Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response

Area of Science:

• Virology
• Immunology
• Structural Biology

Background:

• Open Reading Frame 9b (Orf9b) is a SARS-CoV and SARS-CoV-2 protein.
• Orf9b interacts with the mitochondrial receptor Tom70 (Translocase of Outer Membrane 70).
• This interaction is crucial for suppressing the innate immune system, specifically the type 1 interferon response.

Purpose of the Study:

• To develop a biophysical model quantifying Orf9b's conformational changes and Tom70 binding.
• To investigate how lipid binding and mutations in SARS-CoV-2 variants affect the Orf9b:Tom70 equilibrium.
• To understand the molecular mechanisms underlying Orf9b-mediated immune suppression.

Main Methods:

• Biophysical modeling to quantify conformational switching and binding kinetics.
• Analysis of Orf9b homodimer and Orf9b:Tom70 complex structures.
• Characterization of lipid binding effects on Orf9b monomer:dimer equilibrium.
• Assessment of mutations in variants of concern on Orf9b's interaction with Tom70.

Main Results:

• A biophysical model was developed to describe Orf9b's conformational switch between homodimeric and monomeric states.
• Lipid binding to the Orf9b homodimer significantly stabilizes the dimer form, reducing dissociation rate by ~100-fold.
• Mutations in SARS-CoV-2 variants of concern can alter specific rate constants without substantially impacting Tom70 binding affinity.
• Perturbations in coupled equilibria affect Orf9b's apparent affinity for Tom70.

Conclusions:

• Orf9b conformational dynamics and Tom70 binding are key to its immune suppression.
• Lipid interactions and viral mutations can modulate Orf9b function by altering its equilibrium dynamics.
• Understanding these molecular mechanisms provides insights into coronavirus pathogenesis and potential therapeutic targets for interferon signaling modulation.