We investigate the complexation behavior between a semiflexible charged polymer and an oppositely charged sphere with parameters appropriate for the DNA-histone system. We determine the ground state of a simple free energy expression (which includes electrostatic interactions on a linear level) numerically and use symmetry arguments to divide the obtained DNA configuration into broad classes, thereby obtaining global phase diagrams. We pay specific attention to the effects of salt concentration, DNA length variation, DNA charge renormalization, and externally applied force on the obtained complex structures.
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http://dx.doi.org/10.1103/PhysRevE.66.011918 | DOI Listing |
Soft Matter
January 2025
Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA.
Microrheology has become an indispensable tool for measuring the dynamics of macromolecular systems. Yet, its ability to characterize polymer dynamics across spatiotemporal scales, which vary among polymers and concentration regimes, is limited by the selection of probe morphologies and sizes. Here, we introduce semiflexible M13 phage as a powerful microrheological probe able to circumvent these constraints to robustly capture the dynamics of polymeric solutions across decades of concentrations, sizes, and ionic conditions.
View Article and Find Full Text PDFBiochim Biophys Acta Gen Subj
January 2025
Computational Structural Biology Laboratory, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; Bioinformatics Centre, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India. Electronic address:
Conformational switching in RNA binding proteins (RBPs) is crucial for regulation of RNA processing and transport. Dysregulation or mutations in RBPs and broad RNA processing abnormalities are related to many human diseases including neurodegenerative disorders. Here, we review the role of protein-RNA conformational switches in RBP-RNA complexes.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Institute for Theoretical Physics IV, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany.
J Chem Phys
December 2024
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
In this study, we present a novel orientation discretization approach based on the rhombic triacontahedron for Monte Carlo simulations of semiflexible polymer chains, aiming at enhancing structural analysis through rheo-small-angle scattering (rheo-SAS). Our approach provides a more accurate representation of the geometric features of semiflexible chains under deformation, surpassing the capabilities of traditional lattice structures. Validation against the Kratky-Porod chain system demonstrated superior consistency, underscoring its potential to significantly improve the precision of uncovering geometric details from rheo-SAS data.
View Article and Find Full Text PDFChem Commun (Camb)
December 2024
Institut de Sciences des Matériaux de Mulhouse, CNRS UMR 7361, 15 rue Jean Starcky, 68057 Mulhouse, France.
In the development of functional materials, side chains are traditionally incorporated into the primary chemical structure to induce liquid-crystalline behavior or to enhance solubility for improved processability. However, emerging evidence suggests that side chains play a far more complex role. This study presents a case of a double helical supramolecular structure formed by star-shaped mesogens in the absence of specific interactions.
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