Biology subjects

Silvernail, I.

Publications and source records attributed to Silvernail, I..

3 recordsLinked to original sources

bioRxiv2026

Charge Imbalance Drives Salt-Optimized Nucleosome Phase Separation under Physiological Conditions

Liquid-liquid phase separation (LLPS) of chromatin contributes to genome organization and regulates genome accessibility to control gene expression. Despite advances in identifying the environmental conditions that promote chromatin condensation, the specific molecular interactions that initiate condensate formation, as well as the physical mechanisms by which DNA mechanics and epigenetic modifications modulate the resulting interaction network, remain unclear. Here, we utilize a residue-resolution, coarse-grained protein-DNA model to simulate nucleosome interactions across diverse ionic and structural conditions. Our simulations reveal non-monotonic salt-dependent phase-separation behavior, with optimal nucleosome condensation occurring under physiological salt conditions. Such a behavior was caused by the charge-imbalanced polyampholytic nature of nucleosomes, which drives competition between local protein-DNA attractions and global DNA-DNA repulsion. We further demonstrate that the conformational flexibility of nucleosomal DNA promotes unwrapping of DNA from the histone core, thereby strengthening histone-DNA interactions and enhancing condensate formation. Finally, we show that acetylation of histone H3 and H4 tails significantly reduces inter-nucleosomal interactions and increases nucleosome dynamics within condensates. Together, our study establishes a quantitative link between microscopic molecular interactions and macroscopic material properties, providing new insights into how mechanical constraints and epigenetic modifications could cooperatively tune genome architecture.

biophysics↗

bioRxiv2024

Interpretable Protein-DNA Interactions Captured by Structure-based Optimization

Sequence-specific DNA recognition underlies essential processes in gene regulation, yet methods for simultaneous predictions of genomic DNA recognition sites and their binding affinity remain lacking. Here, we present the Interpretable protein-DNA Energy Associative (IDEA) model, a residue-level, interpretable biophysical model capable of predicting binding sites and affinities of DNA-binding proteins. By fusing structures and sequences of known protein-DNA complexes into an optimized energy model, IDEA enables direct interpretation of physicochemical interactions among individual amino acids and nucleotides. We demonstrate that this energy model can accurately predict DNA recognition sites and their binding strengths across various protein families. Additionally, the IDEA model is integrated into a coarse-grained simulation framework that quantitatively captures the absolute protein-DNA binding free energies. Overall, IDEA provides an integrated computational platform that alleviates experimental costs and biases in assessing DNA recognition and can be utilized for mechanistic studies of various DNA recognition processes.

biophysics↗

bioRxiv2024

A practical guide to time-resolved fluorescence microscopy and spectroscopy

Time-correlated single photon counting (TCSPC) coupled with confocal microscopy is a versatile biophysical tool that enables real-time monitoring of biomolecular dynamics across many timescales. With TCSPC, Fluorescence correlation spectroscopy (FCS) and pulsed interleaved excitation-Forster resonance energy transfer (PIE-FRET) are collected simultaneously on diffusing molecules to extract diffusion characteristics and proximity information. This article is a guide to calibrating FCS and PIE-FRET measurements with several biological samples including liposomes, streptavidin-coated quantum dots, proteins, and nucleic acids for reliable determination of diffusion coefficients and FRET efficiency. The FRET efficiency results are also compared to surface-attached single molecules using fluorescence lifetime imaging microscopy (FLIM-FRET). Combining the methods is a powerful approach to revealing mechanistic details of biological processes and pathways.

biophysics↗