Article
Biochemistry & Molecular Biology
Pranay Amruth Maroju, Ramakrishnan Ganesan, Jayati Ray Dutta
Summary: In this study, a facile solution-based method was used to surface derivatize poly(& epsilon;-caprolactone) films and electrospun fibers with lysozyme, aiming to impart antimicrobial properties and examine the impact on enzymatic degradation. The derivatized films and fibers showed high antibacterial efficacy against Escherichia coli and Staphylococcus aureus. The degradation rate experienced a slight decrease upon lysozyme derivatization, but this reduction was effectively countered by the inclusion of Tween-20.
MACROMOLECULAR BIOSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
A. Diaz Casas, J. J. Cordoba, B. J. Ferrer, S. Balakrishnan, J. E. Wurm, B. Pastrana-Rios, W. J. Chazin
Summary: This article reports the characterization of the interaction between human CM and hPrp40A. It is shown that CaM binds to FF3 in a Ca2+-dependent manner, forming an extended non-globular state. These results are important for understanding the complex interplay of Ca2+ signaling and Ca2+ sensor proteins in modulating Prp40A-Htt function.
Article
Biochemistry & Molecular Biology
Shuay Abdullayev, Priyanka Kadav, Purnima Bandyopadhyay, Francisco Javier Medrano, Gabriel A. Rabinovich, Tarun K. Dam, Antonio Romero, Rene Roy
Summary: Lactose and N-Acetyllactosamine have been widely used ligands for galectins, but with limited selectivity. In this study, simultaneous modifications at the anomeric position, C-2, and O-3' of each sugar were performed, leading to a 3'-O-sulfated N-Acetyllactosamine analog with a significantly increased affinity of 14.7 μM against human Gal-3. The three best compounds contained sulfate groups at the O-3' position, which are in line with the highly cationic character of the Gal-3 binding site.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Construction & Building Technology
O. Linderoth, L. Wadso, D. Jansen
Summary: This study showed that the thermal power of hydration can be measured for up to a year using isothermal calorimetry, and the degree of hydration can be determined with good agreement using various methods.
CEMENT AND CONCRETE RESEARCH
(2021)
Article
Polymer Science
Lianlian Fu, Ying Lu, Zhiyong Jiang, Ran Chen, Yongfeng Men
Summary: The study investigates the structural evolution and temperature dependence of crystal thickness in high-density polyethylene (HDPE) under different crystallization methods. It was found that stretched HDPE processed much thinner crystalline lamellae, while samples crystallized isothermally exhibited better stability.
Article
Chemistry, Applied
Wei Liao, Emilie Dumas, Abdelhamid Elaissari, Adem Gharsallaoui
Summary: This study investigated the formation mechanism of multilayer emulsions in oil-in-water systems by using isothermal titration calorimetry (ITC) and dynamic light scattering (DLS) techniques. The results showed that ITC could provide more accurate information about the polymer concentration effect. The titration experiment confirmed that low methoxyl pectin (LMP) mainly bound sodium caseinate (CAS)-coated droplets through electrostatic forces, and stable multilayer emulsions were obtained by titrating CAS-stabilized droplets into LMP.
FOOD HYDROCOLLOIDS
(2023)
Review
Chemistry, Multidisciplinary
Jayesh Sonje, Seema Thakral, Susan Krueger, Raj Suryanarayanan
Summary: This review summarizes the applications of differential scanning calorimetry (DSC) and scattering techniques in protein formulation design and characterization. Scattering techniques include wide angle X-ray diffractometry (XRD), small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS). While DSC is valuable for understanding thermal behavior of the excipients, XRD provides critical information about physical state of solutes during freezing, annealing and in the final lyophile. However, complementary techniques like small-angle scattering are needed to detect biomolecule-related transitions.
PHARMACEUTICAL RESEARCH
(2023)
Article
Chemistry, Applied
B. Goderis, D. M. Dries, M. A. Nivelle, J. A. Delcour
Summary: The gelatinization process of maize and potato starch granules in excess water was studied using various measurement techniques. The crystallinity of both starches disappeared during gelatinization, with temporarily remaining blocklets observed. Differences in the gelatinization process between maize and potato starches may be related to the speed and completeness of granular conversion.
FOOD HYDROCOLLOIDS
(2022)
Article
Multidisciplinary Sciences
Michael Wagener, Stephan Foerster
Summary: The scattering of various types of radiation by matter is widely used for structural characterization. With the advancement of beam sources and detectors, scattering patterns can now be acquired quickly and at large sizes. However, the slow analysis of these patterns has become a bottleneck. In this study, an algorithm based on hypergeometric functions is introduced, providing a significant increase in computational speed compared to current methods. This algorithm enables real-time experiment feedback, analysis of large scattering datasets, and generation of training data for machine learning.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Shams T. A. Islam, Jie Zhang, Fabio Tonin, Renske Hinderks, Yanthi N. Deurloo, Vlada B. Urlacher, Peter-Leon Hagedoorn
Summary: Lignin valorization through laccase catalysis can release aromatic products, but different enzymes exhibit significant variations in conversion efficiency and rate. Trametes versicolor laccase follows Michaelis-Menten kinetics in converting Kraft lignin, with specific thermodynamic and kinetic parameters, making it a promising tool for guiding enzymatic lignin valorization strategies.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Physical
Pablo F. Garrido, Margarida Bastos, Adrian Velazquez-Campoy, Alfredo Amigo, Philippe Dumas, Angel Pineiro
Summary: The injection of air into an isothermal titration calorimeter's sample cell allows for accurate determination of the surface tension of the target liquid, despite the periodic contribution from bubbles. The new algorithm successfully identifies and analyzes these contributions, improving the analysis of calorimetric signals.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Rasool Nasseri, Christine Moresoli, Aiping Yu, Zhongshun Yuan, Chunbao Charles Xu
Summary: The effect of interphase properties on the crystallization behavior of blends of poly(lactic acid) (PLA)/acetylated starch (AS) with different degrees of substitution (DSs) was investigated. It was found that the crystallization rate varied for different DSs of AS in the PLA/AS blends under isothermal and non-isothermal conditions. The interphase properties and thickness played a role in interrupting crystallization, while hydrogen bonding and hydrophobic interactions facilitated crystallization under non-isothermal conditions.
Article
Chemistry, Physical
Badri Narayanan Narasimhan, Alexander W. Dixon, Bradley Mansel, Andrew Taberner, Jitendra Mata, Jenny Malmstrom
Summary: This study investigates hydrogels made with semi-interpenetrating networks of oligomerized polyphenol tannic acid and poly(acrylamide). The presence of micron-sized hydrogen bonded clusters in the hydrogels and the breaking of these clusters above a critical solution temperature are observed using small angle X-ray scattering and small and ultra-small angle neutron scattering. Polarized optical microscopy shows enhanced anisotropy for gels with oligomerized tannic acid, and rheological studies reveal self-healing behavior of the gels. The findings from this study contribute to the rational design of hydrogels for biomedical applications.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Review
Pharmacology & Pharmacy
Iago Dillion Lima Cavalcanti, Francisco Humberto Xavier Junior, Nereide Stela Santos Magalhaes, Mariane Cajuba de Britto Lira Nogueira
Summary: Isothermal titration calorimetry (ITC) is a technique for evaluating the thermodynamic profiles of connection between two molecules, allowing the experimental design of nanoparticles systems with drugs and/or biological molecules. In the field of pharmaceutical nanotechnology, ITC has been increasingly used to understand the interaction mechanisms in the formation of nanoparticles and the behavior of nanocarriers in in vivo studies. This technique provides quick and easy results to optimize the formulation process of nano-systems.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(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
Chemistry, Multidisciplinary
Petr Konarev, Andrey Yu Gruzinov, Haydyn D. T. Mertens, Dmitri Svergun
Summary: The article presents a general approach for calculating and analyzing SAXS data from lipid mixtures, allowing for the restoration of electron density of lipid bilayers and size distribution of vesicles over the entire angle range. The method is implemented in a computer program, LIPMIX, and demonstrated on layered lipid vesicles undergoing extrusion. This approach is expected to be useful for analyzing various types of lipid-based systems and interactions between target drug molecules and carrier/delivery systems.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Chemistry, Multidisciplinary
D. C. F. Wieland, M. A. Schroer, A. Yu Gruzinov, C. E. Blanchet, C. M. Jeffries, D. Svergun
Summary: Small-angle X-ray scattering is commonly used to study biological macromolecules in solution, with anomalous scattering providing additional information from specific atoms. Despite challenges due to low anomalous scattering effects, pilot ASAXS experiments on dilute macromolecular solutions have been successfully conducted to extract specific anomalous dispersion terms.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Biology
Komal Soni, Georg Kempf, Karen Manalastas-Cantos, Astrid Hendricks, Dirk Flemming, Julien Guizetti, Bernd Simon, Friedrich Frischknecht, Dmitri I. Svergun, Klemens Wild, Irmgard Sinning
Summary: The study investigates the Alu domain of Plasmodium falciparum, a divergent apicomplexan protozoan that causes human malaria, and reveals that it adopts an 'open' Y-shaped conformation unlike its prokaryotic and eukaryotic counterparts. The analysis extends the structural database of Alu domains to protozoan species and shows species-specific differences in the recognition of SRP Alu domains by ribosomes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Petr Konarev, Melissa A. Graewert, Cy M. Jeffries, Masakazu Fukuda, Taisiia A. Cheremnykh, Vladimir V. Volkov, Dmitri Svergun
Summary: SAXS is commonly used for structural analysis of biological macromolecules in solution, and combining SAXS with chromatography setups has become popular in research. The computer program EFAMIX, based on evolving factor analysis (EFA), efficiently restores scattering and concentration profiles of components from mixed SAXS data, proving useful for interpretation and analysis of fractions in the sample.
Biographical-Item
Chemistry, Multidisciplinary
Dmitri Svergun, Jill Trewhella
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2022)
Article
Multidisciplinary Sciences
Ivan Corbeski, Xiaohu Guo, Bruna Eckhardt, Domenico Fasci, Wouter Wiegant, Melissa A. Graewert, Kees Vreeken, Hans Wienk, Dmitri Svergun, Albert J. R. Heck, Haico van Attikum, Rolf Boelens, Titia K. Sixma, Francesca Mattiroli, Hugo van Ingen
Summary: Nucleosome assembly requires specific histone chaperones, but this study found that the acidic domain of DNA repair factor APLF can directly assemble the histone octamer and deposit it on DNA to form nucleosomes, which may be a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.
Article
Biochemistry & Molecular Biology
Maxime Killer, Giada Finocchio, Haydyn D. T. Mertens, Dmitri I. Svergun, Els Pardon, Jan Steyaert, Christian Loew
Summary: Proton-coupled Oligopeptide Transporters (POTs) mediate the uptake of short di- and tripeptides. This study determined the structure of DtpC and provided insights into its ligand specificity using cryogenic electron microscopy (cryo-EM). The research highlights the value of nanobodies for structure determination of low molecular weight integral membrane proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Stefan R. Marsden, Hein J. Wijma, Michael K. F. Mohr, Ines Justo, Peter-Leon Hagedoorn, Jesper Laustsen, Cy M. Jeffries, Dmitri Svergun, Luuk Mestrom, Duncan G. G. McMillan, Isabel Bento, Ulf Hanefeld
Summary: This study reveals a novel mechanism of enzyme activity regulation, which involves the dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. This type of regulation may be widespread but has been largely overlooked.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Tomasz H. Benedyk, Viv Connor, Eve R. Caroe, Maria Shamin, Dmitri I. Svergun, Janet E. Deane, Cy M. Jeffries, Colin M. Crump, Stephen C. Graham
Summary: Herpes simplex virus-1 (HSV-1) alters cellular membrane lipid composition during infection. This study demonstrates that a virus-encoded protein, pUL21, promotes the conversion of ceramide (Cer) to sphingomyelin (SM) by activating CERT. The study also reveals the importance of specific protein-protein interactions in HSV-1 mediated sphingolipid metabolism.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Anna Ostendorp, Steffen Ostendorp, Yuan Zhou, Zoe Chaudron, Lukas Wolffram, Khadija Rombi, Linn von Pein, Sven Falke, Cy M. Jeffries, Dmitri I. Svergun, Christian Betzel, Richard J. Morris, Friedrich Kragler, Julia Kehr
Summary: Long-distance RNA transport via the phloem is crucial for communication between different plant tissues. In this study, the phloem-associated RNA chaperone-like (PARCL) protein was characterized and its role in RNA binding and condensate formation was investigated. The results suggest that the function and structure of PARCL can be regulated by modifications.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
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
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
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)
