The SARS-CoV-2 SSHHPS Recognized by the Papain-like Protease

Viral proteases are highly specific and recognize conserved cleavage site sequences of ∼6–8 amino acids. Short stretches of homologous host–pathogen sequences (SSHHPS) can be found spanning the viral protease cleavage sites. We hypothesized that these sequences corresponded to specific host protein targets since >40 host proteins have been shown to be cleaved by Group IV viral proteases and one Group VI viral protease. Using PHI-BLAST and the viral protease cleavage site sequences, we searched the human proteome for host targets and analyzed the hit results. Although the polyprotein and host proteins related to the suppression of the innate immune responses may be the primary targets of these viral proteases, we identified other cleavable host proteins. These proteins appear to be related to the virus-induced phenotype associated with Group IV viruses, suggesting that information about viral pathogenesis may be extractable directly from the viral genome sequence. Here we identify sequences cleaved by the SARS-CoV-2 papain-like protease (PLpro) in vitro within human MYH7 and MYH6 (two cardiac myosins linked to several cardiomyopathies), FOXP3 (an X-linked Treg cell transcription factor), ErbB4 (HER4), and vitamin-K-dependent plasma protein S (PROS1), an anticoagulation protein that prevents blood clots. Zinc inhibited the cleavage of these host sequences in vitro. Other patterns emerged from multispecies sequence alignments of the cleavage sites, which may have implications for the selection of animal models and zoonosis. SSHHPS/nsP is an example of a sequence-specific post-translational silencing mechanism

Conversion of Bilayers of PS‑<i>b</i>‑PDMS Block Copolymer into Closely Packed, Aligned Silica Nanopatterns

Block copolymer (BCP) self-assembly is an effective and versatile approach for the production of complex nanopatterned interfaces. Monolayers of BCP films can be harnessed to produce a variety of different patterns, including lines, with specific spacings and order. In this work, bilayers of cylinder-forming polystyrene-<i>block</i>-polydimethylsiloxane block copolymer (PS-<i>b</i>-PDMS) were transformed into arrays of silica lines with half the pitch normally attained for conventional monolayers, with the PDMS acting as the source for the SiO_<i>x</i>. The primary hurdle was ensuring the bilayer silica lines were distinctly separate; to attain the control necessary to prevent overlap, a number of variables related to the materials and self-assembly process were investigated in detail. Developing a detailed understanding of BCP film swelling during solvent annealing, blending of the PS-<i>b</i>-PDMS with PS homopolymer, utilization of a surface brush layer, and adjustment of the plasma exposure conditions, distinct and separate silica lines were prepared. On the microscale, the sample coverage of PS-<i>b</i>-PDMS bilayers was investigated and maximized to attain >95% bilayers under defined conditions. The bilayer BCP structures were also amenable to graphoepitaxy, and thus, dense and highly ordered arrays of silica line patterns with tightly controlled width and pitch were fabricated and distributed uniformly across a Si surface

Density doubling of block copolymer templated features

Block copolymers can be used to template large arrays of nanopatterns with periodicities equal to the characteristic spacing of the polymer. Here we demonstrate a technique capitalizing on the multilayered arrangement of cylindrical domains to effectively double the pattern density templated by a given polymer. By controlling the initial thickness of the film and the solvent annealing conditions, it was possible to reproducibly create density doubled lines by swelling the film with solvent until bilayers of horizontal cylinders were obtained. This process was also demonstrated to be compatible with graphoepitaxy.Peer reviewed: YesNRC publication: Ye

Sequential Nanopatterned Block Copolymer Self-Assembly on Surfaces

Bottom-up self-assembly of high-density block-copolymer nanopatterns is of significant interest for a range of technologies, including memory storage and low-cost lithography for on-chip applications. The intrinsic or native spacing of a given block copolymer is dependent upon its size (<i>N</i>, degree of polymerization), composition, and the conditions of self-assembly. Polystyrene-<i>block</i>-polydimethylsiloxane (PS<i>-b</i>-PDMS) block copolymers, which are well-established for the production of strongly segregated single-layer hexagonal nanopatterns of silica dots, can be layered sequentially to produce density-doubled and -tripled nanopatterns. The center-to-center spacing and diameter of the resulting silica dots are critical with respect to the resulting double- and triple-layer assemblies because dot overlap reduces the quality of the resulting pattern. The addition of polystyrene (PS) homopolymer to PS<i>-b</i>-PDMS reduces the size of the resulting silica dots but leads to increased disorder at higher concentrations. The quality of these density-multiplied patterns can be calculated and predicted using parameters easily derived from SEM micrographs of corresponding single and multilayer patterns; simple geometric considerations underlie the degree of overlap of dots and layer-to-layer registration, two important factors for regular ordered patterns, and clearly defined dot borders. Because the higher-molecular-weight block copolymers tend to yield more regular patterns than smaller block copolymers, as defined by order and dot circularity, this sequential patterning approach may provide a route toward harnessing these materials, thus surpassing their native feature density

Density Doubling of Block Copolymer Templated Features

Block copolymers can be used to template large arrays of nanopatterns with periodicities equal to the characteristic spacing of the polymer. Here we demonstrate a technique capitalizing on the multilayered arrangement of cylindrical domains to effectively double the pattern density templated by a given polymer. By controlling the initial thickness of the film and the solvent annealing conditions, it was possible to reproducibly create density doubled lines by swelling the film with solvent until bilayers of horizontal cylinders were obtained. This process was also demonstrated to be compatible with graphoepitaxy