Optimization of Ribosome Footprinting Conditions for Ribo-Seq in Human and Drosophila melanogaster Tissue Culture Cells [PDF]
Frontiers in Molecular Biosciences, 2022 Our understanding of mRNA translation and its regulation has been transformed by the development of ribosome profiling. This approach relies upon RNase footprinting of translating ribosomes in a precise manner to generate an accurate snapshot of ribosome
Katerina Douka +2 more
exaly +4 more sources
Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity
Cell Reports, 2017 In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint).
Songjoon Baek +2 more
exaly +4 more sources
Nanoparticles and photochemistry for native-like transmembrane protein footprinting
Nature Communications, 2021 The intrinsic flexibility of membranes proteins still poses a challenge in determining their active structure. Here the authors describe the development of a method that combines chemical footprinting and mass spectrometry to assist in determining the ...
Jie Sun +5 more
doaj +3 more sources
REVIEW ON PROTEIN FOOTPRINTING AS A TOOL IN STRUCTURAL BIOLOGY [PDF]
Science Heritage Journal, 2023 Structural characterization of proteins is fundamental for understanding their functions and interactions within cellular environments. Protein footprinting has emerged as a powerful and versatile technique in structural biology, providing valuable ...
Oluwatosin Ogundairo +5 more
doaj +2 more sources
Massively multiplex single-molecule oligonucleosome footprinting
eLife, 2020 Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present
Nour J Abdulhay +10 more
doaj +2 more sources
Nature Communications, 2020 Footprinting analysis allows genome-wide investigation of transcription factor (TF) binding on chromatin. Here the authors developed a framework termed TOBIAS aimed at identifying footprints of chromatin-associated proteins from ATAC-seq accessibility ...
Mette Bentsen +11 more
doaj +2 more sources
Improvement of a phylogenetic footprinting method for transcription factor binding sites recognition based on the use of bootstrap trials for the analysis of large bacterial genomic data [PDF]
Вавиловский журнал генетики и селекцииThe rapid development of high-throughput sequencing technologies has led to an explosive accumulation of high-quality bacterial genome sequence data – their number is approaching three million, and this growth continues.
A. M. Mukhin +2 more
doaj +2 more sources
Fast Protein Footprinting by X‑ray Mediated Radical Trifluoromethylation
Journal of the American Society for Mass Spectrometry, 2020 Synchrotron radiolysis generates hydroxyl radicals (•OH) that are successful footprinting reagents. Here, we describe a new reagent for the synchrotron platform, the trifluoromethyl radical (•CF3). The radical is produced by •OH displacement of •CF3 from
Mark R. Chance (196040) +11 more
core +2 more sources
Accurate protein structure prediction with hydroxyl radical protein footprinting data
Nature Communications, 2021 Mass spectrometry-based covalent labeling techniques such as hydroxyl radical protein footprinting (HRPF) provide information about protein tertiary structures.
Sarah E. Biehn, Steffen Lindert
doaj +2 more sources
Radical footprinting in mammalian whole blood [PDF]
Nature CommunicationsHydroxyl Radical Protein Footprinting is a powerful tool to probe protein higher-order structure, protein-protein and protein-ligand interactions. It is mostly performed in vitro, but recent advances have extended its use to live cells, nematodes, and 3D
Mingming Zhao +10 more
doaj +2 more sources