Matt Howard

Congratulations!! 🥳

Check out Jerome's paper! As we push the boundaries of DMS, it is critical that we develop robust ways to score variant effects--and he is doing just that. Excited to put this to use in our upcoming GPCR-DMS endeavors :)

Postdoctoral Fellow - Structural Biology, Deshpande Lab in South San Francisco, California, United States of America | Students & Graduates at Genentech Apply for Postdoctoral Fellow - Structural Biology, Deshpande Lab job with Genentech in South San Francisco, California, United States of America. Students & Graduates at Genentech

We are hiring a #postdoc in the Deshpande lab! Come join us tackle important mechanistic questions in inflammatory signaling. Please share or apply!

careers.gene.com/us/en/job/20...

Structures of the PI3Kα/KRas complex on lipid bilayers reveal the molecular mechanism of PI3Kα activation PI3Kα is a potent oncogene that converts PIP2 to PIP3 at the plasma membrane upon activation by receptor tyrosine kinases and Ras GTPases. In the absence of any structures of activated PI3Kα, the mole...

Beautiful work from our colleagues in the Jura & Verba labs here @ UCSF! Cryo-EM structures of PI3Ka / KRas complex in context of lipid nanodiscs. Read on for unexpected dimers & to see how high-rez structural biology w/ the right reconstitutions can inform mechanism! www.biorxiv.org/content/10.1...

It is important at this pivotal moment to @standupforscience.bsky.social. Looking forward to sharing my thoughts on why this should be a national priority at tomorrow’s rally in SF:

Endocytosis sculpts distinct cAMP signal transduction by endogenously coexpressed GPCRs Many G protein-coupled receptors (GPCRs) trigger a second phase of G protein-dependent signaling from internal membranes after agonist-induced endocytosis. However, individual GPCRs differ significant...

New preprint! Here, we explore how endocytosis encodes receptor-specific cAMP/PKA signaling downstream of three endogenously coexpressed GPCRs. www.biorxiv.org/content/10.1...

My lab at
@stanfordmedicine.bsky.social
is recruiting! We are looking for a postdoc at the interface of quantitative proteomics and G protein-coupled receptor (GPCR) biology: postdocs.stanford.edu/prospective/...
#TeamMassSpec #Proteomics #GPCR #Postdoc

Thanks Reid! Looks like they are queued to release with the next PDB update on Jan. 15

Molecular basis of proton sensing by G protein-coupled receptors Howard et al. combine mechanistic deep mutational scanning, cryo-EM, and constant-pH molecular dynamics simulations to provide a holistic view of proton activation in human pH-sensitive GPCRs.

Congrats @willowcoyote.bsky.social @amanglik.bsky.social and all authors on a tour de force dissection of proton-sensing by GPCRs! DMS, cryo-EM, MD -- it has it all! www.cell.com/cell/fulltex...

Thanks Stephanie! Hope all is going will w/your new lab - excited to see all the amazing work to come!

Thanks Joe!

Thanks, glad you enjoyed it!

Thanks Alex!

Thanks for the invite! Excited to share some of our recent work tomorrow 😀

Tagging all the folks who I can find here... @amanglik.bsky.social @willowcoyote.bsky.social @justingenglish.bsky.social @delemottelab.bsky.social ...

Thanks @justingenglish.bsky.social!! Awesome working with you and excited to see where we go in the future 👀

There is certainly more than can be shared here, but I will end it there with a HUGE thanks to everyone involved! This was both a challenging and fun project to be involved in with many great folks without which none of this would be possible. (13/13)

Ultimately, this enabled us to identify residues which change pronation with conformation and pH. Combining our DMS, cryo-EM, MD, and extensive pharmacologic validation (by XP Huang), we were able to devise a comprehensive model for pH activation of GPR68 (12/n)

Well, Darko went above and beyond. He developed a new method which uses coevolutionary information to identify both alternative receptor conformations AND the effect of pH on the conformational ensemble. (11/n)

We needed an inactive-state structure model to fully interpret our results, so we teamed up with
Darko Mitrovic (in @delemottelab.bsky.social lab) to do some molecular dynamics simulations of GPR68 (10/n)

We followed up with a surface expression screen to determine the which mutations alter receptor expression. This allowed to deconvolve the mutational effects on expression vs activation to uncover GOF and LOF activity specific to activation. (9/n)

The result: a comprehensive map of each mutation's effect on pH activation. (8/n)

We then generated a mutational library of GPR68 using the DIMPLE platform developed in @willowcoyote.bsky.social's lab and screened it using our cAMP FACS assay (7/n)

Using GPR68 as our model, we set out to use mutational scanning to determine the effect of every mutation on proton activation. We developed a new FACS-based method to measure Gs coupled receptor activation (enabled by a new TRE's from @justingenglish.bsky.social ) (6/n)

We needed to ascribe a functional role for each residue in proton activation. Unfortunately, these receptors are littered with an enormous number polar and charged residues which may be implicated. (5/n)

To start, Nick Hoppe (in @amanglik.bsky.social's lab) set out to determine the 3D architecture of each human proton sensor (GPR4, GPR65, and GPR68) using cryo-EM. These provided insights into the architecture and arrangement of putative proton-sensing residues in the active-state (4/n)

We wanted to determine the location and identities of all residues involved in coordinating protons to drive receptor activation. (3/n)

We have known for some time that several GPCRs respond to changes in pH. However, unlike small molecules, peptides, and other stimuli, protons are a bit wonky--we can't directly see them with standard approaches. (2/n)

Happy New Year! (and first post here 😀) Excited to share the final version of our work where we combine deep mutational scanning, cryo-EM, and molecular dynamics to further resolve the mechanisms of pH sensing in GPCRs.

🧵(1/n)

www.cell.com/cell/fulltex...

A massively parallel reporter assay library to screen short synthetic promoters in mammalian cells Nature Communications - Context-dependent, responsive synthetic promoters are crucial for a wide range of applications, yet currently available options are limited. Here, authors develop a library...

Happy Thanksgiving y'all! I'm thankful for my whole lab, team, and collaborators this year. Our updated and final version of the TRE MPRA system is online today. If you have time between turkey bites have a gander.

rdcu.be/d1OTf