Article
Multidisciplinary Sciences
Soon-Keat Ooi, Shigeo Sato, Chieri Tomomori-Sato, Ying Zhang, Zhihui Wen, Charles A. S. Banks, Michael P. Washburn, Jay R. Unruh, Laurence Florens, Ronald C. Conaway, Joan W. Conaway
Summary: PARP1 has multiple functions in ALC1-dependent nucleosome remodeling beyond simply synthesizing PAR chains, as shown by investigation of separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Philip Saumer, Martin Scheffner, Andreas Marx, Florian Stengel
Summary: In this study, the researchers established intact chromatosomes containing site-specifically modified linker histone H1.2 variants and identified the specific cellular interactomes and proteome-wide impact of these modifications. The data supports the role of chromatin-bound H1 as a regulatory protein with distinct functions and provides a valuable resource for future investigations of histone epigenetic modifications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Stephanie L. Johnson, Geeta J. Narlikar
Summary: In this study, a single molecule biophysical assay was used to investigate the mechanism of chromatin remodelers. The results showed that ATP hydrolysis by the molecular motors promoted coordination and played a key role in directional sliding.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Oncology
Xun-Xi Lu, Wen-Xiao Yang, Yu -Chen Pei, Hong Luo, Xiao-Guang Li, Yun-Jin Wang, Guo-Liang Zhang, Hong Ling, Zhi-Ming Shao, Xin Hu
Summary: Dysregulation of RNA-binding proteins (RBPs) is a characteristic of cancer. Investigating the functions and mechanisms of abnormal RBPs can help identify new cancer biomarkers and treatment strategies. In this study, SNRPC was identified as an oncogenic modulator in triple-negative breast cancer (TNBC). SNRPC upregulation was associated with poor prognosis, and its inhibition impaired TNBC cell proliferation, migration, and invasion. SNRPC also contributed to the stability of U1 snRNP and the transcriptional program controlled by RNA Pol II. Knockdown of SNRPC reduced the expression of oncogenes and inhibited TNBC progression via the TNFAIP2-Rac1-β-catenin signaling pathway.
Article
Biology
Drake A. Donovan, Johnathan G. Crandall, Vi N. Truong, Abigail L. Vaaler, Thomas B. Bailey, Devin Dinwiddie, Orion G. B. Banks, Laura E. McKnight, Jeffrey N. McKnight
Summary: The study revealed that Isw2 functions as an obligately targeted nucleosome remodeler in vivo by interacting physically with sequence-specific factors. These data support an 'interacting barrier model' where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.
Article
Biochemistry & Molecular Biology
Ji-Yun Shang, Yu-Jia Lu, Xue-Wei Cai, Yin-Na Su, Chao Feng, Lin Li, She Chen, Xin-Jian He
Summary: The accessory subunits of the INO80 chromatin remodeling complex interact with different domains of the INO80 protein, playing roles in chromatin remodeling and transcriptional activation. These interactions are essential for maintaining the balance between vegetative growth and flowering in plants under various environmental conditions.
Article
Chemistry, Multidisciplinary
Xiaojing Huang, Hari Kamadurai, Piro Siuti, Ezaz Ahmed, Jack L. Bennett, William A. Donald
Summary: Molecular glues stabilize interactions between E3 ligases and novel substrates to promote substrate degradation, facilitating the inhibition of traditionally undruggable protein targets. Efficient approaches for discovering and characterizing the effects of molecular glues on protein interactions are required to accelerate the discovery of novel agents.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Ana M. Matia-Gonzalez, Ibtissam Jabre, Emma E. Laing, Andre P. Gerber
Summary: RNA-binding proteins (RBPs) play a substantial role in post-transcriptional regulation during stress adaptation. Recent studies have revealed the reconfiguration of the RNA-binding proteome (RBPome) and RNA-enzyme interactions in response to cellular stress, showing coordinated remodeling of RNA-binding enzymes, particularly in central carbon metabolism, and paralogous specific alterations of enzyme-RNA interactions. The results suggest a coordinated cross talk between RNA-enzyme interactions and intermediary metabolism to maintain physiological and molecular balance under oxidative stress, possibly through specialization of paralogous genes during evolution.
Article
Chemistry, Multidisciplinary
Fanny Laporte, Yves Chenavier, Alexandra Botz, Christelle Gateau, Colette Lebrun, Sarah Hostachy, Claude Vidaud, Pascale Delangle
Summary: This study proposes a simple and efficient fluorescence-based method to assess the affinity of proteins and peptides for uranyl, providing a reliable and reproducible assessment for understanding the toxicity of this cation and developing decorporation strategies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Elena Gomez-Marin, Melanija Posavec-Marjanovic, Laura Zarzuela, Laura Basurto-Cayuela, Jose A. Guerrero-Martinez, Gonzalo Arribas, Rosario Yerbes, Maria Ceballos-Chavez, Manuel Rodriguez-Paredes, Mercedes Tome, Raul Duran, Marcus Buschbeck, Jose C. Reyes
Summary: The study reveals that PHF14 and HMG20A cooperate in regulating pathways involved in epithelial-mesenchymal plasticity, impacting cell migration, invasion, and cell-cell adhesion abilities. The PHF14-HMG20A complex modulates the Hippo pathway through direct interaction with the TEAD1 transcription factor.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Nazar Mashtalir, Hai T. Dao, Akshay Sankar, Hengyuan Liu, Aaron J. Corin, John D. Bagert, Eva J. Ge, Andrew R. D'Avino, Martin Filipovski, Brittany C. Michel, Geoffrey P. Dann, Tom W. Muir, Cigall Kadoch
Summary: This study identified the effects of chromatin features on mSWI/SNF activities and interactions, as well as the combinatorial contributions of complex module components, reader domains, and nucleosome engagement properties to the localization of complexes.
Article
Multidisciplinary Sciences
Chengwei Zeng, Yiren Jian, Soroush Vosoughi, Chen Zeng, Yunjie Zhao
Summary: RNA-protein complexes play vital roles in various cellular processes. The authors develop a deep-learning-based method called DRPScore to identify native-like structures of RNA-protein complexes. DRPScore outperforms existing methods and shows significant improvements in accuracy, especially for unbound cases.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Ramakrishnan Natesan, Kripa Gowrishankar, Lakshmi Kuttippurathu, P. B. Sunil Kumar, Madan Rao
Summary: This study proposes a model of in vivo chromatin as an active polymer and finds that activity drives chromatin to a nonequilibrium steady state, with conformations consistent with measurements on intrachromosomal contact probabilities and chromosomal compaction. The contact exponents at steady state systematically vary with changes in the nature of activity and turnover rates, and the steady state configuration of active chromatin in two dimensions resembles a space-filling Peano curve, potentially impacting genome information storage optimization.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Richard W. Baker, Janice M. Reimer, Peter J. Carman, Bengi Turegun, Tsutomu Arakawa, Roberto Dominguez, Andres E. Leschziner
Summary: The study reveals that the interaction between Sth1 and the nucleosome acidic patch enhances chromatin remodeling function, and large conformational changes are part of Sth1 regulation and RSC assembly.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Christopher Lambert, Katharina Schmidt, Marius Karger, Marc Stadler, Theresia E. B. Stradal, Klemens Rottner
Summary: The eukaryotic actin cytoskeleton is a dynamic network composed of monomeric and filamentous forms of actin, as well as actin-binding proteins (ABPs). Small molecular inhibitors have been used to study the importance of actin filaments for cellular processes, by interfering with the interactions and turnover of the actin cytoskeleton. This review aims to summarize the available information on the structural features of cytochalasans and their effects on cell morphology and actin cytoskeleton organization.
Article
Biochemistry & Molecular Biology
Christophe Papin, Stephanie Le Gras, Abdulkhaleg Ibrahim, Hatem Salem, Mohammad Mahdi Karimi, Isabelle Stoll, Iva Ugrinova, Maria Schroder, Emeline Fontaine-Pelletier, Ziad Omran, Christian Bronner, Stefan Dimitrov, Ali Hamiche
Summary: Epigenetic modifications and nucleosome positioning are important in gene expression regulation. CpG density, promoter activity, and histone marks accumulation are correlated. CGI boundaries define chromatin promoter regions for epigenetic modifications, while H2A.Z presence is not related to transcriptional control.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Emi Haladjova, Ivaylo Dimitrov, Nadejda Davydova, Jordana Todorova, Iva Ugrinova, Aleksander Forys, Barbara Trzebicka, Stanislav Rangelov
Summary: Novel N-substituted polyacrylamides, including block copolymers with polylactide, exhibit good water solubility, self-assemble into stable micelles, and show promise for gene delivery and regulation as DNA nanocarriers. The behavior and properties of these nanocarriers are highly dependent on the characteristics of the polymer micelles and the length of DNA chains. Systems exhibit low cytotoxicity and high cellular uptake ability.
Article
Polymer Science
Zornica Todorova, Oyundari Tumurbaatar, Jordana Todorova, Iva Ugrinova, Neli Koseva
Summary: A novel phosphorus-containing biocompatible and biodegradable star-shaped polymer was designed and successfully synthesized as a precursor for sugar or drug conjugates. Specific synthetic procedures were employed to transform the phosphoryl polymer into phosphorus-containing glycopolymer and drug conjugates.
EUROPEAN POLYMER JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Emi Haladjova, Varvara Chrysostomou, Maria Petrova, Iva Ugrinova, Stergios Pispas, Stanislav Rangelov
Summary: The physicochemical characteristics and biological performance of polyplexes based on two identical copolymers bearing tertiary amino or quaternary ammonium groups were evaluated and compared. The quaternized copolymer exhibited stronger binding affinity to DNA, resulting in larger particles carrying more DNA molecules per particle, and showed higher transfection efficiency in comparison to the parent copolymer.
MACROMOLECULAR BIOSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Radostina Kalinova, Miroslava Valchanova, Ivaylo Dimitrov, Sevdalina Turmanova, Iva Ugrinova, Maria Petrova, Zlatina Vlahova, Stanislav Rangelov
Summary: The study evaluated the potential of linear polyglycidol-based copolymers for gene therapy, demonstrating their ability to condense DNA into stable nanoparticles through electrostatic interactions. Modified copolymers showed low to moderate cytotoxicity on human cancer cell lines. Cell internalization evaluation confirmed the successful delivery of DNA into cancer cells by the polyplexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Maria Petrova, Iva Ugrinova, Evdokia Pasheva
Summary: The receptor for advanced glycation end products (RAGE) is a cell surface multiligand receptor that is upregulated in various pathological processes. The balance between soluble and full-length RAGE may play a key role in RAGE-induced dysfunction. Different cancer cell lines show differential expression of RAGE forms, with less invasive cancers expressing less membrane-bound RAGE and more invasive cancers predominantly expressing full-length receptor.
COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES
(2022)
Article
Multidisciplinary Sciences
Jordana Todorova, Maria Petrova, Evdokia Pasheva, Iva Ugrinova
Summary: The receptor RAGE has two forms and plays a role in lung cancer. The expression of RAGE in lung cancer cells is related to the prognosis and invasive ability. The nuclear protein HMGB1 can stimulate the expression of RAGE.
COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES
(2022)
Article
Mathematics
Svetozar Margenov, Nedyu Popivanov, Iva Ugrinova, Tsvetan Hristov
Summary: This study examines the epidemiological parameters of COVID-19 in Bulgaria using an extended SEIRS model and proposes a short-term prediction strategy. The findings can provide insights for analyzing COVID-19 data in other countries worldwide.
Article
Biochemistry & Molecular Biology
Maria Schroder, Maria Petrova, Zlatina Vlahova, Georgi M. Dobrikov, Ivaylo Slavchev, Evdokia Pasheva, Iva Ugrinova
Summary: The successful design of antitumour drugs often involves combining different biologically active subunits to affect multiple cellular regulatory pathways, leading to higher efficacy. In this study, two ferrocene derivatives, DK-164 and CC-78, were tested for their cytotoxic potential on lung cancer cell lines. DK-164 showed selective cytotoxicity towards cancer cells, while CC-78 exhibited higher cytotoxicity without selectivity. The different cellular mechanisms induced by these compounds in lung cancer cells provide insights into the specific functions of functional groups in ferrocene compounds and can guide the design of new antitumour drugs.
Article
Chemistry, Medicinal
Maria Petrova, Zlatina Vlahova, Maria Schroder, Jordana Todorova, Alexander Tzintzarov, Anastas Gospodinov, Lyudmila Velkova, Dimitar Kaynarov, Aleksandar Dolashki, Pavlina Dolashka, Iva Ugrinova
Summary: This study reports the antitumor activity of biologically active compounds isolated from the hemolymph of marine snail Rapana venosa on human breast cancer cell lines. The fraction with Mw 50-100 kDa (HRv 50-100) showed promising antitumor activity, inducing cell death, altering cell morphology, inducing autophagy, and activating p53. Synergistic effects were observed when HRv 50-100 was combined with cis-platin. The main proteins in the active fraction were identified and showed homology with known proteins with antitumor potential in other mollusc species.
Article
Pharmacology & Pharmacy
Maria Schroeder, Maria Petrova, Georgi M. Dobrikov, Georgy Grancharov, Denitsa Momekova, Petar D. Petrov, Iva Ugrinova
Summary: The development of new anticancer drugs with higher efficacy and lower side effects is a major challenge for medical research. A newly synthesized organometallic compound, DK164, shows promising antiproliferative activity against breast and lung cancer cells, but faces solubility issues in biological fluids. In this study, we successfully prepared a micellar form of DK164, which greatly improves its solubility in aqueous medium, and evaluated its physicochemical parameters and biological activity.
Article
Mathematics
Svetozar Margenov, Nedyu Popivanov, Iva Ugrinova, Tsvetan Hristov
Summary: Bulgaria has the lowest COVID-19 vaccination rate in the EU and the second-highest COVID-19 mortality rate globally. This study aims to understand the reasons behind this situation and analyze the disease's development over time. The extended time-dependent SEIRS-VB model is used, which incorporates vaccination and vital dynamics. The study includes developing numerical simulation tools, solving inverse problems for parameter identification, and proposing a methodology for selecting the closest discrete model to the differential SEIRS-VB model. Bulgarian COVID-19 data are used for validation, and mathematical analysis is conducted to illustrate biological properties and perform sensitivity analysis.
Article
Chemistry, Physical
Emi Haladjova, Maria Petrova, Iva Ugrinova, Aleksander Forys, Barbara Trzebicka, Stanislav Rangelov
Summary: A one pot synthesis method using phospholipid liposomes to fabricate hollow spherical nucleic acids (SNAs) is reported. These SNAs are characterized by their vesicular cores and surface-bound DNA oligonucleotide strands, and they exhibit high binding affinity to complementary nucleic acids and cross the cell membrane without transfection agents.
Article
Biotechnology & Applied Microbiology
Jordana Todorova, Lazar I. Lazarov, Maria Petrova, Alexander Tzintzarov, Iva Ugrinova
Summary: The study compared the reaction of two lung cancer cell lines and found that cannabidiol led to a dose-dependent increase in apoptosis in p53 positive A549 cells, while the level of apoptosis in p53 negative H1299 cells was lower and not dose-dependent. However, the total cell viability was similar for the two cell lines, which was due to the increased necrosis observed in H1299 cells.
BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT
(2021)
Article
Multidisciplinary Sciences
Tihomira Stoyanova, Veselina Uzunova, Albena Momchilova, Rumiana Tzoneva, Iva Ugrinova
Summary: Erufosine treatment induces apoptosis, G2/M cell cycle arrest, actin cytoskeleton destruction, and inhibition of cell motility in a dose-dependent manner in triple negative breast cancer cells. Erufosine may be effective as an anti-tumour agent against breast cancer.
COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES
(2021)
