dennishuang.bsky.social
PhD student at Bugaj Lab UPenn | synbio | protein engineering | optogenetics | thermogenetics | systems bio | love weird dynamics, information flow, network structures of all systems | everything BcLOV4
40 posts
245 followers
517 following
Prolific Poster
Conversation Starter
comment in response to
post
Oh wow, this is awesome! So the left-right handedness is actually a spectrum? And that’s why some ppl only do a fraction of things with left hand but not all?
comment in response to
post
Big thank you to all the coauthors! Especially Yueying and Carol!
comment in response to
post
See our thread here! bsky.app/profile/denn...
comment in response to
post
Grateful for a true collaboration with @nmrkaygee.bsky.social lab at CUNY, with @malvinf.bsky.social and @Kevin Gardner leading the in vitro studies. Huge thank you to Lukasz for all the support! This work was also only possible with funding for curiosity-driven research by NIH, NSF, and Penn.
comment in response to
post
Many questions (what benefits of protein dynamics for the host fungus?) and implications (better/new opto or thermo proteins). Overall, intra-protein network motifs provide a new way to think about compact, dynamic computation on the protein level.
comment in response to
post
Indeed, 1 A.A. mutation from each of these hotspots dramatically extended the pulsatory response (>18 hrs vs 10s of min), suggesting evolutionary tuning of dynamics.
comment in response to
post
Remarkably, sequence analysis found these *exact same hotspots* had co-evolved in BcLOV4 homologs, implying function.
comment in response to
post
Structural studies (limited proteolysis, HDX-MS by the Gardner lab) identified temperature-sensitive hot-spots in DUF.
comment in response to
post
What about the temperature-sensitive inhibitory Node C? We mapped this to the mysterious “Domain of Unknown Function” (DUF). We still call it DUF even though function is now known :P.
comment in response to
post
We then mapped the network nodes: The light-sensing LOV domain (A) regulates a charged clustering region (B), which drives PM binding. Aside: this inspired an entire toolset for single-protein translocation to various compartments. Preprint soon!
comment in response to
post
The inter-domain IFFL idea started as a hunch, but models made several non-intuitive predictions that we then confirmed experimentally through mutations that altered the energetics of LOV domain interactions.
comment in response to
post
Answer: smaller-scale networks of interactions between the protein’s domains. Light response (A) quickly activates a region for plasma membrane (PM) binding (B), but also enables a temp.-sensitive domain (C) to inhibit the PM-binding region more slowly.
comment in response to
post
Step-to-pulse response – adaptation – is common in all kinds of networks, often through an incoherent feed-forward loop (IFFL). Node A quickly activates Node B but also —more slowly— Node C, which inhibits Node B. Result: a pulse of B. But how can a single protein do it w/o a larger network?
comment in response to
post
Why does BcLOV4 turn itself off despite constant light stimulation, and why does this depend on temperature? The answer could make better optogenetic and thermogenetic tools, and itself was a fascinating puzzle.
comment in response to
post
Thank you Rita!