Article
Biochemical Research Methods
Ran Liu, Ye-Fan Hu, Jian-Dong Huang, Xiaodan Fan
Summary: A Bayesian model is proposed to jointly infer core locations, binding affinity, and binding thresholds, providing accurate determination for each MHC. Simulation studies showed desirable estimation accuracy and robustness of the model, outperforming commonly used thresholds when applied to real data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Immunology
Wei-Feng Wang, Xiao-Yong Xie, Yan Huang, Yin-Kang Li, Hong Liu, Xiu-Li Chen, Huan-Ling Wang
Summary: A novel antimicrobial peptide called Tatritin was discovered, which showed broad-spectrum antimicrobial activity and the ability to recognize and inhibit pathogenic microorganisms. It also demonstrated sensitivity to drug-resistant bacterial strains in both in vivo and in vitro experiments. Due to these characteristics, Tatritin can be used as a new type of drug for infection treatment or as an immune enhancer in animals.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Hiromasa Taniguchi, Yugo Ishimime, Kosuke Minamihata, Pugoh Santoso, Takuya Komada, Hendra Saputra, Kazuki Uchida, Masahiro Goto, Toki Taira, Noriho Kamiya
Summary: Fungal infections affect over one billion people worldwide and cause millions of deaths each year. The use of Amphotericin B, a commonly-used antifungal drug, is limited due to its side effects. Researchers have developed a simple and effective strategy to enhance the antifungal activity of Amphotericin B by modifying it with a lipid-modified protein. This approach could potentially improve the widespread use of the drug.
MOLECULAR PHARMACEUTICS
(2022)
Article
Microbiology
Claudia Feurstein, Vera Meyer, Sascha Jung
Summary: Antimicrobial peptides (AMPs) are promising alternatives to antibiotics to fight multidrug-resistant microorganisms, but there are still limited predictions about their structure-activity relationships and common properties across different taxonomic groups. The current study reveals the structural diversity of AMPs in different taxonomic groups, which will assist in future peptide screens in unexplored microorganisms.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Lay-Sun Ma, Wei-Lun Tsai, Florensia Ariani Damei, Raviraj M. Kalunke, Meng-Yun Xu, Yu-Han Lin, Hui-Chun Lee
Summary: Maize secretory protein AFP1 inhibits the growth and germination of the biotrophic fungus U. maydis by binding to its surface and interfering with enzyme activity of chitin deacetylases. AFP1 also exhibits inhibitory activity against S. cerevisiae by interacting with cell surface glycoproteins.
Article
Microbiology
Gang Liu, Dong-Yun Zuo, Peng Yang, Wei-Jie He, Zheng Yang, Jing-Bo Zhang, Ai-Bo Wu, Shu-Yuan Yi, He-Ping Li, Tao Huang, Yu-Cai Liao
Summary: A novel wheat gene TaArl6ip4 induced by DON was identified in this study, which exhibits antifungal function and DON affinity, potentially playing a key role in Fusarium-wheat interactions.
Article
Biotechnology & Applied Microbiology
Vahideh Gougerdchi, Ebrahim Dorani, Mostafa Valizadeh, Mohammadreza Zamani
Summary: This study reports the increased resistance to Sclerotinia stem rot in transgenic tomatoes expressing the chimeric chit42 gene with the Serratia marcescens chitinase binding domain. The overexpression of the chimeric chitinase enhanced plant resistance against the fungal disease, and reduced lesion sizes caused by S. sclerotiorum. This is the first evaluation of transgenic tomato lines for resistance to S. sclerotiorum using Trichoderma chitinase with a chitin binding domain.
PLANT CELL TISSUE AND ORGAN CULTURE
(2022)
Article
Chemistry, Medicinal
Fang Luan, Zhenhua Xu, Kai Wang, Xin Qi, Zhanyong Guo
Summary: Novel water-soluble chitin derivatives, SCT and SPCT, were synthesized as antioxidant and antifungal agents. The derivatives were characterized and their antioxidant and antifungal activities were evaluated. The results showed that SPCT had the highest antioxidant and antifungal abilities, and the efficacy increased with the chain length of the substituents. This derivatization strategy provides a feasible way to broaden the utilization of chitin and has significant implications for minimizing waste and realizing the high-value utilization of aquatic product wastes.
Article
Physics, Atomic, Molecular & Chemical
Rajpal Vangala, Laurence A. Angel
Summary: Three analog methanobactin peptides were studied for their reactivity with various metal ions, showing different binding preferences for different metals. The complexes formed at different pH values exhibited distinct characteristics, with negatively charged complexes formed through ion-ion interactions and positively charged complexes through ion-dipole metal binding. Fluorescence quenching qualitatively agreed with the mass spectrometry results, revealing the solution-phase metal binding behavior of methanobactin peptides.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2021)
Article
Biochemistry & Molecular Biology
James P. Tam, Jiayi Huang, Shining Loo, Yimeng Li, Antony Kam
Summary: Coffee processing waste contains novel microproteins with cell-penetrating and metal ion-binding abilities, including a ginsentide-like microprotein that can target intracellular proteins. These findings suggest that coffee by-products could be a potential source of bioactive peptides for targeting intracellular proteins.
Article
Cell Biology
Yu Wei Zhang, Julian Mess, Nadim Aizarani, Pankaj Mishra, Carys Johnson, Mari Carmen Romero-Mulero, Jasmin Rettkowski, Katharina Schoenberger, Nadine Obier, Karin Jaecklein, Nadine M. Woessner, Maria-Eleni Lalioti, Talia Velasco-Hernandez, Katarzyna Sikora, Ralph Waesch, Bernhard Lehnertz, Guy Sauvageau, Thomas Manke, Pablo Menendez, Sebastian Gottfried Walter, Susana Minguet, Elisa Laurenti, Stefan Guenther, Dominic Gruen, Nina Cabezas-Wallscheid
Summary: This study uses single-cell RNA sequencing to investigate the dormancy state of HSCs in human bone marrow and identifies the GPRC5C receptor and its signaling pathway with hyaluronic acid as important factors in maintaining dormancy.
NATURE CELL BIOLOGY
(2022)
Article
Fisheries
Aika Sekimoto, Tsuyoshi Ohira, Atsushi Shigematsu, Takuji Okumura, Miyuki Mekuchi, Kenji Toyota, Hiroyuki Mishima, Ryoya Kawamura, Kaito Hatano, Umi Kawago, Yoichiro Kitani, Toshio Sekiguchi, Thumronk Amornsakun, Jun Hirayama, Atsuhiko Hattori, Hajime Matsubara, Nobuo Suzuki
Summary: This study investigates the calcification mechanism of the exoskeleton of kuruma prawns and identifies CAP-1 as a peptide involved in chitin-binding and anti-calcification activities. CAP-1 mRNA expression in the prawns changes during molting, indicating its important role in exoskeleton calcification.
Article
Fisheries
Aika Sekimoto, Tsuyoshi Ohira, Atsushi Shigematsu, Takuji Okumura, Miyuki Mekuchi, Kenji Toyota, Hiroyuki Mishima, Ryoya Kawamura, Kaito Hatano, Umi Kawago, Yoichiro Kitani, Toshio Sekiguchi, Thumronk Amornsakun, Jun Hirayama, Atsuhiko Hattori, Hajime Matsubara, Nobuo Suzuki
Summary: The study found that kuruma prawn CAP-1 has chitin-binding and anti-calcification activities, and its mRNA expression level changes significantly during molting.
Article
Chemistry, Applied
Daisuke Yamanaka, Kento Suzuki, Masahiro Kimura, Fumitaka Oyama, Yoshiyuki Adachi
Summary: In this study, we developed a reliable method for chitin detection using a luciferase-fragment complementation assay. The use of a CatD mutant allowed for higher sensitivity and structure-specific detection of chitin. Furthermore, a sandwich ELISA using modified CatD showed a low detection limit for soluble chitin.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemistry & Molecular Biology
Dhruv C. Rathod, Sonali M. Vaidya, Marie-T. Hopp, Toni Kuehl, Diana Imhof
Summary: Heme plays a dual role in biological processes, functioning as a prosthetic group of hemoproteins and also regulating biochemical pathways through transient association with proteins. However, the mechanisms of heme recognition and complex formation with target proteins are poorly understood. This report focuses on evaluating mammalian heme-regulated proteins and their heme-binding motifs (HBMs), particularly the Cys-Pro dipeptide motifs. This analysis provides insights into the sequence and structural anomalies observed during transient heme binding and protein regulation.
Article
Geochemistry & Geophysics
O. Dimitrov, K. Z. Vacheva, A. M. Korzhenkov, Chr Kouzov, A. S. Larkov, A. N. Ovsuchenko, B. K. Ranguelov, E. A. Rogozhin, A. A. Strelnikov
Summary: The ruins of Odessos in Varna, Bulgaria have shown significant damage and destruction in the ancient building constructions, indicating the occurrence of strong earthquakes in the past. Medieval builders recognized the possibility of earthquakes and implemented measures to absorb seismic vibrations. Archaeological research has identified multiple periods of construction and determined the age and direction of past seismic events, providing valuable data for seismic hazard assessment.
IZVESTIYA-PHYSICS OF THE SOLID EARTH
(2022)
Article
Biotechnology & Applied Microbiology
A. E. Kuvarina, Yu A. Roshka, E. A. Rogozhin, D. A. Nikitin, A. Kurakov, V. S. Sadykova
Summary: The study found that the representatives of psychrotolerant micromycetes, especially Penicillium vulpinum KPB F-290, have the potential to produce antibiotics that are active against opportunistic fungi and bacteria. The isolated active fractions belong to the group of antimicrobial compounds, including ss-lactam antibiotics and peptides.
APPLIED BIOCHEMISTRY AND MICROBIOLOGY
(2022)
Article
Geochemistry & Geophysics
A. M. Korzhenkov, E. Deev, L. A. Korzhenkova, Jiao Liu, Y. Mazeika, E. A. Rogozhin, A. A. Strelnikov, I. Turova, M. T. Usmanova, A. B. Fortuna
Summary: This study explored the historical and paleoseismic deformations in the southern Issyk-Kul depression, revealing 10 strong seismic events during the Holocene. The findings suggest that these seismic events migrated from west to east and back, potentially impacting the evolution of civilizations in the region. The obtained data can be used for creating a New Map of Seismic Zoning for the Issyk-Kul Region.
IZVESTIYA-PHYSICS OF THE SOLID EARTH
(2022)
Article
Biochemistry & Molecular Biology
Anna S. Barashkova, Dmitry Y. Ryazantsev, Eugene A. Rogozhin
Summary: This study investigates the structural determinants of antimicrobial activity in plant alpha-hairpinins peptides. The researchers found that spatial structure, surface charge, and hydrophobicity level all contribute to the antimicrobial properties of these peptides. Through the synthesis and testing of different forms of alpha-hairpinins peptides, they demonstrate that alterations in the peptide structure and amino acid substitutions result in weakened antimicrobial activity. Additionally, this study provides the first description of the antibacterial activity of cereal alpha-hairpinins against Gram-positive bacteria.
Article
Biochemistry & Molecular Biology
Anastasia E. Kuvarina, Irina A. Gavryushina, Maxim A. Sykonnikov, Tatiana A. Efimenko, Natalia N. Markelova, Elena N. Bilanenko, Sofiya A. Bondarenko, Lyudmila Y. Kokaeva, Alla V. Timofeeva, Marina V. Serebryakova, Anna S. Barashkova, Eugene A. Rogozhin, Marina L. Georgieva, Vera S. Sadykova
Summary: This study investigated the production of active antibiotic compounds by alkaliphilic fungi and identified a novel form of antifungal peptaibol.
Article
Biotechnology & Applied Microbiology
Alexey S. Vasilchenko, Darya Poshvina, Roman Yu Sidorov, Aleksandr Iashnikov, Eugene A. Rogozhin, Anastasia V. Vasilchenko
Summary: Bacterial intercellular communication through quorum sensing is a common mechanism for regulating bacterial colonization and survival. This study discovered plant-derived quorum sensing inhibitors from oak bark, which reduced the production of acyl-HSL and decreased bacterial cellulolytic and protease activity. The treatment also suppressed QS-related genes and conferred resistance to soft-rot symptoms in pre-treated potato tubers. The identification of biologically active molecules in the oak bark extract suggests its potential for bacterial control during potato storage.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Microbiology
Anastasia E. Kuvarina, Eugene A. Rogozhin, Maxim A. Sykonnikov, Alla Timofeeva, Marina Serebryakova, Natalia Fedorova, Lyudmila Y. Kokaeva, Tatiana A. Efimenko, Marina L. Georgieva, Vera S. Sadykova
Summary: This study identified a hydrophobin, Sa-HFB1, from an alkaliphilic fungus, which exhibited potential antifungal effects against pathogenic and opportunistic fungi strains, especially the clinical isolate Cryptococcus neoformans.
Article
Chemistry, Medicinal
Victoria A. Buchelnikova, Eugene A. Rogozhin, Anna S. Barashkova, Anatoly S. Buchelnikov, Maxim P. Evstigneev
Summary: Experimental evidence suggests that the presence of C-60 fullerene clusters in aqueous solution can alter the activity of biologically relevant compounds, making them a promising nanoplatform for drug delivery. In this study, the interaction between fullerene clusters and the antibiotic topotecan (TPT) was investigated. The results showed that fullerene clusters can selectively deliver pH-sensitive drug forms.
CHEMICAL RESEARCH IN TOXICOLOGY
(2022)
Article
Microbiology
Darya V. V. Poshvina, Diana S. S. Dilbaryan, Sergey P. P. Kasyanov, Vera S. S. Sadykova, Olda A. A. Lapchinskaya, Eugene A. A. Rogozhin, Alexey S. S. Vasilchenko
Summary: Gausemycin A, a novel lipoglycopeptide, exhibits bactericidal activity against methicillin-resistant Staphylococcus aureus. The resistant variant S. aureus 5812R, which is 80 times more resistant compared to the parent strain, showed cross-resistance to multiple antibiotics. Whole genome sequencing revealed genetic mutations and deletions in S. aureus 5812R, as well as changes in the composition of fatty acids in the cell membrane. The combination of Gausemycin A and ciprofloxacin demonstrated a synergistic effect against S. aureus 5812R.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Medicinal
Tatyana O. O. Mizgina, Sergey N. N. Baldaev, Galina N. N. Likhatskaya, Valentina I. I. Molchanova, Maxim S. S. Kokoulin, Alina P. P. Filshtein, Eugene A. A. Rogozhin, Irina V. V. Chikalovets, Marina P. P. Isaeva, Oleg V. V. Chernikov
Summary: C-type lectins (CTLs), such as GYL in the bivalve Glycymeris yessoensis, play key roles in adhesion between cells, turnover of serum glycoproteins, and innate immune system reactions. This study cloned the cDNA of GYL and identified eight isoforms. It was found that GYL is a glycoprotein with two N-glycosylation sites, and its glycan portion consists of various sugars. The study also determined the natural carbohydrate ligands for GYL and reconstructed its glycotopes.
Article
Biochemistry & Molecular Biology
Rimma S. Kalina, Irina N. Gladkikh, Anna A. Klimovich, Yulia V. Kozhevnikova, Aleksandra N. Kvetkina, Eugene A. Rogozhin, Sergey G. Koshelev, Sergey A. Kozlov, Elena V. Leychenko
Summary: A novel beta-hairpin fold peptide AnmTX Sco 9a-1 was isolated from Stomphia coccinea, which showed non-toxicity but had stimulating effects on mice's exploratory motivation, reduced anxiety, and demonstrated anti-inflammatory and analgesic effects.
Article
Biotechnology & Applied Microbiology
D. Yu. Ryazantsev, E. Yu. Khodzhaev, A. E. Kuvarina, A. S. Barashkova, E. A. Rogozhin
Summary: Using a combination of solid-phase extraction, affinity chromatography, and analytical reverse-phase HPLC, a new linear peptide was isolated from dog-grass (Elytrigia repens) ears that does not contain cysteine residues. Identification of its primary structure by Edman automated degradation made it possible to reveal the presence of several polyglycine regions, each consisting of six to eight residues, between which short fragments consisting of polar amino-acid residues are localized. The C-terminal fragment of the molecule is a positively charged site enriched in arginine and histidine residues. The structural features of this peptide determine its functionality.
APPLIED BIOCHEMISTRY AND MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anna S. Barashkova, Alexey N. Smirnov, Elena S. Zorina, Eugene A. Rogozhin
Summary: Black cumin contains antimicrobial peptides, including three novel peptides, that have been isolated and characterized. These peptides show a broad spectrum of antimicrobial activity against plant pathogens, making them potential candidates for the development of next-generation biopesticides for agricultural use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
S. N. Gavrilov, A. S. Barashkova, T. A. Cherdyntseva, M. I. Prokofeva, O. V. Tresvyatskii, D. A. Lukianov, A. A. Nikandrova, T. Haertle, A. Yu. Merkel, E. A. Bonch-Osmolovskaya, E. A. Rogozhin
Summary: The study focuses on the search for new antimicrobial compounds and their producers due to the increasing antibiotic resistance in pathogenic microorganisms. Halophilic microorganisms, especially actinomycetes, are considered as promising producers of antibiotics. Three different approaches were used to identify potential antimicrobial compounds in halophilic and halotolerant microorganisms from extreme ecosystems. Metagenomic analysis revealed putative antimicrobial biosynthetic clusters in uncultured lineages of bacteria and archaea from subsurface thermal mineral waters. Enrichment cultures from deep oceanic sediments identified potential producers of antimicrobial compounds as members of the class Desulfuromonadia. Additionally, a new species of soil natronophilic streptomycetes, Streptomyces sp. ACA25, was characterized for antimicrobial activity against gram-positive bacteria, and the pathways for biosynthesis of antibiotics were identified.
Article
Food Science & Technology
Anna S. Barashkova, Dmitry Yu. Ryazantsev, Anna S. Zhuravleva, Vladimir V. Sharoyko, Eugene A. Rogozhin
Summary: This study successfully obtained a recombinant chimeric protein named trx-NsW2 through the heterologous expression of the antimicrobial peptide nigellothionin from black cumin seeds. The protein was purified and achieved a total yield of 650 mg/L of bacterial culture. The fusion protein trx-NsW2 exhibited fungistatic activity against Aspergillus niger and showed low cytotoxicity towards normal and tumor cell lines at certain concentrations, even stimulating cytokinesis.