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Thermodynamics of nucleosome breathing and positioning.
J Chem Phys
January 2025
Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
Nucleosomes are fundamental units of chromatin in which a length of genomic DNA is wrapped around a histone octamer spool in a left-handed superhelix. Large-scale nucleosome maps show a wide distribution of DNA wrapping lengths, which in some cases are tens of base pairs (bp) shorter than the 147 bp canonical wrapping length observed in nucleosome crystal structures. Here, we develop a thermodynamic model that assumes a constant free energy cost of unwrapping a nucleosomal bp.
View Article and Find Full Text PDFUse of Collagen in Cosmetic Products.
Curr Issues Mol Biol
March 2024
Chair and Department of Pharmaceutical Technology, Faculty of Pharmacy, Poznan University of Medical Sciences, 3 Rokietnicka, 60-806 Poznan, Poland.
Collagen (CLG) belongs to the family of fibrillar proteins and is composed of left-handed α polypeptide chains, which, twisting around themselves and their axis, form a right-handed superhelix. In the chemical structure, it contains mainly proline, hydroxyproline, glycine, and hydroxylysine. It occurs naturally in the dermis in the form of fibers that provide the skin with proper density and elasticity.
View Article and Find Full Text PDFCryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations.
Cell Discov
May 2021
Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors.
View Article and Find Full Text PDFRegulation of the gyr operon of Mycobacterium tuberculosis by overlapping promoters, DNA topology, and reiterative transcription.
Biochem Biophys Res Commun
July 2018
Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India. Electronic address:
DNA gyrase introduces negative supercoils into DNA to maintain topological homeostasis. The genes encoding gyrase, gyrB and gyrA, form a dicistronic operon in Mycobacterium tuberculosis (Mtb) and other actinobacteria. Earlier work indicated that DNA relaxation stimulates the expression of the gyr genes, a phenomenon termed relaxation-stimulated transcription (RST).
View Article and Find Full Text PDFStructure of a 13-fold superhelix (almost) determined from first principles.
IUCrJ
March 2015
Molecular Design and Chemical Biology, F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel, Switzerland.
Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2). For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide.
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