Article
Biochemistry & Molecular Biology
Natalia Stach, Abdulkarim Karim, Przemyslaw Golik, Radoslaw Kitel, Katarzyna Pustelny, Natalia Gruba, Katarzyna Groborz, Urszula Jankowska, Sylwia Kedracka-Krok, Benedykt Wladyka, Marcin Drag, Adam Lesner, Grzegorz Dubin
Summary: By studying the substrate specificity and structure of SplF, it was found that the enzyme has a strict preference for long aliphatic sidechains at the P1 subsite and significant selectivity for aromatic residues at P3, with its crystal structure defining the structural basis of this substrate specificity. Comparisons with other Spl proteases suggest that the spl operon encodes a unique extracellular proteolytic system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Shan Tang, Adam T. Beattie, Lucie Kafkova, Gianluca Petris, Nicolas Huguenin-Dezot, Marc Fiedler, Matthew Freeman, Jason W. Chin
Summary: This study proposes a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps, which can capture substrates of hydrolases in complex mixtures and live mammalian cells.
Article
Immunology
Dorothee Kretschmer, Ricarda Breitmeyer, Cordula Gekeler, Marco Lebtig, Katja Schlatterer, Mulugeta Nega, Mark Stahl, Daphne Stapels, Suzan Rooijakkers, Andreas Peschel
Summary: Neutrophil serine proteases can effectively degrade some of the most potent staphylococcal toxins, while Staphylococcus aureus secretes proteins that inhibit the degradation of toxins by proteases. This helps the prominent human pathogen S. aureus to preserve the function of toxins and activate infection processes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Fisheries
Zhirong Fu, Srinivas Akula, Anna-Karin Olsson, Lars Hellman
Summary: In this study, we characterized the extended cleavage specificity and hematopoietic expression pattern of the chicken serine protease cathepsin G-like. Using substrate phage display and a panel of recombinant substrates, we identified a consensus sequence for this protease and found a preference for specific amino acids in the substrate. Immunohistochemical analysis confirmed the presence of cathepsin G-like in thrombocytes of chicken white blood cells.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2022)
Article
Cell Biology
Andrew Michael Frey, Dale Chaput, Lindsey Neil Shaw
Summary: In this study, two N-terminomics methods were applied to investigate the cleavage of human serum proteins by the S. aureus V8 protease, leading to the discovery of 85 host-protein targets, including complement, iron sequestration, clotting cascade, and host protease inhibitor proteins. The protease V8 disrupts host protein function through cleavage sites, providing insights into its role in S. aureus pathogenesis.
Article
Biochemistry & Molecular Biology
Qian Chen, Junwei Zhou, Zhixiang Yang, Jiahui Guo, Zimin Liu, Xinyi Sun, Qingshi Jiang, Liurong Fang, Dang Wang, Shaobo Xiao
Summary: This study systematically investigated the substrate specificity switch mechanism of arterivirus 3CLpro and identified specific amino acid exchanges that can lead to the switch. These findings contribute to a better understanding of the biological characteristics and transmission mechanisms of arteriviruses and porcine reproductive and respiratory syndrome virus.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Faying Zhang, Hui Zheng, Yufan Xian, Haoyue Song, Shengchen Wang, Yueli Yun, Li Yi, Guimin Zhang
Summary: SUMO modification is an important post-translational regulation process in eukaryotes. The SUMO protease, Ulp1, is responsible for the maturation and deconjugation of SUMO protein. The diglycine motif is not strictly required for Ulp1 cleavage, and the P1' position of Smt3 (Ala) plays a vital role in maintaining Ulp1's precise cleavage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Ahmad Mourad, Thomas L. Holland, Nicholas A. Turner
Summary: This commentary reflects on the impact of clopidogrel use on clinical outcomes in patients with Staphylococcus aureus bacteremia, as analyzed in a recent study.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Immunology
Rahel Dani, Gabor Oroszlan, Robert Martinusz, Bence Farkas, Bernadett Dobos, Evelin Vadas, Peter Zavodszky, Peter Gal, Jozsef Dobo
Summary: Complement factor D (FD) is a self-inhibited protease that is continuously converted from pro-FD by circulating active MASP-3. FD has low activity towards free FB but is highly efficient towards C3bB. The cleavage rate of FB is enhanced 20 million-fold when it forms a complex with C3b.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Jiewei Cui, Minjuan Zhou, Ying Li, Zhixin Liang, Yanqin Li, Ling Yu, Yang Liu, Yuan Liang, Liangan Chen, Changxi Yang
Summary: A quantum dots immunofluorescence biosensor was successfully developed for S. aureus detection, demonstrating high specificity and sensitivity. The biosensor has a low detection limit and can effectively distinguish other pathogens.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Andreza Alves Belo, Dayane L. Naves de Souza, Marcella Nunes De Melo-Braga, Leticia Lopes de Souza, Denis A. Molina Molina, Patricia D. Vaz de Melo, Martin R. Larsen, Clara Guerra-Duarte, Carlos Chavez-Olortegui
Summary: This study successfully generated a neutralizing antibody against Bothrops snake venom in Brazil, specifically targeting its coagulant activity. The use of monoclonal antibodies for immunoaffinity chromatography proved to be an effective technique for purifying bioactive toxins from the venom.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Chemistry, Multidisciplinary
Matthew D. Lloyd, Maksims Yevglevskis, Amit Nathubhai, Tony D. James, Michael D. Threadgill, Timothy J. Woodman
Summary: Racemases and epimerases are important enzymes in biotechnology and drug research, with potential applications. Research focuses on their catalytic mechanisms and development of corresponding inhibitors, including rational design of inhibitors and development of transition-state mimics.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Biochemistry & Molecular Biology
Ilka Jorde, Jens Schreiber, Sabine Stegemann-Koniszewski
Summary: Bronchial asthma, affecting more than 300 million patients worldwide, is primarily characterized by a Th2-mediated immune response against aeroallergens and is commonly observed in asthmatic children and adults. Recent studies have highlighted the association between respiratory colonization with Staphylococcus aureus (S. aureus), a Gram-positive bacterium, and the development of atopic respiratory diseases. Understanding the pathophysiological aspects and the impact of S. aureus toxins could potentially lead to new preventive strategies for allergic asthma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ken-ichi Miyazono, Keiko Kubota, Kenji Takahashi, Masaru Tanokura
Summary: Proteases are vital enzymes for life and have significant industrial importance. Understanding the substrate recognition mechanisms of proteases is crucial for enhancing their applications. This study determined the crystal structure of the prolyl endoprotease PEP and revealed the importance of its unique catalytic pocket structure in recognizing protein substrates.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Pharmacology & Pharmacy
Mengli Jin, Shuyue Zhu, Yating Tang, Xiangri Kong, Xingye Wang, Yufen Li, Shuang Jiang, Lin Wei, Chunjie Hu, Bingmei Wang, Wu Song
Summary: Antimicrobial resistance (AMR) is a global health threat, and there is a need for new anti-infective agents. Ayanin, a flavonoid extracted from Callicarpa nudiflora, was found to be an inhibitor of MRSA ClpP, suggesting its potential therapeutic effect against MRSA infections.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pawel Niedzialkowski, Magdalena Bojko, Jacek Ryl, Anna Wcislo, Marta Spodzieja, Katarzyna Magiera-Mularz, Katarzyna Guzik, Grzegorz Dubin, Tad A. Holak, Tadeusz Ossowski, Sylwia Rodziewicz-Motowidlo
Summary: This study successfully demonstrates the modification of a gold electrode with BMS-8 compound for interaction with PD-L1, and further investigates the selectivity of the electrode for other proteins. The work provides a new approach for electrochemical detection of immune checkpoint proteins.
BIOELECTROCHEMISTRY
(2021)
Article
Cell Biology
Ewelina Dobosz, Georg Lorenz, Andrea Ribeiro, Vivian Wuerf, Marta Wadowska, Jerzy Kotlinowski, Christoph Schmaderer, Jan Potempa, Mingui Fu, Joanna Koziel, Maciej Lech
Summary: Research has shown that depletion of MCPIP1 in macrophages and granulocytes can trigger severe autoimmune diseases like systemic lupus, affecting adaptive immune responses. This phenomenon is related to systemic autoinflammation and suggests that abnormal macrophage activation plays a significant role in the loss of immune tolerance.
DISEASE MODELS & MECHANISMS
(2021)
Article
Biochemistry & Molecular Biology
Ravi R. Sonani, Katarzyna Kurpiewska, Krzysztof Lewinski, Grzegorz Dubin
Summary: The glycosomal malate dehydrogenase from Trypanosoma cruzi displays a distinct sequence and structural feature, providing an anchor point for the development of specific inhibitors and potential trypanocidal drugs in the future.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Ophthalmology
Emilie Hage Mogensen, Ebbe Toftgaard Poulsen, Ida B. Thogersen, Kazuhiro Yamamoto, Annemarie Bruel, Jan J. Enghild
Summary: This article introduces a simplified LRP1 purification protocol, and uses the purified LRP1 to map its unknown interactome in the human cornea. The results suggest a novel role for LRP1 in regulating corneal immune response, structure, and transparency.
EXPERIMENTAL EYE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Liqiang Song, John D. Perpich, Chenggang Wu, Thierry Doan, Zuzanna Nowakowska, Jan Potempa, Peter J. Christie, Eric Cascales, Richard J. Lamont, Bo Hu
Summary: This study reveals the structure and assembly of P. gingivalis T9SS and its correlation with the development of periodontal disease. The T9SS shows unique structure and mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Nadia Sukusu Nielsen, Alessandra Zarantonello, Seandean Lykke Harwood, Kathrine Tejlgard Jensen, Katarzyna Kjoge, Ida B. Thogersen, Leif Schauser, Jesper Lykkegaard Karlsen, Gregers R. Andersen, Jan J. Enghild
Summary: This study investigates the protease-inhibitory mechanism of human A2ML1 and determines the structures of its native and protease-cleaved conformations. The functional unit of A2ML1 is a monomer that depends on covalent binding of the protease to achieve inhibition. Structural analysis shows that disruption of the bait region triggers conformational changes, resulting in protease inhibition.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Stanislaw Malicki, Barbara Pucelik, Edyta Zyla, Malgorzata Benedyk-Machaczka, Wojciech Galan, Anna Golda, Alicja Sochaj-Gregorczyk, Marta Kaminska, Joao Crispim Encarnacao, Barbara Chruscicka, Hans-Peter Marti, Tony Jialiang Chen, Katarzyna Magiera-Mularz, Bartosz Zieba, Tad A. Holak, Janusz M. Dabrowski, Anna Czarna, Joanna Koziel, Piotr Mydel, Grzegorz Dubin
Summary: In this study, a molecular probe based on aptamer was developed, which specifically recognizes human PD-L1. The probe showed excellent potential in cancer imaging in both in vitro and in vivo experiments.
Article
Biochemistry & Molecular Biology
Filipe Menezes, Grzegorz Maria Popowicz
Summary: In this study, three semi-empirical methods were used to model the interactions between the corannulene pincer and fullerenes. The results showed that these methods provided better agreement with experimental data compared to higher-level methods, at a significantly lower computational cost. Additionally, dynamical simulations were used to gain a more comprehensive understanding of the behavior of the corannulene pincer with fullerenes.
Letter
Multidisciplinary Sciences
Seandean Lykke Harwood, Gregers Rom Andersen, Jan J. Enghild
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Weronika Sowinska, Mateusz Wawro, Debolina D. Biswas, Jakub Kochan, Katarzyna Pustelny, Aleksandra Solecka, Angela S. Gupta, Karli Mockenhaupt, Jaroslaw Polak, Borys Kwinta, Tomasz Kordula, Aneta Kasza
Summary: The precise functions of Regnase-2 (Reg-2/ZC3H12B/MCPIP2) and its regulatory mechanisms remain unclear. This study shows that Reg-2 actively controls neuroinflammation in nontransformed cells, particularly primary astrocytes. It downregulates the mRNA levels of proinflammatory cytokines IL-1 beta and IL-6, as well as regulates the expression of Regnase-1 (Reg-1/ZC3H12A/MCPIP1). The expression levels of Reg-2 and Reg-1 are inversely related and their imbalance is associated with glioblastoma progression and patient prognosis.
Article
Multidisciplinary Sciences
Soren K. Amstrup, Sui Ching Ong, Nicholas Sofos, Jesper L. Karlsen, Ragnhild B. Skjerning, Thomas Boesen, Jan J. Enghild, Bjarne Hove-Jensen, Ditlev E. Brodersen
Summary: Using cryogenic electron microscopy, researchers discovered that PhnJ mediates the binding of the ATP-binding cassette proteins PhnK and PhnL to the core complex, and ATP hydrolysis leads to structural rearrangement and opening of the complex. This study sheds light on the breakdown of phosphonate in bacteria and provides insights into the mechanism of the large carbon-phosphorus lyase enzyme.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Christian E. Rusbjerg-Weberskov, Mette Liere Johansen, Jan S. Nowak, Daniel E. Otzen, Jan Skov Pedersen, Jan J. Enghild, Nadia Sukusu Nielsen
Summary: Human periostin is a matricellular protein that plays important roles in extracellular matrix remodeling, tumor development, and inflammatory diseases. The C-terminal domain of periostin interacts with other domains and proteins, potentially contributing to the pathogenesis of diseases such as atopic dermatitis.
Article
Microbiology
Katarzyna Szczesniak, Florian Veillard, Carsten Scavenius, Kamila Chudzik, Kinga Ferenc, Matthias Bochtler, Jan Potempa, Danuta Mizgalska
Summary: In certain bacteria, the glutaminyl cyclase (QC) is crucial for protein stability and bacterial growth. QC converts glutamine residues to pyroglutamate, protecting proteins from degradation. However, the loss of QC results in the loss of Q-rule substrates, leading to the inability of bacteria to survive.
Article
Biochemistry & Molecular Biology
Zsombor Prucsi, Agnieszka Zimny, Alicja Plonczynska, Natalia Zubrzycka, Jan Potempa, Maja Sochalska
Summary: Periodontitis is a chronic inflammatory disease caused by dysbiotic oral microbiome, and Porphyromonas gingivalis is identified as a key pathogen. The mechanism by which P. gingivalis secretes the enzyme PPAD to contribute to the inflammation loop is not fully understood. This study reveals that PPAD promotes neutrophil survival and pro-inflammatory cytokine secretion, while enhancing the resilience of bacteria to phagocytosis, thus sustaining a chronic inflammatory state.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Interdisciplinary Applications
Zhonghua Xia, Pavel Karpov, Grzegorz Popowicz, Michael Sattler, Igor Tetko
Summary: Small-molecule drug design aims to identify inhibitors that can specifically bind to an enzyme's active site. Traditional methods rely on static structures to identify binding pockets, but small molecules can induce the opening of dynamic pockets. This study assessed the features in molecules that can induce cryptic pocket opening and developed a model to design inducers for undruggable proteins.