A specific cosedimentation of proteins and their complexes with DNA at low temperature (M-band technique) has been demonstrated. Model experiments with reconstituted SV40 DNA-topoisomerase I and SV40 DNA-E. coli RNA polymerase complexes demonstrated the potential and capacities of the method. It allows fractionation of DNA-protein complexes from naked DNA and has greater range, higher reproducibility and lower background values than similar methods.
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J Chem Inf Model
January 2025
Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States.
Coarse-grained models have become ubiquitous in biomolecular modeling tasks aimed at studying slow dynamical processes such as protein folding and DNA hybridization. These models can considerably accelerate sampling but it remains challenging to accurately and efficiently restore all-atom detail to the coarse-grained trajectory, which can be vital for detailed understanding of molecular mechanisms and calculation of observables contingent on all-atom coordinates. In this work, we introduce FlowBack as a deep generative model employing a flow-matching objective to map samples from a coarse-grained prior distribution to an all-atom data distribution.
View Article and Find Full Text PDFAntioxidants (Basel)
December 2024
Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
Cancer metabolism is sustained both by enhanced aerobic glycolysis, characteristic of the Warburg phenotype, and oxidative metabolism. Cell survival and proliferation depends on a dynamic equilibrium between mitochondrial function and glycolysis, which is heterogeneous between tumors and even within the same tumor. During oxidative phosphorylation, electrons from NADH and FADH originated in the tricarboxylic acid cycle flow through complexes of the electron transport chain.
View Article and Find Full Text PDFMethods Mol Biol
December 2024
Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
Transcriptional regulation allows cells to execute developmental programs, maintain homeostasis, and respond to intra- and extracellular signals. Central to these processes are promoters, which in eukaryotes are sequences upstream of genes that bind transcription factors (TFs) and which recruit RNA polymerase to initiate mRNA synthesis. Valuable tools for studying promoters include reporter genes, which can be used to indicate when and where genes are activated.
View Article and Find Full Text PDFMethods Mol Biol
December 2024
Genome Integrity and Cancers, UMR 9019 CNRS, Université-Paris-Saclay, Gustave Roussy, Villejuif, France.
Homologous recombination (HR) is a high-fidelity DNA repair pathway that uses a homologous DNA sequence as a template. Recombinase proteins are the central HR players in the three kingdoms of life. RecA/RadA/Rad51 assemble on ssDNA, generated after the processing of double-strand breaks or stalled replication forks into an active and dynamic presynaptic helical nucleofilament.
View Article and Find Full Text PDFSubcell Biochem
December 2024
School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
The ageing process involves a gradual decline of chromosome integrity throughout an organism's lifespan. Telomeres are protective DNA-protein complexes that cap the ends of linear chromosomes in eukaryotic organisms. Telomeric DNA consists of long stretches of short "TTAGGG" repeats that are conserved across most eukaryotes including humans.
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