Mac Kevin Braza

✨✨ 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...

✨ 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/...

Tuesday, March 25, 2025 7PM-9PM PST. Poster Board #: 1234 at Hall B2/C - San Diego Convention Center.

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.

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/...

@westpasoftware.bsky.social is partnering with @mdanalysis.bsky.social for Google Summer of Code this year. Please help spread the word!

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...

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...

spike protein domains and mutations in VOCs

Fiona's tang fish named Dorry matches the spike colors

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...

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

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…

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...