Trapped-ion quantum simulation of electron transfer models with tunable dissipation.

Electron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. The exact simulation of these reactions is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. Here, we experimentally simulate a paradigmatic model of molecular electron transfer using a multispecies trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently.

Chromatin folding through nonuniform motorization by responsive motor proteins.

Chromatin is partially structured through the effects of biological motors. "Swimming motors" such as RNA polymerases and chromatin remodelers are thought to act differentially on the active parts of the genome and the stored inactive part. By systematically expanding the many-body master equation for chromosomes driven by swimming motors, we show that this nonuniform aspect of motorization leads to heterogeneously folded conformations, thereby contributing to chromosome compartmentalization.

Real-Time Visualization of Protein Microenvironment Changes with High Spatial Resolution in Live Cells via Site-Specific Incorporation of Rotor-Based Fluorescent Noncanonical Amino Acids.

Traditional methods, such as the use of fluorescent protein fusions and environment-sensitive fluorophores, have limitations when studying protein microenvironment changes at the finest spatial resolution. These techniques often rely on bulky proteins or tags restricted to the N- or C-terminus, which can disrupt the natural behavior of the target protein and dramatically limit the ability of their method to investigate noninvasively microenvironment effects. To overcome these challenges, we have developed an innovative strategy to visualize microenvironment changes of protein substructures in real-time by genetically incorporating environment-sensitive noncanonical amino acids (ncAAs) containing rotor-based fluorophores (RBFs) at specific positions within a protein of interest.

Predicting protein conformational motions using energetic frustration analysis and AlphaFold2.

Proteins perform their biological functions through motion. Although high throughput prediction of the three-dimensional static structures of proteins has proved feasible using deep-learning-based methods, predicting the conformational motions remains a challenge. Purely data-driven machine learning methods encounter difficulty for addressing such motions because available laboratory data on conformational motions are still limited.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds.