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Creators/Authors contains: "Li, Yunfeng"

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  1. Abstract

    Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

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  2. Abstract

    Molecular sieving may occur when two molecules compete for a nanopore. In nearly all known examples, the nanopore is larger than the molecule that selectively enters the pore. Here, we experimentally demonstrate the ability of single-wall carbon nanotubes with a van der Waals pore size of 0.42 nm to separate n-hexane from cyclohexane—despite the fact that both molecules have kinetic diameters larger than the rigid nanopore. This unexpected finding challenges our current understanding of nanopore selectivity and how molecules may enter a tight channel. Ab initio molecular dynamics simulations reveal that n-hexane molecules stretch by nearly 11.2% inside the nanotube pore. Although at a relatively low probability (28.5% overall), the stretched state of n-hexane does exist in the bulk solution, allowing the molecule to enter the tight pore even at room temperature. These insights open up opportunities to engineer nanopore selectivity based on the molecular degrees of freedom.

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  3. Abstract SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome. 
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    Free, publicly-accessible full text available November 14, 2023
  4. Defects in liquid crystals serve as templates for nanoparticle (NP) organization; however, NP assembly in cholesteric (Ch) liquid crystals is only beginning to emerge. We show interactive morphogenesis of NP assemblies and a Ch liquid crystalline host formed by cellulose nanocrystals (CNCs), in which both the host and the guest experience marked changes in shape and structure as a function of concentration. At low NP loading, Ch-CNC droplets exhibit flat-ellipsoidal packing of Ch pseudolayers, while the NPs form a toroidal ring- or two cone–shaped assemblies at droplet poles. Increase in NP loading triggers reversible droplet transformation to gain a core-shell morphology with an isotropic core and a Ch shell, with NPs partitioning in the core and in disclinations. We show programmable assembly of droplets carrying magnetic NPs. This work offers a strategy for NP organization in Ch liquid crystals, thus broadening the spectrum of architectures of soft nanostructured materials. 
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  5. Abstract

    The electrical double layer is known to spontaneously form at the electrode‐electrolyte interface, impacting many important chemical and physical processes as well as applications including electrocatalysis, electroorganic synthesis, nanomaterial preparation, energy storage, and even emulsion stabilization. However, it has been challenging to study this fundamental phenomenon at the molecular level because the electrical double layer is deeply “buried” by the bulk electrolyte solution. Here, we report a quantitative probing of the electrical double layer of ionic liquids from the solid side of a photoelectron‐transparent graphene‐carbon nanotube hybrid membrane electrode using X‐ray photoelectron spectroscopy. The membrane window is ultrathin (1‐1.5 nm), large (~1 cm2), and robust, enabling a tight seal of the electrolyte and quantitative measurement with excellent photoelectron signals. Byoperandomonitoring the population changes of cations and anions in response to the applied electrical potentials, we experimentally resolve the chemical structure and dynamics of the electrical double layer, which corroborate results from molecular dynamics simulations.


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