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JOURNAL ARTICLE
Simone Parisi, Becciolini Andrea, Ditto Maria Chiara, Lo Gullo Alberto, Larosa Maddalena, Scolieri Palma, Addimanda Olga, Reta Massimo, Paroli Marino, Caccavale Rosalba, Visalli Elisa, Foti Rosario, Amato Giorgio, De Lucia Francesco, Dal Bosco Ylenia, Foti Roberta, Farina Antonella, Girelli Francesco, Bernardi Simone, Camellino Dario, Bianchi Gerolamo, Colina Matteo, Andracco Romina, Mansueto Natalia, Ferrero Giulio, Del Medico Patrizia, Molica Colella Aldo, Franchina Veronica, Molica Colella Francesco, Lumetti Federica, Sandri Gilda, Salvarani Carlo, Priora Marta, Ianniello Aurora, Nucera Valeria, Santilli Daniele, Lucchini Gianluca, Giuditta Adorni, Di Donato Eleonora, Bravi Elena, Platè Ilaria, Arrigoni Eugenio, Bezzi Alessandra, Focherini Maria Cristina, Mascella Fabio, Bruzzese Vincenzo, Ravagnani Viviana, Fiorenza Alessia, Rovera Guido, Vitetta Rosetta, Marchetta Antonio, Volpe Alessandro, Ometto Francesca, Ariani Alarico, Fusaro Enrico
OBJECTIVES: The persistence in therapy of rheumatoid arthritis drugs and particularly bDMARD is a limiting factor for their long-term use. The randomized controlled trials (RCTs) may not reflect real-world contexts due to strict inclusion and exclusion criteria. Baricitinib, which targets both JAK1 and JAK2, has been used in Italy for several years. The aim of this multi-center study is to assess the real world persistence on therapy of baricitinib in RA patients and to identify predictive factors of baricitinib's survival rate...
2024: Curr Res Pharmacol Drug Discov
#42
JOURNAL ARTICLE
Jinsha Huang, Xiaoman Xie, Wanlin Zheng, Li Xu, Jinyong Yan, Ying Wu, Min Yang, Yunjun Yan
BACKGROUND: Biodiesel, an emerging sustainable and renewable clean energy, has garnered considerable attention as an alternative to fossil fuels. Although lipases are promising catalysts for biodiesel production, their efficiency in industrial-scale application still requires improvement. RESULTS: In this study, a novel strategy for multi-site mutagenesis in the binding pocket was developed via FuncLib (for mutant enzyme design) and Rosetta Cartesian_ddg (for free energy calculation) to improve the reaction rate and yield of lipase-catalyzed biodiesel production...
February 24, 2024: Biotechnol Biofuels Bioprod
#43
Daniele Sola, Carlo Smirne, Francesco Bruggi, Chiara Bottino Sbaratta, Aubin Cardin Tamen Njata, Guido Valente, Maria Cristina Pavanelli, Rosetta Vitetta, Mattia Bellan, Lorenzo De Paoli, Mario Pirisi
Adult-onset Still's disease (AOSD) is a rare systemic inflammatory disorder. Diagnosis can take a long time, especially in the presence of confounding factors, and it is, to some extent, a process of exclusion. AOSD has life-threating complications ranging from asymptomatic to severe, such as macrophage activation syndrome (MAS), which is also referred to as hemophagocytic lymphohistocytosis (HLH). This condition is correlated with cytokine storm production and monocyte/macrophage overactivation and typically occurs with rash, pyrexia, pancytopenia, hepatosplenomegaly and systemic involvement...
January 29, 2024: Life
#44
REVIEW
Mihail Celeski, Annunziata Nusca, Valeria Maria De Luca, Giorgio Antonelli, Valeria Cammalleri, Rosetta Melfi, Fabio Mangiacapra, Elisabetta Ricottini, Paolo Gallo, Nino Cocco, Raffaele Rinaldi, Francesco Grigioni, Gian Paolo Ussia
Takotsubo syndrome (TTS) is a clinical condition characterized by temporary regional wall motion anomalies and dysfunction that extend beyond a single epicardial vascular distribution. Various pathophysiological mechanisms, including inflammation, microvascular dysfunction, direct catecholamine toxicity, metabolic changes, sympathetic overdrive-mediated multi-vessel epicardial spasms, and transitory ischemia may cause the observed reversible myocardial stunning. Despite the fact that TTS usually has an acute coronary syndrome-like pattern of presentation, the absence of culprit atherosclerotic coronary artery disease is often reported at coronary angiography...
January 26, 2024: Journal of Cardiovascular Development and Disease
#45
REVIEW
Doo Nam Kim, Andrew D McNaughton, Neeraj Kumar
This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions...
February 15, 2024: Bioengineering
#46
JOURNAL ARTICLE
Sijie Chen, Tong Lin, Ruchira Basu, Jeremy Ritchey, Shen Wang, Yichuan Luo, Xingcan Li, Dehua Pei, Levent Burak Kara, Xiaolin Cheng
We introduce a computational approach for the design of target-specific peptides. Our method integrates a Gated Recurrent Unit-based Variational Autoencoder with Rosetta FlexPepDock for peptide sequence generation and binding affinity assessment. Subsequently, molecular dynamics simulations are employed to narrow down the selection of peptides for experimental assays. We apply this computational strategy to design peptide inhibitors that specifically target β-catenin and NF-κB essential modulator...
February 21, 2024: Nature Communications
#47
Jessica Wei, Jeonghyeon Moon, Yoshiaki Yasumizu, Le Zhang, Khadir Radassi, Nicholas Buitrago-Pocasangre, M Elizabeth Deerhake, Nicholas Strauli, Alan Chan, Ann Herman, Rosetta Pedotte, Catarina Raposo, Björn Tackenberg, Isaiah Yim, Jenna Pappalardo, Erin E Longbrake, Tomokazu S Sumida, Pierre-Paul Axisa, David A Hafler
Multiple sclerosis (MS) is a complex genetically mediated autoimmune disease of the central nervous system where anti-CD20-mediated B cell depletion is remarkably effective in the treatment of early disease. While previous studies investigated the effect of B cell depletion on select immune cell subsets using flow cytometry-based methods, the therapeutic impact on patient immune landscape is unknown. In this study, we explored how a therapy-driven " in vivo perturbation " modulates the diverse immune landscape by measuring transcriptomic granularity with single-cell RNA sequencing (scRNAseq)...
February 9, 2024: bioRxiv
#48
JOURNAL ARTICLE
Rui Zhang, Haohao Yan, Zhicheng Liu, Xiaoli Liu, Gangan Yan, Xiaoping Liu, Yunyu Chen
The conventional peptide substrates of SARS-CoV-2 main protease (Mpro) are frequently associated with high cost, unstable kinetics, and multistep synthesis. Hence, there is an urgent need to design affordable and stable Mpro substrates for pharmacological research. Herein, we designed a functional Mpro substrate based on a dimerization-dependent red fluorescent protein (ddRFP) for the evaluation of Mpro inhibitors in vitro . The codon-optimized DNA fragment encoding RFP-A1 domain, a polypeptide linker containing Mpro cleavage sequence (AVLQS), and the RFP-B1 domain was subcloned into the pET-28a vector...
February 25, 2024: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
#49
JOURNAL ARTICLE
Hope Woods, Julia Koehler Leman, Jens Meiler
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanodiscs, or liposomes...
March 2024: Protein Science
#50
JOURNAL ARTICLE
Rosetta Ragusa, Arianna Di Molfetta, Alberto Mercatanti, Letizia Pitto, Antonio Amodeo, Maria Giovanna Trivella, Milena Rizzo, Chiara Caselli
BACKGROUND: Ventricular assist device (VAD) implant represents a therapeutic option for pediatric patients with end-stage heart failure (HF). Heart unloading by VAD can modify several molecular pathways underlying cardiac function in HF. Among them, the potential role of microRNA (miRNAs) in response to VAD implant is emerging. This study was aimed at investigating in HF pediatric patients the effect of VAD-modified miRNAs on the adiponectin (ADPN) system, known to exert cardioprotective actions...
February 2024: JHLT Open
#51
Marissa Dolorfino, Rituparna Samanta, Anastassia Vorobieva
Recent deep-learning (DL) protein design methods have been successfully applied to a range of protein design problems, including the de novo design of novel folds, protein binders, and enzymes. However, DL methods have yet to meet the challenge of de novo membrane protein (MP) and the design of complex β-sheet folds. We performed a comprehensive benchmark of one DL protein sequence design method, ProteinMPNN, using transmembrane and water-soluble β-barrel folds as a model, and compared the performance of ProteinMPNN to the new membrane-specific Rosetta Franklin2023 energy function...
February 1, 2024: bioRxiv
#52
JOURNAL ARTICLE
Héctor Cruz, Alejandro Llanes, Patricia L Fernández
Many protein-protein interactions involve the binding of short protein segments to peptide-binding domains. Usually, such interactions require the recognition of linear motifs with variable conservation. The combination of highly conserved and more variable regions in the same ligands often contributes to the multispecificity of binding, a common property of enzymes and cell signaling proteins. Characterization of amino acid preferences of peptide-binding domains is important for the design of mediators of protein-protein interactions (PPIs)...
January 26, 2024: Journal of Visualized Experiments: JoVE
#53
JOURNAL ARTICLE
Franco Vicariotto, Patrizia Malfa, Elisa Viciani, Federica Dell'Atti, Diletta F Squarzanti, Andrea Marcante, Andrea Castagnetti, Rosetta Ponchia, Laura Governini, Vincenzo De Leo
The menopausal transition marks a significant physiological shift in women. Menopause-related symptoms can significantly affect a woman's quality of life and probiotics have emerged as a promising avenue. This study aims to investigate the benefits of probiotics in improving vaginal well-being and microbiota composition in post-menopausal women. A prospective observational clinical trial was carried out enrolling 50 post-menopausal healthy women, aged between 45 and 65 years old, taking a supplement containing Lactiplantibacillus plantarum PBS067, Bifidobacterium animalis subsp...
January 30, 2024: Nutrients
#54
JOURNAL ARTICLE
Claudio Gambardella, Federico Maria Mongardini, Maddalena Paolicelli, Francesco Saverio Lucido, Salvatore Tolone, Luigi Brusciano, Simona Parisi, Rosetta Esposito, Francesco Iovino, Luca Nazzaro, Francesco Pizza, Ludovico Docimo
Background. Obesity is a prevalent condition associated with various comorbidities, impacting mortality, fertility, and quality of life. Its relationship with type 2 diabetes mellitus (DMII) is well established, with nearly 44% prevalence. Bariatric surgery has proven crucial for treating both obesity and DMII. The comparison between surgical techniques, such as sleeve gastrectomy (SG) and one anastomosis gastric bypass (OAGB), remains controversial in terms of glycemic control efficacy. This retrospective study aimed to assess DMII remission efficacy between SG and OAGB after 36 months...
February 4, 2024: Journal of Clinical Medicine
#55
JOURNAL ARTICLE
Matt Sinclair, Richard A Stein, Jonathan H Sheehan, Emily M Hawes, Richard M O'Brien, Emad Tajkhorshid, Derek P Claxton
Mediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein glucose-6-phosphate catalytic subunit 1 (G6PC1) regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 causes glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown...
February 2024: PNAS Nexus
#56
JOURNAL ARTICLE
Neeraj K Gaur, Zeenat Khakerwala, Ravindra D Makde
The world of medicine demands from the research community solutions to the emerging problem of SARS-CoV-2 variants and other such potential global pandemics. With advantages of specificity over small molecule drugs and designability over antibodies, miniprotein therapeutics offers a unique solution to the threats of rapidly emerging SARS-CoV-2 variants. Unfortunately, most of the promising miniprotein binders are de novo designed and it is not viable to generate molecules for each new variant. Therefore in this study, we demonstrate a method for design of miniprotein mimics from the interaction interphase of human angiotensin converting enzyme 2 (ACE2)...
February 5, 2024: Journal of Biomolecular Structure & Dynamics
#57
JOURNAL ARTICLE
Nishanthika Thenmozhi Kulasekaran, Sai Hariharan Sankara Subramanian, Mary Leema Thilakam, Dharani Gopal, Jung Kul Lee, Jeya Marimuthu
Type III polyketide synthases (type III PKSs) are single homodimeric enzymes that produce diverse products such as phloroglucinol, pyrones, resorcinols and chalcones which are biotechnologically important molecules. In an attempt to identify new type III PKS from extreme environments, the deep-sea sediment metagenome from Bay of Bengal was screened for type III PKS genes. BLASTX analyses of Nanopore sequence derived metagenome with the in-house created PKS database revealed a full length type III PKS from a 5 kb fragment...
February 1, 2024: Journal of Bioscience and Bioengineering
#58
JOURNAL ARTICLE
Alexandra Claveria, Dona Bachour, Joy Y Balta, Rosetta Antonacci, Nicole M Ventura, Geoffroy P J C Noel
Donor-centered education offers students the opportunity to not only acquire visual and tactile experiences for applying anatomical knowledge but also a chance for students to reflect upon fundamental humanistic principles. The exploration of differences in students' viewpoints on body donation and the utilization of body donors in their education remains unexplored across various healthcare professional programs, which has an impact on student learning and experience. This study aimed to qualitatively examine the similarities and differences in student perspectives regarding body donation across three healthcare professional programs...
February 1, 2024: Anatomical Sciences Education
#59
JOURNAL ARTICLE
J Cheng, Z Li, Y Liu, C Li, X Huang, Y Tian, F Shen
OBJECTIVE: To analyze the interaction between PML protein and TAB1 protein using bioinformatic approaches and experimentally verify the results. METHODS: Using Rosetta software, a 3D model of TAB1 protein was constructed through a comparative modeling approach; the secondary structure of PML protein was retrieved in the PDB database and its crystal structure and 3D structure were resolved. Zdock 3.0.2 software was used to perform protein-protein docking of PML and TAB1, and the best conformation was extracted for molecular structure analysis of the docking model...
January 20, 2024: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
#60
JOURNAL ARTICLE
Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y Hara, Yoko Hirono-Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda
Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E. coli strains have distinct metabolic capacities. In this study, two proteins were overexpressed in four E. coli strains (MG1655(DE3), W3110(DE3), BL21star(DE3), and Rosetta(DE3)), and their effects on metabolic burden were investigated...
January 27, 2024: Journal of Bioscience and Bioengineering
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