Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia.

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.

Predicting the offshore distribution and abundance of marine birds with a hierarchical community distance sampling model.

Proposed offshore wind energy development on the Atlantic Outer Continental Shelf has brought attention to the need for baseline studies of the distribution and abundance of marine birds. We compiled line transect data from 15 shipboard surveys (June 2012-April 2014), along with associated remotely sensed habitat data, in the lower Mid-Atlantic Bight off the coast of Delaware, Maryland, and Virginia, USA. We implemented a recently developed hierarchical community distance sampling model to estimate the seasonal abundance of 40 observed marine bird species. Treating each season separately, we included six oceanographic parameters to estimate seabird abundance: three static (distance to shore, slope, sediment grain size) and three dynamic covariates (sea surface temperature [SST], salinity, primary productivity). We expected that avian bottom-feeders would respond primarily to static covariates that characterize seafloor variability, and that surface-feeders would respond more to dynamic covariates that quantify surface productivity. We compared the variation in species-specific and community-level responses to these habitat features, including for rare species, and we predicted species abundance across the study area. While several protected species used the study area in summer during their breeding season, estimated abundance and observed diversity were highest for nonbreeding species in winter. Distance to shore was the most common significant predictor of abundance, and thus useful in estimating the potential exposure of marine birds to offshore development. In many cases, our expectations based on feeding ecology were confirmed, such as in the first winter season, when bottom-feeders associated significantly with the three static covariates (distance to shore, slope, and sediment grain size), and surface-feeders associated significantly with two dynamic covariates (SST, primary productivity). However, other cases revealed significant relationships between static covariates and surface-feeders (e.g., distance to shore) and between dynamic covariates and bottom-feeders (e.g., primary productivity during that same winter). More generally, we found wide interannual, seasonal, and interspecies variation in habitat relationships with abundance. These results show the importance of quantifying detection and determining the ecological drivers of a community's distribution and abundance, within and among species, for evaluating the potential exposure of marine birds to offshore development.

The E3 Ubiquitin Ligase, CHIP/STUB1, Inhibits Aggregation of Phosphorylated Proteoforms of Microtubule-associated Protein Tau (MAPT).

Hyper-phosphorylated tau accumulates as insoluble fibrils in Alzheimer's disease (AD) and related dementias. The strong correlation between phosphorylated tau and disease has led to an interest in understanding how cellular factors discriminate it from normal tau. Here, we screen a panel of chaperones containing tetratricopeptide repeat (TPR) domains to identify those that might selectively interact with phosphorylated tau. We find that the E3 ubiquitin ligase, CHIP/STUB1, binds 10-fold more strongly to phosphorylated tau than unmodified tau. The presence of even sub-stoichiometric concentrations of CHIP strongly suppresses aggregation and seeding of phosphorylated tau. We also find that CHIP promotes rapid ubiquitination of phosphorylated tau, but not unmodified tau, in vitro. Binding to phosphorylated tau requires CHIP's TPR domain, but the binding mode is partially distinct from the canonical one. In cells, CHIP restricts seeding by phosphorylated tau, suggesting that it could be an important barrier in cell-to-cell spreading. Together, these findings show that CHIP recognizes a phosphorylation-dependent degron on tau, establishing a pathway for regulating the solubility and turnover of this pathological proteoform.

Rare antibody phage isolation and discrimination (RAPID) biopanning enables identification of high-affinity antibodies against challenging targets.

In vitro biopanning platforms using synthetic phage display antibody libraries have enabled the identification of antibodies against antigens that were once thought to be beyond the scope of immunization. Applying these methods against challenging targets remains a critical challenge. Here, we present a new biopanning pipeline, RAPID (Rare Antibody Phage Isolation and Discrimination), for the identification of rare high-affinity antibodies against challenging targets. RAPID biopanning uses fluorescent labeled phage displayed fragment antigen-binding (Fab) antibody libraries for the isolation of high-affinity binders with fluorescent activated sorting. Subsequently, discriminatory hit screening is performed with a biolayer interferometry (BLI) method, BIAS (Biolayer Interferometry Antibody Screen), where candidate binders are ranked and prioritized according to their estimated kinetic off rates. Previously reported antibodies were used to develop the methodology, and the RAPID biopanning pipeline was applied to three challenging targets (CHIP, Gαq, and CS3D), enabling the identification of high-affinity antibodies.

Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine.

Viruses are responsible for some of the most deadly human diseases, yet available vaccines and antivirals address only a fraction of the potential viral human pathogens. Here, we provide a methodology for managing human herpesvirus (HHV) infection by covalently inactivating the HHV maturational protease via a conserved, non-catalytic cysteine (C161). Using human cytomegalovirus protease (HCMV Pr) as a model, we screened a library of disulfides to identify molecules that tether to C161 and inhibit proteolysis, then elaborated hits into irreversible HCMV Pr inhibitors that exhibit broad-spectrum inhibition of other HHV Pr homologs. We further developed an optimized tool compound targeted toward HCMV Pr and used an integrative structural biology and biochemical approach to demonstrate inhibitor stabilization of HCMV Pr homodimerization, exploiting a conformational equilibrium to block proteolysis. Irreversible HCMV Pr inhibition disrupts HCMV infectivity in cells, providing proof of principle for targeting proteolysis via a non-catalytic cysteine to manage viral infection.

Offshore observations of eastern red bats (Lasiurus borealis) in the Mid-Atlantic United States using multiple survey methods.

Little is known about the migration and movements of migratory tree-roosting bat species in North America, though anecdotal observations of migrating bats over the Atlantic Ocean have been reported since at least the 1890s. Aerial surveys and boat-based surveys of wildlife off the Atlantic Seaboard detected a possible diurnal migration event of eastern red bats (Lasiurus borealis) in September 2012. One bat was sighted approximately 44 km east of Rehoboth Beach, Delaware during a boat-based survey. Eleven additional bats were observed between 16.9 and 41.8 km east of New Jersey, Delaware, and Virginia in high definition video footage collected during digital aerial surveys. Observations were collected incidentally as part of a large baseline study of seabird, marine mammal, and sea turtle distributions and movements in the offshore environment. Digital survey methods also allowed for altitude estimation for several of these bats at >100 m above sea level. These observations provide new evidence of bat movements offshore, and offer insight into their flight heights above sea level and the times of day at which such migrations may occur.