Roberto Chica Lab
@chicalab.bsky.social
Our research group at the University of Ottawa specializes in computational enzyme design. mysite.science.uottawa.ca/rchica/
We can design "static" binders routinely now, but design of "dynamic" shape-changing proteins has remained quite hard. Jeffrey Chang and I asked: why can't we couple small-molecule binding to shape change? After all, natural proteins do it every day. In a new preprint, we show how it can be done. 🧵
Can protein dynamics help guide protein engineering? Our latest paper shows that a simple NMR peak intensity analysis can reveal functional dynamics hotspots, helping to uncover promising engineering targets. With @thompson-lab.bsky.social and Natalie Goto. doi.org/10.1093/prot...
Mapping functional dynamics hotspots for protein engineering with NMR peak intensity analysis
Abstract. Structural dynamics play a crucial role in protein function, and tuning these dynamics through mutagenesis has emerged as a promising strategy fo
academic.oup.com
A new paper presents CANVAS, a computational workflow that converts minimal de novo TIM barrels into enzymes by designing structural lids that generate tailored active sites www.nature.com/articles/s41...
Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes - Nature Chemical Biology
The TIM barrel is nature’s most versatile enzyme fold, yet de novo variants lack functional active sites. Minimal de novo TIM barrels have now been converted into enzymes by designing structural lids ...
nature.com
Excited to share our latest with @birtehoecker.bsky.social: CANVAS, a de novo enzyme design strategy that builds active sites by adding tailored lids to minimal TIM barrels. Several designs reached kcat values of 13–26 s⁻¹, on par with the median natural enzyme. www.nature.com/articles/s41...
Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes - Nature Chemical Biology
The TIM barrel is nature’s most versatile enzyme fold, yet de novo variants lack functional active sites. Minimal de novo TIM barrels have now been converted into enzymes by designing structural lids ...
nature.com
Today out in Nature Chemical Biology @springernature.com. Thanks for great collaboration @chicalab.bsky.social
Roberto Chica Lab@chicalab.bsky.social · 6mo ago1/6 Thrilled to announce our updated preprint on the CANVAS method for de novo enzyme design, in collaboration with @birtehoecker.bsky.social. We show how CANVAS builds custom lids onto minimal TIM barrels, transforming them into efficient catalysts. www.biorxiv.org/content/10.1...
Only 2 weeks left to benefit from early-bird registration rate! The 6th Protein Engineering Canada Conference will be held on June 22-24 in Ottawa, Canada. More information here: event.fourwaves.com/pec2026/pages
6th Protein Engineering Canada (PEC) Conference
Join 6th Protein Engineering Canada (PEC) Conference, June 22-24, 2026. Learn more on Fourwaves.
event.fourwaves.com
Excited to share Sampleworks led by @karsonchrispens.bsky.social with @diffuseproject.bsky.social. It's a modular framework connecting structure predictors to experimental data and guidance methods. Swap predictors or guidance methods. All open and made to be built upon. t.co/fvNHH3gfVu
https://diffuse.science/posts/sampleworks/
t.co
I had a great time nerding out about protein design with @nickpolizzi.bsky.social, and an enormous thanks to @biotechtv.bsky.social and @massbio.bsky.social for hosting us! www.biotechtv.com/post/chris-b...
AI Proteins Founder & CEO Chris Bahl and Dana-Farber Cancer Institute Investigator Nick Polizzi discuss the current state of protein design and new innovations that are around the corner
Both experts in the field, one with an academic view and one from industry, they discuss what can be done today with protein design, new innovations coming in the next year or two, and how they think ...
biotechtv.com
1/6 Thrilled to announce our updated preprint on the CANVAS method for de novo enzyme design, in collaboration with @birtehoecker.bsky.social. We show how CANVAS builds custom lids onto minimal TIM barrels, transforming them into efficient catalysts. www.biorxiv.org/content/10.1...
1/ Save the date! The 6th Protein Engineering Canada Conference will be held on June 22-24 in Ottawa, Canada. Abstract submission and registration are open! More information here: event.fourwaves.com/pec2026/pages
1/ Save the date! The 6th Protein Engineering Canada Conference will be held on June 22-24 in Ottawa, Canada. Abstract submission and registration are open! More information here: event.fourwaves.com/pec2026/pages
Thrilled to share that our latest article is now out in final form! A great collaboration with @fraserlab.com and @silviaosuna.bsky.social. Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release www.nature.com/articles/s41...
Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release - Nature Communications
Distal mutations, though far from the active site, enhance Kemp eliminase catalysis by tuning conformational dynamics that facilitate substrate binding and product release, thereby promoting the full catalytic cycle.
nature.com
Our latest article is now published online! In collaboration with @thompson-lab.bsky.social, Marc Garcia-Borràs, and @ferranfeixas.bsky.social. Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step pubs.acs.org/doi/full/10....
Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step
Amino acid residues distant from an enzyme’s active site are known to influence catalysis, but their mechanistic contributions to the catalytic cycle remain poorly understood. Here, we investigate the...
pubs.acs.org
In collaboration with @birtehoecker.bsky.social, we’ve unlocked enzymatic activity in a minimal de novo TIM barrel by designing a custom lid for catalysis! 🧵👇 #ProteinDesign #EnzymeDesign Customizing the Structure of a Minimal TIM Barrel to Create a De Novo Enzyme www.biorxiv.org/content/10.1...
Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme
The TIM barrel is the most prevalent fold in natural enzymes, supporting efficient catalysis of diverse chemical reactions. While de novo TIM barrels have been successfully designed, their minimalisti...
biorxiv.org
Join us! We are looking for a new team member (PhD student) with strong background in organic chemistry. 🙏 RETWEET (We want to recruit internationally) Organic chemistry meets #DirectedEvolution Highly interdisciplinary & passionate research group uni-bielefeld.hr4you.org/job/view/433...
Research Position (PhD) in organic chemistry and b...
<div style="text-align: justify;">The research group „Organic Chemistry and&nb...
uni-bielefeld.hr4you.org
Protein Engineering, Design & Selection (PEDS) invites contributions to a Special Collection titled, “Non-Canonical Amino Acids", with guest editors Prof. Huiwang Ai (Virginia) and Prof. Peng Chen (Peking). Send us your best work! academic.oup.com/peds/pages/c...
Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1... 🧵🧪
Zero-shot design of drug-binding proteins via neural selection-expansion
Computational design of molecular recognition remains challenging despite advances in deep learning. The design of proteins that bind to small molecules has been particularly difficult because it requ...
biorxiv.org
Guess what? TPS has extended the deadline to March 19 to submit abstracts for poster presentations and speaking opportunities at our 39th Annual Symposium. Join us in San Francisco June 26 - 29 for 3.5 days of scientific talks. hashtag#proteinscience hashtag#annualsymposium lnkd.in/g7VKqX7C
How do mutations far from an enzyme's active site influence catalysis? 🤔 Part 2: In collaboration with @fraserlab.bsky.social and @silviaosuna.bsky.social, we investigated this question using de novo Kemp eliminases, revealing effects of distal mutations on the catalytic cycle. 🧵 (1/6)
Whereas beneficial active site mutations to enzymes often improve the chemical transformation itself by preorganizing the active site, mutations to second-shell residues instead tune steps like product release by modifying the broader conformational ensemble www.biorxiv.org/content/10.1...
How do distal mutations contribute to enzyme catalysis? Our new study, in collaboration with @thompson-lab.bsky.social, Marc Garcia-Borràs, and @ferranfeixas.bsky.social, reveals how they optimize structural dynamics & local electric fields to drive the catalytic cycle. 🧵👇
Join us this summer for 3.5 days for science! The Protein Society's 39th Annual Symposium takes place June 26 - 29, in beautiful San Francisco. #proteinscience #annualsymposium #proteinsociety mailchi.mp/proteinsocie...
Register Today for PS39
mailchi.mp
Thrilled to take a break from doom and gloom to share our latest work collaborating with the DeGrado lab! We took a de novo designed protein, screened it for ligand binding using X-rays, and used the hits to evolve two wildly different functions: fluorescent turn-on and Kemp elimination catalysis. 🧵
Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme https://www.biorxiv.org/content/10.1101/2025.01.28.635154v1
Distal mutations in a designed retro-aldolase alter loop dynamics to shift and accelerate the rate-limiting step https://www.biorxiv.org/content/10.1101/2025.01.26.634918v1
Bluetorial-A dream and a bit of a nightmare Serving as Editor-in-Chief at Science was fascinating. I greatly enjoyed working with talented and committed editorial, news, graphics, and production staff. But the inside look into scientific publishing and AAAS was also deeply disillusioning.
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
Looking forward to The Protein Society's 39th Annual Symposium! Honored to co-chair the program planning committee with Margie Sunde, alongside committee stars @clvizcarra.bsky.social and Gary Zhang. Explore the program here: www.proteinsociety.org/program
Program
proteinsociety.org
Protein Society@proteinsociety.bsky.social · 2y agoRegistration is OPEN: The Protein Society's 39th Annual Symposium, June 26 - 29, 2025 in San Francisco. Join us for 3.5 days of protein science, combining critical underpinnings of the field, career development, technical workshops & networking opportunities. www.proteinsociety.org/annual-sympo...
Mireia Solà Colom gave an incredible seminar at @bpdmc.bsky.social last week, and I'm very excited for her to share some details about what we've built at @aiproteins.bsky.social and how well our #miniproteins perform as therapeutics
Boston Protein Design and Modeling Club@bpdmc.org · 2y agofor the folks who weren't able to join for the brilliant presentation by Mireia Solà Colom last week to cap off our 2024 seminar series, you can check out the recording 👇 youtu.be/e6oZgGWjD_0
There is no "committee on science" that will impose a new order or set of incentives. No one is going to "fix" peer review or incentivize it differently in one fell swoop. We have to BE the change - the tools already exist for everyone at every level to make an impact and change the incentives
Harris Wang@harriswang.bsky.social · 2y ago💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)
