approach to determine size-dependent critical quality attributes in nanoparticulate pharmaceutical products, using a combination of AF4 and SAXS techniques. The method provides valuable information for the study and development of drug formulations.
SCIENTIFIC REPORTS
(2023)
