Engineering topics

Heller, William

Publications and source records attributed to Heller, William.

3 records

DOE OSTI2024

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Functional composites by programming entropy-driven nanosheet growth

Here, nanomaterials must be systematically designed to be technologically viable. Driven by optimizing intermolecular interactions, current designs are too rigid to plug in new chemical functionalities and cannot mitigate condition differences during integration. Despite extensive optimization of building blocks and treatments, accessing nanostructures with the required feature sizes and chemistries is difficult. Programming their growth across the nano-to-macro hierarchy also remains challenging, if not impossible. To address these limitations, we should shift to entropy-driven assemblies to gain design flexibility, as seen in high-entropy alloys, and program nanomaterial growth to kinetically match target feature sizes to the mobility of the system during processing. In tis report, following a micro-then-nano growth sequence in ternary composite blends composed of block-copolymer-based supramolecules, small molecules and nanoparticles, we successfully fabricate high-performance barrier materials composed of more than 200 stacked nanosheets (125 nm sheet thickness) with a defect density less than 0.056 µm -2 and about 98% efficiency in controlling the defect type. Contrary to common perception, polymer-chain entanglements are advantageous to realize long-range order, accelerate the fabrication process (<30 min) and satisfy specific requirements to advance multilayered film technology. This study showcases the feasibility, necessity and unlimited opportunities to transform laboratory nanoscience into nanotechnology through systems engineering of self-assembly.

42 ENGINEERING↗

DOE OSTI2013

A new structural framework for integrating replication protein A into DNA processing machinery

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.

59 BASIC BIOLOGICAL SCIENCES↗