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CaML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features.
Protein Sci
February 2025
Department of Physics, University of Washington, Seattle, Washington, USA.
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes.
View Article and Find Full Text PDFEngineered protein G variants for multifunctional antibody-based assemblies.
Protein Sci
February 2025
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.
We have developed a portfolio of antibody-based modules that can be prefabricated as standalone units and snapped together in plug-and-play fashion to create uniquely powerful multifunctional assemblies. The basic building blocks are derived from multiple pairs of native and modified Fab scaffolds and protein G (PG) variants engineered by phage display to introduce high pair-wise specificity. The variety of possible Fab-PG pairings provides a highly orthogonal system that can be exploited to perform challenging cell biology operations in a straightforward manner.
View Article and Find Full Text PDFAdvances in Prenatal Cell-Free DNA Screening for Dominant Monogenic Conditions: A Review of Current Progress and Future Directions in Clinical Implementation.
Prenat Diagn
January 2025
Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
Prenatal cell-free DNA (cfDNA) screening has advanced significantly, extending beyond detecting aneuploidies to sub-chromosomal copy number variations. However, its application for screening dominant single-gene conditions, often caused by de novo variants, remains underutilized in the general obstetric population. This study reviews recent data and experience on prenatal cfDNA screening for dominant monogenic conditions using multiple-gene panels, highlighting its potential to enhance early detection and management of genetic disorders.
View Article and Find Full Text PDFSingle-cell transcriptomics identify a novel macrophage population associated with bone invasion in pituitary neuroendocrine tumors.
J Exp Clin Cancer Res
January 2025
Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
Background: Bone-invasive Pituitary Neuroendocrine Tumors (BI PitNETs) epitomize an aggressive subtype of pituitary tumors characterized by bone invasion, culminating in extensive skull base bone destruction and fragmentation. This infiltration poses a significant surgical risk due to potential damage to vital nerves and arteries. However, the mechanisms underlying bone invasion caused by PitNETs remain elusive, and effective interventions for PitNET-induced bone invasion are lacking in clinical practice.
View Article and Find Full Text PDFSemaphorin-4D signaling in recruiting dental stem cells for vascular stabilization.
Stem Cell Res Ther
January 2025
Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, Prince Philip Dental Hospital, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong, Hong Kong SAR.
Background: Achieving a stable vasculature is crucial for tissue regeneration. Endothelial cells initiate vascular morphogenesis, followed by mural cells that stabilize new vessels. This study investigated the in vivo effects of Sema4D-Plexin-B1 signaling on stem cells from human exfoliated deciduous teeth (SHED)-supported angiogenesis, focusing on its mechanism in PDGF-BB secretion.
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