Biology subjects

Sherer, N.

Publications and source records attributed to Sherer, N..

3 recordsLinked to original sources

bioRxiv2025

Molecular mechanism by which SARS-CoV-2 Orf9b suppresses the Tom70-Hsp90 interaction to evade innate immunity

The Tom70-Hsp90 interaction is critical for activating MAVS-mediated interferon (IFN) production. Upon RNA virus infection, cytosolic Hsp90 recruits key innate immune signaling proteins to MAVS on mitochondria through its interaction with Tom70. To evade this innate immune response, the SARS-CoV-2 protein Orf9b binds to Tom70, thereby disrupting the Tom70-Hsp90 interaction and suppressing IFN production. Despite its importance, the molecular mechanism underlying Orf9b-mediated inhibition of IFN signaling remains unclear. Here, using an integrative approach combining cryo-electron microscopy, 19F NMR spectroscopy, and isothermal titration calorimetry (ITC), we show that Orf9b inhibits Hsp90 binding to Tom70 through a bipartite mechanism. The helix and intrinsically disordered tail of Orf9b sterically block the access of two distinct structural units of Hsp90 to Tom70. We also find that Orf9b-mediated allosteric conformational changes in Tom70 do not contribute to the inhibition of the Hsp90 binding. Comprehensive structural, thermodynamic, and kinetic analyses further reveal that Orf9b primarily slows the association kinetics between Hsp90 and Tom70. Collectively, our results provide a high-resolution mechanistic framework for understanding Orf9b-mediated suppression of the host innate immune response.

biophysics↗

bioRxiv2025

Overcoming effects of heterogeneous binding on BLI analysis

Binding characteristics, such as kon, koff, and KD, are critical for mechanistic study of biomolecular interactions and drug design. Biolayer interferometry (BLI) has become popular due to its simplicity and sensitivity. Despite its widespread use, BLI data analysis is susceptible to various non-ideal features in sensorgrams. One commonly observed issue is a persistent signal drift after the binding process reaches an expected steady state. The basis of this phenomenon, often referred to as heterogeneous binding, remains poorly understood. In this study, we find that analyte aggregation on the biosensor, particularly induced by ligand-analyte complexes, can contribute to heterogeneous binding. We also find that heterogeneous binding affects not only the association phase but also the dissociation process, leading to erroneous binding characteristics. We propose an approach to mitigate the adverse impacts of heterogeneous binding on the BLI analysis. Since accurate binding characterization is fundamental for many biophysical analyses, addressing this issue is crucial.

biophysics↗

bioRxiv2022

The energy landscape reshaped by strain-specific mutations underlies the long-range epistasis in NS1 evolution of influenza A virus

The mechanisms underlying how individual mutations affect the protein energy landscape are crucial for understanding how proteins evolve. However, predicting mutational effects remains challenging because of epistasis--the nonadditive interactions between mutations. Here, we investigate the biophysical mechanism of strain-specific epistasis in the nonstructural protein 1 (NS1) of the influenza A virus (IAV). To understand the molecular basis of epistasis, we conducted comprehensive analyses of four NS1s of IAV strains that emerged between 1918 and 2004. We find that strain-specific mutations of NS1s are near-neutral with respect to the association with the p85{beta} subunit of PI3K. However, the individual residues on the p85{beta}-binding interface show long-range epistatic interactions with strain-specific mutations. We reveal that strain-specific mutations reshaped the energy landscape of NS1, leading to long-range epistasis. Our findings offer a high-resolution mechanism of how near-neutral mutations silently alter the biophysical energy landscapes, resulting in diverse background effects during molecular evolution.

biophysics↗