Mac Kevin Braza
@mackevinbraza.bsky.social
📤 452
📥 2351
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Amaro Lab (UC San Diego), PhD student Biochemistry and Molecular Biophysics | Computational Biology
reposted by
Mac Kevin Braza
Rommie Amaro
9 months ago
✨✨ It's
#glycotime
for
#HIV
Env ✨✨ N-linked glycans modulate flexibility & MPER epitope exposure
#glycotime
Huge effort by
@shehata92.bsky.social
@lcasalino88.bsky.social
with cryoET of Env in VLPs by
@thevillalab.bsky.social
& team 💪 Would love feedback!
www.biorxiv.org/content/10.1...
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reposted by
Mac Kevin Braza
Rommie Amaro
9 months ago
✨ Check out
@mackevinbraza.bsky.social
's new work on full length APOBEC3B, which shows how the NTD modulates active site opening in the CTD Collab w/
@adaozlemdemir.bsky.social
& Aihara, Herzik, & Harris labs
pubs.acs.org/doi/10.1021/...
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I'm presenting my research at the ACS Spring 2025 meeting in San Diego! DM me if you're coming, too!!! 🙌
@rommieamaro.bsky.social
pubs.acs.org/doi/10.1021/...
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Regulatory Interactions between APOBEC3B N- and C-Terminal Domains
APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting our understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared the dynamics of the truncated (A3Bctd) to that of the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD–CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics and potential druggability of fl-A3B, including observations regarding both the active and allosteric sites, which may offer new avenues for therapeutic intervention in cancer.
https://pubs.acs.org/doi/10.1021/acs.jcim.4c02272
9 months ago
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reposted by
Mac Kevin Braza
Lillian Chong
9 months ago
@westpasoftware.bsky.social
is partnering with
@mdanalysis.bsky.social
for Google Summer of Code this year. Please help spread the word!
add a skeleton here at some point
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reposted by
Mac Kevin Braza
Dr. Fiona
9 months ago
Nevertheless, we persisted ❤️ 📣 NEW BIORXIV ALERT!! 🚨 Using WE MD, linguistic pathway clustering, dynamical network analyses, and HDXMS we reveal a hidden allosteric network within the SARS2 spike S1 domain and predict how the D614G mutation impacts this network!
www.biorxiv.org/content/10.1...
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D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes
The SARS-CoV-2 spike glycoprotein binds human epithelial cells and enables infection through a key conformational transition that exposes its receptor binding domain (RBD). Experimental evidence indic...
https://www.biorxiv.org/content/10.1101/2025.03.07.642081v1
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reposted by
Mac Kevin Braza
Rommie Amaro
9 months ago
A behemoth effort from
@fionachembot.bsky.social
in which she does amazing science (showing how VOCs reshape allosteric pathways) while also making the SARS2 spike color palette match her fish Dorry 😍🫠
www.biorxiv.org/content/10.1...
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reposted by
Mac Kevin Braza
Sonya Neal
10 months ago
Incredible work led by Dr. Satarupa Bhaduri, co-authors
@mackevinbraza.bsky.social
and others. This work wouldn't have been possible without our collaborators Dr. Anthony O'Donoghue,
@rommieamaro.bsky.social
@marius-lemberg.bsky.social
and Dr. Kvido Strisovsky
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reposted by
Mac Kevin Braza
Sonya Neal
10 months ago
Our work is finally published! We developed a robust in vitro platform to study a disease relevant membrane protease, notoriously difficult to isolate.This protease has linked to cancer & neurodegen,and our platform opens new doors for structural & drug discovery.
sciencedirect.com/science/arti...
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An in vitro platform for the enzymatic characterization of the rhomboid protease RHBDL4
Rhomboid proteases are ubiquitous intramembrane serine proteases that can cleave transmembrane substrates within lipid bilayers. They exhibit many and…
https://sciencedirect.com/science/article/pii/S0021925825001231?via%3Dihub
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