Article
Biochemical Research Methods
Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo
Summary: The study introduces a new big data platform, FADE, for alignment-free genomic analysis, supporting 18 best-performing AF functions, with faster execution time and user-friendly software design. Additionally, it provides a novel analysis of the informativeness and robustness of AF functions, finding that only a handful of functions out of the 18 included in FADE can actually be used.
Article
Chemistry, Multidisciplinary
Zhongjie Wang, Wenjuan Yuan, Lei Zhang, Ying Zhang, Haojie Lu
Summary: Protein termini play a crucial role in protein stability. Researchers have developed a new method called NAPT to selectively separate protein termini based on charge state differences. They successfully identified thousands of protein N-termini and C-termini from the HeLa cell line.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biophysics
Wenjun Liu, Xuena Zhu, Ling Li, Shanshan Wang, Chen-Zhong Li, Tingbo Liang
Summary: Activation of Cas13 is dependent on crRNA-target RNA hybridization. This study develops a controlled activation system for Cas13 using N-terminus tagging, which suppresses target dependent activation through a composite SUMO tag. This discovery not only enables Cas13-based protease detection, but also provides a novel strategy for precise multi-component activation of Cas13.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Multidisciplinary Sciences
Sabit Ahmed, Afrida Rahman, Md Al Mehedi Hasan, Shamim Ahmad, S. M. Shovan
Summary: The study introduces a computational method named 'iMul-kSite' for predicting multiple protein post-translational modifications, achieving an accuracy of 92.83% and outperforming existing predictors in validation tests. This predictor can serve as a supportive tool for further research in K-PTMs.
SCIENTIFIC REPORTS
(2021)
Article
Food Science & Technology
Xiang Yang, Zhongming Zhang, Weibing Zhang, Haijun Qiao, Pengcheng Wen, Yan Zhang
Summary: Researchers have discovered a new milk-clotting protease with high activity from the midgut of Tenebrio molitor larvae, which could serve as a potential milk coagulant and provide a theoretical basis for the development of insect chymosin.
JOURNAL OF FUNCTIONAL FOODS
(2022)
Article
Chemistry, Physical
Julia Soika, Calum McLaughlin, Tomas Nevesely, Constantin G. Daniliuc, John. J. Molloy, Ryan Gilmour
Summary: This study presents a mild organophotocatalytic N-O bond cleavage method that allows for the cleavage of bonds without harsh conditions. The method demonstrates synthetic utility for a broad range of compounds and enables the synthesis of ambiphilic amide aldehydes with varying chain lengths.
Article
Biochemical Research Methods
Vladimir Naumov, Evgeny Putin, Stefan Pushkov, Ekaterina Kozlova, Konstantin Romantsov, Alexander Kalashnikov, Fedor Galkin, Nina Tihonova, Anastasia Shneyderman, Egor Galkin, Arsenii Zinkevich, Stephanie M. Cope, Ramanathan Sethuraman, Tudor Oprea, Alexander T. Pearson, Savas Tay, Nishant Agrawal, Alexey Dubovenko, Quentin Vanhaelen, Ivan Ozerov, Alex Aliper, Evgeny Izumchenko, Alex Zhavoronkov
Summary: COVIDomic is a multi-omics online platform designed to facilitate the analysis and interpretation of health data collected from COVID-19 patients, including microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification, to determine the origin of the coronavirus strain and the expected severity of the disease.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Energy & Fuels
Shentong Ni, Yang Tang, Guorong Wang, Liu Yang, Bo Lei, Zhidong Zhang
Summary: Equipment failure risk identification and risk assessment are crucial for offshore platform equipment integrity management. This paper proposes a new quantitative risk assessment method based on fuzzy set theory, gray correlation analysis, and fuzzy Borda method. The proposed method effectively captures and aggregates diversity evaluations of FMECA team members and solves the existing issues in quantitative risk assessment. It provides a reference for maintenance decision-making in complex industrial systems.
Article
Chemistry, Medicinal
Xuewu Liang, Chenxia Sun, Chunpu Li, Haolan Yu, Xiaohui Wei, Xuyi Liu, Wei Bao, Yuqiang Shi, Xiaochen Sun, Mirzadavlat Khamrakulov, Chenghua Yang, Hong Liu
Summary: The study identified a novel class of potent MALT1 inhibitors that showed selective cytotoxicity to activated B cell-like diffuse large B cell lymphoma with low micromolar potency. Compound 20c specifically repressed NF-κB signaling and induced cell apoptosis in MALT1-dependent TMD8 cells in a dose-dependent manner, exhibiting good pharmacokinetic properties and antitumor efficacy in xenograft tumor model. This provides valuable lead compounds for further structural optimization and antitumor mechanism study.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Rui Wang, Shuai Wang, Xiaowen Xu, Wei Jiang, Nan Zhang
Summary: A DNA logic platform based on MNAzyme probes was developed for miRNAs logic detection and cancer cells identification. Different types of logic gates were constructed, using MnO2 nanosheets as carriers and cofactor providers, to achieve logic detection of miRNAs and identification of cancer cells.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Priscila Yumi Tanaka Shibao, Milene Ferro, Fernando Fonseca Pereira de Paula, Bruno Salata Lima, Flavio Henrique-Silva
Summary: The main digestive protease Sl-CathL-CS of Sphenophorus levis was identified as a pseudo-cysteine protease that assists in protein digestion by interacting with sugarcane cystatin inhibitors. The study revealed that the mutant Sl-CathL-mutSC, with a reverted serine residue to cysteine, showed protease activity and was inhibited by a cysteine protease inhibitor. Protein ligand docking further highlighted the differences in catalytic sites between native and mutant proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Noemi Miltner, Gergo Kallo, Eva Csosz, Mario Miczi, Tibor Nagy, Mohamed Mahdi, Janos Andras Motyan, Jozsef Tozser
Summary: The main protease (Mpro) of SARS-CoV-2 is crucial for the virus's life cycle. Cleavage of viral polyproteins by Mpro is necessary for virus replication, and cleavage of host proteins may contribute to viral pathogenesis. Identification of host substrates and cleavage sites is important for understanding the enzyme's specificity and improving computational prediction methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Applied
Yong Qiang Zhou, Su Mei Li, Xin Wei, Xin Yang, Jun Wei Xiao, Bo Wen Pan, Shou Xia Xie, Ying Zhou, Jian Yang, Ying Wei
Summary: This study evaluated the antiviral activity of four Potentilla kleiniana extracts and seven compounds against HIV-1 protease, and found that they exhibited inhibitory effects on the enzyme.
NATURAL PRODUCT RESEARCH
(2022)
Article
Microbiology
Abdul Wahaab, Ke Liu, Muddassar Hameed, Muhammad Naveed Anwar, Lei Kang, Chenxi Li, Xiaochun Ma, Abdul Wajid, Yi Yang, Umair Hassan Khan, Jianchao Wei, Beibei Li, Donghua Shao, Yafeng Qiu, Zhiyong Ma
Summary: This study investigated the proteolytic processing of polyprotein mediated by NS2B-NS3 protease in Japanese encephalitis virus (JEV) infection using eukaryotic and prokaryotic cell models. The results showed that cleavage efficiency of cleavage sites by host cell proteases varied, with certain sites being specifically cleaved by JEV NS2B-NS3 protease. These findings provide insight into JEV replication and pathogenesis.
Review
Biochemistry & Molecular Biology
Andrew R. Ghazi, Philipp C. Munch, Di Chen, Jordan Jensen, Curtis Huttenhower
Summary: Microbiology has been studying the significant impacts of subtle genetic differences between closely related microbial strains on their phenotypes and the environments and communities around them. However, detecting and studying these strain-level differences remains challenging. This article provides an in-depth discussion of computational tools and statistical models available for strain-resolved shotgun metagenomic profiling of microbial communities, as well as the limitations and challenges in conducting such studies.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Paolo Ascenzi, Giovanna De Simone, Andrea Pasquadibisceglie, Magda Gioia, Massimo Coletta
Summary: Haptoglobin counteracts the negative effects of extracellular hemoglobin by forming complexes with Hb, displaying Hb-like reactivity. The dissociation of NO from Hp:Hb complexes is biphasic and unaffected by allosteric effectors, indicating a structural similarity in the subunits. The observed functional heterogeneity in the dissociation process is attributed to the different structural arrangements of the subunits in the nitrosylated R-state.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2021)
Article
Allergy
Henry Y. Lu, Mehul Sharma, Ashish A. Sharma, Atilano Lacson, Ashley Szpurko, Joanne Luider, Poonam Dharmani-Khan, Afshin Shameli, Peter A. Bell, Gregory M. T. Guilcher, Victor A. Lewis, Marta Rojas Vasquez, Sunil Desai, Lyle McGonigle, Luis Murguia-Favela, Nicola A. M. Wright, Consolato Sergi, Eytan Wine, Christopher M. Overall, Sneha Suresh, Stuart E. Turvey
Summary: This study identified novel pathogenic biallelic loss-of-function variants in CARD11 in two patients with profound CID. The defects in immune signaling pathways resulted in impaired B and T cell development, compromised antibody responses, and abolished MALT1 paracaspase activity. Hematopoietic stem cell transplantations restored the impaired signaling pathways and led to functional normalization.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Review
Cell Biology
Giulia Alloisio, Chiara Ciaccio, Giovanni Francesco Fasciglione, Umberto Tarantino, Stefano Marini, Massimo Coletta, Magda Gioia
Summary: The complex skeletal organization adapts to external contexts and demonstrates excellent self-renewal capacity. Cells respond to mechanical cues and external stimuli to regulate bone anabolism. Exogenous stimuli can promote mineral apposition, bone formation, and fracture repair, while mechanical forces and signaling factors play a crucial role in modulating bone synthesis.
Article
Chemistry, Multidisciplinary
Matthew Drayton, Morgan A. Alford, Daniel Pletzer, Evan F. Haney, Yoan Machado, Haiming D. Luo, Christopher M. Overall, Jayachandran N. Kizhakkedathu, Robert E. W. Hancock, Suzana K. Straus
Summary: A novel PEG-HDP conjugate was designed targeting MMPs at sites of inflammation and infection, enhancing antimicrobial activity through enzymatic cleavage while improving biocompatibility, demonstrated by strong antibacterial efficacy in a mouse abscess model with high-density MRSA infection.
JOURNAL OF CONTROLLED RELEASE
(2021)
Editorial Material
Biochemical Research Methods
Christopher M. Overall
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Environmental Sciences
Nicolo Venza, Giulia Alloisio, Magda Gioia, Claudio Liguori, Annarita Nappi, Carlotta Danesi, Giuseppina Lagana
Summary: Subjects with obstructive sleep apnea syndrome (OSAS) exhibit slight alkaline pH and reduced antioxidant capacity in saliva, along with increased protein concentration. This may contribute to the development of chronic gingivitis. Further investigations are needed to explore the potential of using salivary fluid for early diagnosis of oral or systemic problems in OSAS patients.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Editorial Material
Biochemical Research Methods
John R. Yates, Ileana M. Cristea, Meng-Qui Dong, Claire E. Eyers, Joshua LaBaer, Jia V. Li, Jeremy K. Nicholson, Christopher M. Overall, Magnus Palmblad, Nikolai Slavov
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jina Yun, Simon Hansen, Otto Morris, David T. Madden, Clare Peters Libeu, Arjun J. Kumar, Cameron Wehrfritz, Aaron H. Nile, Yingnan Zhang, Lijuan Zhou, Yuxin Liang, Zora Modrusan, Michelle B. Chen, Christopher C. Overall, David Garfield, Judith Campisi, Birgit Schilling, Rami N. Hannoush, Heinrich Jasper
Summary: Cellular senescence and the senescence-associated secretory phenotype (SASP) play a role in aging and age-related diseases. The inflammation caused by SASP is believed to contribute to tissue dysfunction in aging and diseased animals. Research using intestinal organoids as a model has found that SASP factors released by senescent fibroblasts disturb stem cell activity and differentiation, leading to impaired crypt formation. It has been discovered that the N-terminal domain of Ptk7, which is secreted by senescent cells, activates non-canonical Wnt/Ca2+ signaling through FZD7 in intestinal stem cells (ISCs), disrupting symmetry breaking and stem cell differentiation. This study provides insight into the mechanism by which cellular senescence contributes to tissue dysfunction in aging and disease.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Peter A. Bell, Christopher M. Overall
Summary: Proteolytic processing, the most common post-translational modification, has a significant impact on protein function. By reanalyzing shotgun proteomics datasets, we found evidence of proteolytic processing in COVID-19, which provides valuable insights for studying protease function and virus-host interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Giulia Alloisio, David Becerril Rodriguez, Marco Luce, Chiara Ciaccio, Stefano Marini, Antonio Cricenti, Magda Gioia
Summary: This study used uniaxial-stretching technology to select a mechanical regimen that can increase the migration of SAOS-2 cells in osteosarcoma. Through confocal and atomic force microscopy, it was found that a 24 h 1 Hz cyclic elongation can induce morphological changes in cells, as well as changes in cell adhesion and migration properties. These changes are independent of osteoblastic differentiation grade.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Aleksander M. Haack, Christopher M. Overall, Ulrich auf dem Keller
Summary: The extracellular matrix (ECM) is composed of proteins secreted by cells and plays a crucial role in maintaining tissue homeostasis and cellular control. Aberrant signaling through the ECM can lead to various pathological conditions. Therefore, characterizing the components of the ECM and developing novel therapeutics are of great importance.
Article
Biochemistry & Molecular Biology
Peter A. Bell, Sophia Scheuermann, Florian Renner, Christina L. Pan, Henry Y. Lu, Stuart E. Turvey, Frederic Bornancin, Catherine H. Regnier, Christopher M. Overall
Summary: Researchers developed a bioinformatics-led substrate discovery workflow to expand the known substrate repertoire of MALT1. They identified seven new MALT1 substrates using their approach and confirmed their functions in NF-κB regulation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Oncology
K. Juurikka, A. Dufour, K. Pehkonen, B. Mainoli, P. Campioni Rodrigues, N. Solis, T. Klein, P. Nyberg, C. M. Overall, T. Salo, P. Astrom
Summary: In this study, we identified FXYD5 as a novel substrate of MMP8, which when cleaved by MMP8 or silenced with siRNA, leads to increased cell adhesion and reduced motility in HSC-3 and SCC-25 tongue cancer cells. The findings suggest that targeting FXYD5, a known prognostic factor in OTSCC, may have therapeutic potential in cancer treatment.
Article
Medicine, Research & Experimental
Lindsay B. Alcaraz, Aude Mallavialle, Timothee David, Danielle Derocq, Frederic Delolme, Cindy Dieryckx, Caroline Mollevi, Florence Boissiere-Michot, Joelle Simony-Lafontaine, Stanislas Du Manoir, Pitter F. Huesgen, Christopher M. Overall, Sophie Tartare-Deckert, William Jacot, Thierry Chardes, Severine Guiu, Pascal Roger, Thomas Reinheckel, Catherine Moali, Emmanuelle Liaudet-Coopman
Summary: This study identified a novel crosstalk between proteases and matricellular proteins in the tumor microenvironment through limited SPARC proteolysis, revealing a novel targetable 9-kDa bioactive SPARC fragment for new TNBC treatments. The research paves the way for developing strategies to target bioactive fragments from matricellular proteins in TNBC.