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
Cell Biology
Eugeny E. Orlov, Alexey M. Nesterenko, Daria D. Korotkova, Elena A. Parshina, Natalia Yu Martynova, Andrey G. Zaraisky
Summary: This study investigates the genes involved in scaling of embryonic patterning and identifies mmp3 as a key regulator. Mmp3 regulates the scaling of dorsal-ventral patterning by degrading certain embryonic inducers. This research not only sheds light on the mechanism of patterning scaling but also provides evidence for identifying scalers in embryos of other species.
DEVELOPMENTAL CELL
(2022)
Article
Chemistry, Multidisciplinary
Tzu-Yi Tai, Fanrui Sha, Xiaoliang Wang, Xingjie Wang, Kaikai Ma, Kent O. Kirlikovali, Shengyi Su, Timur Islamoglu, Satoshi Kato, Omar K. Farha
Summary: This study presents the first systematic investigation on the thermodynamics of protein immobilization in metal-organic frameworks (MOFs). It demonstrates that MOFs provide a hydrophobic stabilizing microenvironment for proteins, leading to an entropically driven encapsulation process. Among a series of Zr-MOFs, pyrene-based NU-1000 exhibits the most favorable encapsulation process for insulin.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Thermodynamics
Ziga Medos, Isidora Cobanov, Marija Bester-Rogac, Bojan Sarac
Summary: This research paper examines the issues associated with power compensation isothermal titration calorimetry, highlighting the possibility of obtaining different enthalpy values with different instruments and setting parameters. It emphasizes that modern calorimeters' dynamic power compensation mode may lead to overcompensation of heat effects, resulting in experimental results heavily reliant on chosen parameters. To avoid these problems, the paper suggests checking raw signals and conducting experiments with low or disabled power compensation when observing switching effects.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2021)
Article
Biochemistry & Molecular Biology
Dominique Manikowski, Georg Steffes, Jurij Froese, Sebastian Exner, Kristina Ehring, Fabian Gude, Daniele Di Iorio, Seraphine V. Wegner, Kay Grobe
Summary: Morphogens play a crucial role in cell differentiation in a concentration dependent manner. In the case of Hedgehog (Hh) morphogens, they spread from their source to guide growth and pattern formation in the Drosophila wing disc. Heparan sulfate (HS) expression is essential for this process, and it has been found that HS directly regulates Hh signaling and spread in the wing disc epithelium. Interfering with this regulation alters Hh signaling range and gradient robustness.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Developmental Biology
Takayoshi Yamamoto, Toki Kaneshima, Kohei Tsukano, Tatsuo Michiue
Summary: The nervous system is derived from three neuroectodermal regions and their differentiation is regulated by morphogens. The role of the extracellular component heparan sulfate (HS) in regulating morphogen gradients in neural patterning is still debated. This study focused on Hs6st1, an HS modification enzyme, and found that it selectively regulates morphogen distribution in neuroectodermal patterning. The results suggest that cell-autonomous 6-O sulfation of HS affects neuroectodermal patterning through both morphogen accumulation and dispersal.
DEVELOPMENTAL BIOLOGY
(2023)
Article
Cell Biology
Takayoshi Yamamoto, Yuta Kambayashi, Kohei Tsukano, Tatsuo Michiue
Summary: Neural tissue is derived from three precursor regions: neural plate, neural crest, and preplacodal ectoderm. Morphogen-mediated signaling regulates the determination of these regions. Heparan sulfate (HS) proteoglycan plays a role in regulating morphogen distribution. Ndst1, an enzyme highly expressed in early development, modifies HS. This study shows that Ndst1 is involved in ectodermal patterning and activates the Wnt signaling pathway.
DEVELOPMENT GROWTH & DIFFERENTIATION
(2023)
Article
Polymer Science
Jacek J. Walkowiak, Rohit Nikam, Matthias Ballauff
Summary: The effective charge of highly charged polyelectrolytes is significantly lowered by a condensation of counterions. This effect is more pronounced for divalent ions. Our study on dendritic polyglycerol sulfate (dPGS) demonstrates that the interactions between dPGS and divalent ions (Mg2+ and Ca2+) show no ion specificity but clear competition between monovalent and divalent ions. These findings support the latest theoretical studies and indicate the sequential replacement of monovalent ions with divalent ions.
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)
Article
Biochemistry & Molecular Biology
Mimosa Sillanpaa, Marica T. T. Engstroem, Petri Taehtinen, Rebecca J. J. Green, Jarmo Kapyla, Anu Nareaho, Maarit Karonen
Summary: Plant tannins have anthelmintic and antiparasitic activities and can be used as complementary nutrients alongside commercial anthelmintics. The interactions between tannins and anthelmintics are limited and can have both synergistic and antagonistic effects depending on the tannin type and method used. Hydrolysable tannins can directly interact with the anthelmintic thiabendazole, and this interaction is strengthened by increasing the number of free galloyl groups and the overall molecular flexibility of tannins.
Article
Chemistry, Applied
Paola Peluso, David Landy, Lamia Nakhle, Roberto Dallocchio, Alessandro Dessi, Sulaiman Krait, Antonio Salgado, Bezhan Chankvetadze, Gerhard K. E. Scriba
Summary: The complex formation between daclatasvir and gamma-CD or TM-beta-CD was studied using isothermal titration calorimetry and molecular modeling. The results showed that a 2:1 complex was predominantly formed with gamma-CD, while a 1:1 complex was formed to a lesser extent. In contrast, the TM-beta-CD complex had a stoichiometry of 1:1. The complex formation with gamma-CD did not require dissociation of the daclatasvir dimer and had a binding constant of 1.67x10^7 M-2, while the weak TM-beta-CD complex required dissociation of the daclatasvir dimer and had a binding constant of 371 M-1.
CARBOHYDRATE POLYMERS
(2023)
Article
Chemistry, Physical
Mathilde Coquil, Nathalie Boubals, Magali Duvail, Marie-Christine Charbonnel, Jean-Francois Dufreche
Summary: Despite the challenges in describing liquid-liquid extraction due to various organization phenomena, a new methodology combining microcalorimetric measurements and molecular modeling has been proposed to better understand the interactions in these complex fluids.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Polymer Science
Thomas Baetz, Marcel Enke, Stefan Zechel, Martin D. Hager, Ulrich S. Schubert
Summary: The selective complexation of metal ions plays a key role in developing versatile supramolecular architectures, and the incorporation of orthogonal binding concepts into polymeric matrices has been investigated. By utilizing end-functionalized poly(N-isopropylacrylamide) carrying zinc-porphyrin and a terpyridine ligand, the polymer can simultaneously interact with different ligands, showcasing successful transfer of orthogonality into functional polymeric architecture.
MACROMOLECULAR CHEMISTRY AND PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Rabindranath Jana, Sayeed Ashique Ahmed, Debabrata Seth
Summary: In this study, the interaction between three well-known bile salts and CB7 was investigated using ITC, and significant thermodynamic parameters of the complexation process were obtained. The results showed that the degree of hydroxylation and conjugation of bile salts greatly influenced the binding affinity with CB7.
Article
Physics, Multidisciplinary
Monica Corea, Rogelio Jimenez-Juarez, Gabriela Martinez-Mejia, Maria de Jesus Martinez-Ortiz, Jose Manuel del Rio
Summary: The study experimentally analyzed the influence of the stock solution concentration on the geometrical characteristics of the titration curve, and found that the magnitude and shape of the heat titration depend on the stock solution concentration until reaching a limiting value. Qualitative analysis suggested that the limiting value is substance-dependent.
Review
Biochemistry & Molecular Biology
Lidia P. Kurochkina, Pavel I. Semenyuk, Olga S. Sokolova
Summary: It has been discovered that some bacterial viruses also encode their own chaperonins, in addition to being characteristic of prokaryotes, eukaryotes, and archaea. The biochemical properties and structures of these new phage chaperonins have been compared with other known group I and group II chaperonins.
BIOCHEMISTRY-MOSCOW
(2022)
Article
Cell Biology
Eugeny E. Orlov, Alexey M. Nesterenko, Daria D. Korotkova, Elena A. Parshina, Natalia Yu Martynova, Andrey G. Zaraisky
Summary: This study investigates the genes involved in scaling of embryonic patterning and identifies mmp3 as a key regulator. Mmp3 regulates the scaling of dorsal-ventral patterning by degrading certain embryonic inducers. This research not only sheds light on the mechanism of patterning scaling but also provides evidence for identifying scalers in embryos of other species.
DEVELOPMENTAL CELL
(2022)
Editorial Material
Biochemistry & Molecular Biology
Natalia Y. Martynova, Elena A. Parshina, Andrey G. Zaraisky
Summary: Zyxin, initially recognized as a minor actin cytoskeleton protein, not only regulates actin filaments assembly and repair but also plays a crucial role in gene expression and cell differentiation, particularly during embryogenesis process.
Article
Biochemistry & Molecular Biology
Elena A. Parshina, Eugeny E. Orlov, Andrey G. Zaraisky, Natalia Y. Martynova
Summary: Zyxin protein plays an important role in regulating the expression of maternal genes during early embryo development by affecting mRNA stability, especially in the regulation of retinoic acid signal pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Polymer Science
Pavel Semenyuk, Diana Evstafyeva, Vladimir Izumrudov, Vladimir Muronetz
Summary: The effect of sulfated or sulfonated polymers on amyloid conversion and aggregation of prion protein was investigated. The results showed that these polymers induce amyloid conversion of the prion protein, possibly by destabilizing its native structure. Short polymers enhanced further aggregation, while high-molecular poly(styrene sulfonate) inhibited amyloid fibrils formation. The protein-polymer complexes formed after incubation with poly(styrene sulfonate) had significantly lower amyloidogenic capacity and inhibited the cytotoxicity of soluble oligomers. This suggests that sulfonated polymers could be a promising platform for the development of anti-prion and anti-amyloidosis therapeutics.
Article
Biochemistry & Molecular Biology
Pavel Semenyuk
Summary: This study utilized replica exchange molecular dynamics simulations to predict the binding sites and effects of low-molecular ligands on the behavior of alpha-synuclein. The accuracy of this approach was confirmed by its agreement with experimental data, demonstrating its potential in the screening of new drug candidates and understanding the mechanism of anti- and pro-amyloid activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Polymer Science
Vladimir Muronetz, Denis Pozdyshev, Pavel Semenyuk
Summary: This review discusses the application of polyelectrolytes, particularly synthetic polyanions and polycations, for immobilizing enzymes and regulating their properties. It focuses on the use of polyelectrolytes to create complex systems such as self-regulated enzyme-polyelectrolyte complexes, artificial chaperones, polyelectrolyte brushes, layer-by-layer immobilization, and others. The review also includes a section on molecular modeling of protein-polyelectrolyte interactions.
Article
Biochemistry & Molecular Biology
Olga S. Sokolova, Evgeny B. Pichkur, Ekaterina S. Maslova, Lidia P. Kurochkina, Pavel Semenyuk, Petr Konarev, Valeriya R. Samygina, Tatiana B. Stanishneva-Konovalova
Summary: Chaperonins are a family of molecular chaperones that assist in protein folding. They are categorized into two groups, and a potential new group has recently been identified in giant bacteriophages. Using cryo-EM, researchers determined the structure of a new chaperonin encoded by gene 228 of phage AR9 B. subtilis, revealing similarities and differences with known chaperonins.
Article
Biochemistry & Molecular Biology
Anna A. Efimova, Anton S. Popov, Alexey V. Kazantsev, Pavel I. Semenyuk, Irina M. Le-Deygen, Nikolay V. Lukashev, Alexander A. Yaroslavov
Summary: pH-sensitive liposomes with embedded AMS showed rapid cargo release when pH was altered, but the mechanism is not yet fully understood. This article presents the details of fast cargo release based on ATR-FTIR spectroscopy and molecular modeling. The findings are relevant to the potential use of AMS-containing pH-sensitive liposomes for drug delivery.
Article
Multidisciplinary Sciences
Alexey M. Nesterenko, Dmitry A. Korzhenevskii, Vasilisa M. Tereshchuk, Olga M. Kudryashova, Vsevolod V. Belousov, Arina G. Shokhina
Summary: Ferroptosis is an iron-dependent programmed cell death that differs from apoptosis and necroptosis and plays a crucial role in neurodegenerative diseases and tumorigenesis. It is characterized by massive lipid oxidation and perturbation of multiple metabolic pathways. This study aims to obtain proteomic data from different time points of ferroptotic death to understand its primary and delayed phases and the genes involved in ferroptosis and protein regulation.
Article
Biochemistry & Molecular Biology
Alina Volkova, Pavel Semenyuk
Summary: Phospho-hirudin and succinylated hirudin have potential value as anticoagulant drugs in clinical practice.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Computer Science, Information Systems
Olga M. Kudryashova, Alexey M. Nesterenko, Dmitry A. Korzhenevskii, Valeriy K. Sulyagin, Vasilisa M. Tereshchuk, Vsevolod V. Belousov, Arina G. Shokhina
Summary: Ferroptosis is a form of non-apoptotic cell death that involves lipid oxidation driven by iron. It plays critical roles in the pathogenesis of neurodegenerative diseases and therapy-resistant cancer cells. This study developed a high-quality shotgun proteome sequencing method to analyze the effects of three chemical agents on ferroptosis induction.
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)