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Concatemer-assisted stoichiometry analysis: targeted mass spectrometry for protein quantification.
Life Sci Alliance
March 2025
https://ror.org/0168r3w48 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
Large multiprotein machines are central to many biological processes. However, stoichiometric determination of protein complex subunits in their native states presents a significant challenge. This study addresses the limitations of current tools in accuracy and precision by introducing concatemer-assisted stoichiometry analysis (CASA).
View Article and Find Full Text PDFHistone N-tails modulate sequence-specific positioning of nucleosomes.
J Biol Chem
December 2024
National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:
Spatial organization of chromatin is essential for cellular functioning. However, the precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA still remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo.
View Article and Find Full Text PDFRemodeling of Individual Nucleosomes in Nucleosome Arrays.
Methods Mol Biol
December 2024
Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
Adenosin triphosphate (ATP)-dependent nucleosome remodeling factors sculpt the nucleosomal landscape of eukaryotic chromatin. They deposit, evict, or reposition nucleosomes along DNA in a process termed nucleosome sliding. Remodeling has traditionally been analyzed using mononucleosomes as a model substrate.
View Article and Find Full Text PDFPhase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography.
View Article and Find Full Text PDFForce transmission through the inner kinetochore is enhanced by centromeric DNA sequences.
bioRxiv
November 2024
Department of Biochemistry, University of Washington, Seattle, United States.
Previously, we reconstituted a minimal functional kinetochore from recombinant proteins that was capable of transmitting force from dynamic microtubules to nucleosomes containing the centromere-specific histone variant Cse4 (Hamilton et al. 2020). This work revealed two paths of force transmission through the inner kinetochore: through Mif2 and through the Okp1/Ame1 complex (OA).
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