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Protein Target Search Diffusion-association/dissociation Free Energy Landscape around DNA Binding Site with Flanking Sequences.
Biophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFProtein prenylation in mechanotransduction: implications for disease and therapy.
Trends Pharmacol Sci
January 2025
Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China. Electronic address:
The process by which cells translate external mechanical cues into intracellular biochemical signals involves intricate mechanisms that remain unclear. In recent years, research into post-translational modifications (PTMs) has offered valuable insights into this field, spotlighting protein prenylation as a crucial mechanism in cellular mechanotransduction and various human diseases. Protein prenylation, which involves the covalent attachment of isoprenoid groups to specific substrate proteins, profoundly affects the functions of key mechanotransduction proteins such as Rho, Ras, and lamins.
View Article and Find Full Text PDFPostoperative pancreatic fistula risk assessment using digital pathology based analyses at the parenchymal resection margin of the pancreas - Results from the randomized multicenter RECOPANC trial.
HPB (Oxford)
December 2024
Institute for Surgical Pathology, Medical Center - University of Freiburg, Germany; Core Facility for Histopathology and Digital Pathology, University of Freiburg, Germany; Faculty of Medicine, University of Freiburg, Germany. Electronic address:
Background: In pancreatic surgery Postoperative pancreatic fistula (POPF) represents the most dreaded complication, for which pancreatic texture is acknowledged as one of the strongest predictors. No consensual objective reference has been defined to evaluate the pancreas composition. The presented study aimed to mine histology data of the pancreatic tissue composition with AI assist and correlate it with clinic-pathological parameters derived from the RECOPANC study.
View Article and Find Full Text PDFUsing synthetic biology to express nitrogenase biosynthesis pathway in rice and to overcome barriers of nitrogenase instability in plant cytosol.
Trends Biotechnol
January 2025
College of Biological Sciences, China Agricultural University, Beijing 100193, China. Electronic address:
Engineering nitrogen fixation in cereals could reduce usage of chemical nitrogen fertilizers. Here, a nitrogenase biosynthesis pathway comprising 13 genes (nifB nifH nifD nifK nifE nifN nifX hesA nifV nifS nifU groES groEL) was introduced into rice by transforming multigene vectors and subsequently by sexual crossing between transgenic rice plants. Genome sequencing analysis revealed that 13 nif genes in F hybrid rice lines L12-13 and L8-17 were inserted at two loci on rice chromosome 1.
View Article and Find Full Text PDFPathological diagnosis of central nervous system tumours in adults: what's new?
Pathology
December 2024
Department of Pathology, Amsterdam University Medical Centers/VUmc, Amsterdam, The Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
In the course of the last decade, the pathological diagnosis of many tumours of the central nervous system (CNS) has transitioned from a purely histological to a combined histological and molecular approach, resulting in a more precise 'histomolecular diagnosis'. Unfortunately, translation of this refinement in CNS tumour diagnostics into more effective treatment strategies is lagging behind. There is hope though that incorporating the assessment of predictive markers in the pathological evaluation of CNS tumours will help to improve this situation.
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