Neel Shah

Post-Translational Modifications Remodel Proteome-Wide Ligandability Post-translational modifications (PTMs) vastly expand the diversity of human proteome, dynamically reshaping protein activity, interactions, and localization in response to environmental, pharmacologi...

Excited to share a new preprint from the lab. We show that PTMs like phosphorylation & glycosylation dynamically reshape proteome-wide ligandability in cells, including proteins like KRAS. Great collaboration with the Huang Lab, @forlilab.bsky.social and BMS. www.biorxiv.org/content/10.1...

Shah lab at a picnic on the Great Hill at Central Park

Had a great lab retreat today in Central Park, with team-building games, great conversations, and lots of laughs, followed by delicious food/drinks. Gearing up for my State of the Lab address tmrw, where I’ll recap our past year and discuss what’s on the horizon! So lucky to have this awesome group!

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...

Dr. Anne van Vlimmeren giving her thesis defense talk.

Congrats to PhD #5 from our lab, Dr. Anne van Vlimmeren, who successfully defended her dissertation yesterday!!! Check out some of Anne's thesis work on the diverse structural/functional consequences of SHP2 mutations: PMIDs 39012820, 40661614, 40631144, 40631229.

Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein and peptide C termini Nature Chemistry - In living systems, ATP provides an energetic driving force for protein synthesis and modification. Now, an engineered enzymatic tool has been developed for high-yield, ATP-driven...

Excited to share our latest: we engineered the reactivity of a bacterial E1-like enzyme for ATP-driven modification of C termini. Our tool mimics the logic of peptide bond formation in biology for precision modification of proteins in vitro. 🧪https://rdcu.be/ewN7C

Today marks the 5-year anniversary of congressman John Lewis’ death. He wrote an essay to be published at the time of his death.

“When you see something that is not right, you must say something. You must do something. Democracy is not a state. It is an act…”

It’s worth a read 👇

Goodnight 💚

Our lab website is live tamirlab.org 😁

The Story of Samuel L Jackson In 2016 I was watching an episode of the Tonight Show with Jimmy Fallon. One of the guests on the show was Samuel L. Jackson, and as he made his entrance he struck a pose where he made a letter "L" with one of his hands before bringing it up to his chin. I thought "Well I guess his enantiomer would have to make a "D" with his hands.".

The story behind the most recognisable ChemScrapes meme. #chemsky

Ziyuan (Jason) Jiang giving his thesis presentation.

Dr. Jiang toasting his completed PhD defense!

The Shah Lab. Back row (left to right): Annalise, Loren, Katherine, Yethmie, Anne Front row (left to right): Devon, Minhee, Andrew, Jason, Anya, Neel

Jason and Neel

Congratulations to Dr. Ziyuan (Jason) Jiang, the 4th PhD from our lab! He gave a stellar thesis defense presentation on SHP2 deep mutational scanning, structure, and dynamics. We even managed to squeeze in a new lab photo in the midst of all of the excitement and celebrations!

I am beyond excited and honored to receive a BWF CASI! This amazing program will support my transition from postdoc to faculty as I continue to develop new modeling frameworks for elucidating and programming cellular behaviors.

Happy 11th birthday to @andolab.bsky.social ! 🎂 🥳 Also happy to share that I'm a full prof as of July 1 -- thanks to my awesome group, past and present.

We're now looking to grow the team! Looking for someone with amazing protein skills and postdocs excited about evolutionary questions!

Three cartoon drawings of SHP2 conformational equilibria: 1. wild-type SHP2 mostly rests in an auto-inhibited state, but when it is not auto-inhibited, it accesses an ensemble of active conformations 2. SHP2 E76K has a highly destabilized auto-inhibited state mostly rests in an active state, which is actually an ensemble of active conformations 3. SHP2 E139D is not as activating as E76K, because it does not destabilize the auto-inhibited state. Rather it stabilizes a specific active conformation where the N-SH2 position is constrained.

A neat upshot of this mechanism is that, unlike other activating mutations, which destabilize auto-inhibited SHP2 and yield an ensemble of active states, the active state of E139D is more conformationally constrained. Ultimately, this impacts the phosphoprotein binding specificity of this mutant.

In this paper, we show that the mechanistically mysterious disease mutation E139D in the C-SH2 domain of SHP2 activates the enzyme by stabilizing an active conformation not seen in any SHP2 crystal structures. We corroborate this with extensive modeling, simulations, mutagenesis, and biochemistry.

We're ending the week on a high note, with one more preprint, led by senior grad students Anne and Jason, with contributions from undergrad Anya, and our long-time collaborator Deepti Karandur!

Overall, we think this work provides a new way of thinking about and studying mutational effects on SHP2 that could be applied to other signaling enzymes that have many mechanistically diverse disease mutations.

And finally, different mutations at hotspot residue Q510 have different phenotypic outcomes defined by the identity and physical properties of the substituted amino acid, which cause changes in autoinhibition, basal activity, substrate specificity, and overall stability.

We find that two mutants, T507K and Q510K, phenocopy one another by causing cells to exist in a unique basal state. It turns out these mutants both alter phosphatase substrate specificity in the same way, which we show biochemically.

In the rest of the paper, we dig into the molecular mechanisms causing divergent outcomes by different mutations. Among the highlights, we find that cancer mutant R138Q, with a defective SH2 domain, is largely unresponsive to EGF but still drives expression of some oncogenes.

UMAP graphs derived from the RNAseq data for 9 mutants and SHP2 WT expressing cells, showing that different amounts of EGF yield different cell states (first three graphs, with EGF stimulation state largely changing along UMAP2). The fourth UMAP graph higlights 5 different clusters, with clsuter 1 largely containing unstimulated cells and cluster 5 containing maximally stimulated cells.

Occupancy of each cluster by each mutant at different EGF doses. Notable outliers are R138Q, which almost always stays in cluster 1 (non-responsive to EGF), and T507K/Q510K, which never occupy cluster 1.

Through some data analysis (read the paper!) we identified 5 distinct clusters of cell states and found that different mutants occupy different cell states as a function of EGF stimulation

volcano plot showing SHP2 WT vs SHP2 KO gene expression profiles.

EGF-dependent gene expression in SHP2 WT expressing cells.

Through this experiment, we first identified a core SHP2-dependent transcriptome and identified key EGF-response programs that are SHP2 dependent.

To get at this question, Anne and Ross designed as simple but elegant experiment, where they reconstituted SHP2 knock-out HEK293 cells with different SHP2 variants, stimulated with EGF for different doses/timepoints, and then did multiplexed single cell transcriptomics.

9 different SHP2 disease-associated mutations and their structural/functional effects, mapped onto the auto-inhibited structure of SHP2.

SHP2 is mutated in developmental disorders and cancers. We are (compulsively) focused on understanding the diverse ways that mutations dysregulate this enzyme: changes in catalytic activity, dynamics, stability, interactions, etc. But do these different mechanism yield different downstream outcomes?

Check out our latest preprint, from Anne van Vlimmeren in my group and Ross Giglio in @jlmcfalinefigueroa.bsky.social's lab. We used single-cell transcriptomics, biochemistry, and structural analysis, to reveal how mechanistically distinct SHP2 disease mutations yield different cellular states.

A Potent Inhibitor of Caspase-8 Based on the IL-18 Tetrapeptide Sequence Reveals Shared Specificities between Inflammatory and Apoptotic Initiator Caspases Caspases are a family of cysteine proteases that act as molecular scissors to cleave substrates and regulate biological processes, such as programmed cell death and inflammation. Extensive efforts hav...

New paper online at ACS Bio & Med Chem Au with @taabaman.bsky.social! New peptide probes and inhibitors for caspase 8
pubs.acs.org/doi/10.1021/...

What the fuck NY?! Donate $10 to Skype a Scientist so we don’t lose to fucking FLORIDA.

Fro the last few years, as part of a final assignment in my senior biophysical chem class I ask students to share a class-related memes, with ones they make themselves highly encouraged!
For everyone's enjoyment, here are some of my favorites!
#chemistry #biochemistry #sigfigs #units 🧪

And of course, we could not have done this without NIH funding that has been critical for supporting my students’ training and my career, and for giving us the resources to shed light on some aspects of the molecular basis of human diseases.

Excited to see this paper out in its final form, and huge congrats to first author Ziyuan (Jason) Jiang just a week before his thesis defense. This work has become an invaluable resource in our lab for SHP2 projects, and we hope it resonates with the whole field.

www.nature.com/articles/s41...

Despite ~20 years in/around #chembio research, I went to my first Bioorganic GRC this week. This community is amazing and so supportive. I feel energized (and tired, lol) and find myself rooting for the next generation of chemical biologists. Sooooo much awesome science - We can’t/won’t be stopped!

It’s been a weird, unproductive week at the lab and I’m feeling a little down. So here are 10 cool facts about vision: