fraserlab.bsky.social
Professor and Chair @UCSF/@UCSF_BTS - dynamic structural biology and open science - (he/him) - fraserlab.com
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We’re excited to push this work forward with CJ's next two papers. But in the meantime, we'd love to receive feedback from the community. Please reach out!
www.biorxiv.org/content/10.1...
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These results suggest that stabilizing Orf9b’s (lipid-bound) dimeric state could be a future therapeutic target. Disrupting lipid interactions might bias Orf9b towards a form that can’t bind Tom70, restoring immune activation.
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CJ measured key rate constants that constrained a model to show how lipid binding shifts Orf9b’s equilibrium towards the homodimer, preventing Tom70 interaction. The lipid-free form comes to equilibrium in seconds, whereas the lipid-bound form takes hours-days!
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The key was a collaboration between graduate student CJ San Felipe & Michael Grabe using ordinary differential equations to model this process.
grabelab.org/software
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Here, we developed a quantitative biophysical model to describe the coupled equilibria of Orf9b dimerization and Tom70 binding, revealing how lipid binding tunes the system.
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Subsequently, Klim Verba led the cryo-EM structure of the Orf9b-Tom70 complex, revealing that Orf9b undergoes a dramatic conformational switch upon binding. It is a beta-rich homodimer on its own, but adopts an alpha-helical fold when bound to Tom70.
pmc.ncbi.nlm.nih.gov/articles/PMC...
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This story builds on the foundational work of the QBI QCRG/AVIDD center, which identified Tom70 as a binding partner of Orf9b in a landmark SARS-CoV-2 interactome study.
pmc.ncbi.nlm.nih.gov/articles/PMC...
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We show that Orf9b exists in a dynamic equilibrium between a homodimeric and monomeric state. The monomer binds to the mitochondrial protein Tom70, suppressing immune responses. Lipid binding to Orf9b stabilizes the homodimer, acting as a switch to slow down Tom70 engagement.
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4/4 Awardee @willowcoyote.bsky.social is unraveling the interactions between genetic mutations🧬 + the environment (ie, exposures like drugs💊 or viruses). His project may transform how we study diseases with complex etiologies.
🎉Congrats Dr. Coyote-Maestas!
🙏 #HFScout Taekjip Ha
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I’m just looking for preprints to read! Anything to improve on yesterday
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I guess that’s really only five preprints so now I’m even more depressed about the thievery going on around Genentech hall!
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Priyanka contributed some 🌽 genetics www.biorxiv.org/content/10.1...
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@karsonchrispens.bsky.social sound a new cryoem heterogeneous reconstruction preprint www.biorxiv.org/content/10.1...
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Tushar added the chlamy tomo community annotation paper www.biorxiv.org/content/10.1...
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Sofia added @paulrobustelli.bsky.social idp docking preprint www.biorxiv.org/content/10.1...
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I started with @poojaasthana.bsky.social ‘s latest from our group www.biorxiv.org/content/10.1...
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I regret to inform the world that we are at 10 cookies consumed but only 4 preprints posted...
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Huge credit to Pooja Asthana for leading this work, along with Sonya Lee, @ccmm.bsky.social, and Ian Seiple (😭 now😭 at 😭 Scripps 😭).
www.biorxiv.org/content/10.1...
Excited for feedback!
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While we found promising starting points, this is just the beginning! Much like beta-lactamase inhibitors potentiate beta-lactam antibiotics, we think that developing Vat inhibitors could restore streptogramin efficacy.
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Using X-ray crystallography-based fragment screening, we mapped VatD’s key binding sites and identified small-molecule fragments that can serve as leads.
This builds on our 2020 Seiple collaboration, where we modified streptogramins to overcome resistance.
www.ncbi.nlm.nih.gov/pmc/articles...
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Streptogramins are promising antibiotics for treating resistant bacterial infections, but their efficacy is threatened by Vat enzymes, which inactivate streptogramins by acetylation (blocking a key interaction with the ribosome). So we set out to block the blocker!
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It truly is a Keedy inspired and connected work!
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Indeed. Old school. All part of checking the actual principles of catalysis which I think is a big strength of this paper
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there is even some MD in there for you!
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Bill and I are so excited about combining fragment screening + protein design to navigate chemical & sequence space in tandem!
We think this mimics how evolution explores generalist binding sites to generate new functions.
Link to preprint: www.biorxiv.org/content/10.1...
We welcome feedback!
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We (mostly Sagar Bhattacharya!) ensured that KABLE worked for the RIGHT REASONS.
- Mutagenesis confirmed Asp49 as the essential active site residue
- Disrupting key orienting H-bonds also eliminated activity
- kcat/KM for analogs scaled with the electron-withdrawing nature of leaving groups
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Next, we took inspiration from more polar fragments binding lower in the original binding site and designed KABLE (Kemp eliminase ALBE). With a few additional mutations from a single round of screening it has a catalytic efficiency (600,000 M⁻¹s⁻¹) on par with the natural enzymes.
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Yuda Chen noticed that some of the fragments resembled coumarins. So they redesigned the binding site and created FABLE (Fluorescent ABLE) —a protein that binds turn-on fluorophores.
ABLE->FABLE generalist to a specialist sensor with 100-fold turn-on fluorescence enhancement!
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Lena Bergmann and Galen Correy used X-ray crystallography as a binding assay.
ABLE turned out to be a generalist, binding 43 fragments in two distinct conformations.
(side note, Nick and Justin Biel started this as COVID hit... but it paused until Lena picked it back up!)
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We started with ABLE, a simple helical bundle that Nick Polizzi had designed as a postdoc to bind the drug apixaban (pmc.ncbi.nlm.nih.gov/articles/PMC...) with high specificity compared to analogs. But could it do more? Enter crystallographic fragment screening...