Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

Structure and dynamics of a nucleosome core particle based on Widom 603 DNA sequence

Nucleosomes are fundamental elements of chromatin organization that participate in compacting genomic DNA and serve as targets for the binding of numerous regulatory proteins. Currently, over 500 different nucleosome structures are known. Despite the large number of nucleosome structures, all of them were formed on only about twenty different DNA sequences. Using cryo-electron microscopy, we determined the structure of the nucleosome formed on a high-affinity Widom 603 DNA sequence at 4 Å resolution; an atomic model was built. We proposed an integrative modeling approach to study the nucleosomal DNA unwrapping based on the cryoelectron microscopy (cryo-EM) data. We also demonstrated the DNA unwrapping of the Widom 603 nucleosome using small angle X-ray scattering and single particle Förster resonance energy transfer measurements. Our results are consistent with the asymmetry of nucleosomal DNA unwrapping. Our data revealed the dependence of nucleosome structure and dynamics on the sequence of nucleosomal DNA.

d-Orbital Single Electron Filling O─O π* Bonds on WO3S1 Sites for Highly Selective Generation of Hydroxyl Radicals

Hydroxyl radical (•OH) stemming from dissolved oxygen (O2) via photocatalysis is very attractive, but its poor selectivity and generation efficiency greatly limit its application. Herein, a kind of tungsten single site co-coordinated with O and S atoms (WO3S1) is established on ZnIn2S4 (W-ZIS). The strong interactions in WO3S1 shift the d-band center toward the Fermi level, enhancing the adsorption of O2. These interactions improve the accumulation of photo-generated electrons on WO3S1, facilitating the dissociation of O─O bonds in crucial intermediates and promoting the selective conversion from O2 into •OH. This brings a state-of-the-art selectivity (40.2%) and generation efficiency (1668.90 mmol. g-1. L-1. h-1) of •OH production. Experimental results and theoretical simulations have elucidated that O2 can be reduced by d-orbitals single electron (↑, _, _, _, _, _) of WO3S1 transfer to 2p-orbital O─O pi anti-bonding (π*: px and py), initially activating O2. Additionally, WO3S1 sites facilitate the cleavage of H2O, optimizing proton adsorption through W─O orbital coupling in WO3S1 and promoting the transformation of oxygen-containing intermediates. More importantly, d-orbitals single electron can fill O─O π* bond in •OOH intermediate, weakening the covalency of the O─O bond, mitigating the formation of H2O2 and shortening the pathway for •OH generation.).

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Molecular recognition of nucleosomes by binding partners

Nucleosomes represent the elementary units of chromatin packing and hubs in epigenetic signaling pathways. Across the chromatin and over the lifetime of the eukaryotic cell, nucleosomes experience a broad repertoire of alterations that affect their structure and binding with various chromatin factors. Dynamics of the histone core, nucleosomal and linker DNA, and intrinsic disorder of histone tails add further complexity to the nucleosome interaction landscape. In light of our understanding through the growing number of experimental and computational studies, we review the emerging patterns of molecular recognition of nucleosomes by their binding partners and assess the basic mechanisms of its regulation.

Structure and Properties of High and Low Free Volume Polymers Studied by Molecular Dynamics Simulation

Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low permeability polyetherimides (PEIs) and highly permeable Si-containing polytricyclononenes. All calculations were made with 32 independent models for each polymer. In both cases, the accessible free volume (AFV) increases with decreasing probe size. However, for a zero-size probe, the curves for both types of polymers cross the ordinate in the vicinity of 40%. The size distribution of free volume in PEI and highly permeable polymers differ significantly. In the former case, they are represented by relatively narrow peaks, with the maxima in the range of 0.5–1.0 Å for all the probes from H2 to Xe. In the case of highly permeable Si-containing polymers, much broader peaks are observed to extend up to 7–8 Å for all the gaseous probes. The obtained size distributions of free volume and accessible volume explain the differences in the selectivity of the studied polymers. The surface area of AFV is found for PEIs using Delaunay tessellation. Its analysis and the chemical nature of the groups that form the surface of free volume elements are presented and discussed.