Cole DeForest
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coledeforest.bsky.social
Cole DeForest
@coledeforest.bsky.social
1.9K followers 530 following 23 posts
Weyerhaeuser Associate Professor of Chemical Engineering & Bioengineering, University of Washington | User-Programmable Biomaterials | Photochemistry | Optogenetics | Protein Engineering

http://www.coledeforest.com
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Check out our new paper entitled "Boolean Logic-based Controlled Release of Bioactive Proteins with Diversified Inputs", live in @angewandtechemie.bsky.social !

Growth factors, enzymes, nanobodies, and cytokines can now be "logically" delivered!

📜: onlinelibrary.wiley.com/doi/10.1002/...
Stimuli-responsive biomaterials hold great promise in controlled therapeutic delivery, tissue engineering, and biosensing applications. Recently, molecular assembly via autonomous compilation has been employed to create topologically specified protein cargos that can be site-specifically tethered to and conditionally released from biomaterials following user-programmable Boolean logic. Prior implementation has been confined to simple fluorescent protein outputs and model protease inputs. In this manuscript, we extend the applicability of this framework by assembling all 7 unique logical operations emanating from a YES/OR/AND 3-input operator set to deliver bioactive proteins spanning diverse categories: growth factors (epidermal growth factor), model enzymes (β-lactamase, NanoLuciferase, and thioredoxin A), therapeutic nanobodies (anti-human epidermal growth factor receptor 2), de novo-engineered cytokines (Neoleukin), and fluorescent proteins (mGreenLantern). In so doing, we demonstrate programmable biomacromolecule release from material anchors in response to precise combinations of three orthogonal protease actuators while maintaining native bioactivity. Through inclusion of a photocleavable protein motif, we further establish that visible light can be employed as an additional input in specifying logic-based protein release. We anticipate these methods will powerfully expand opportunities for targeted therapeutic delivery and beyond.
November 21, 2025 at 9:17 PM
coledeforest.bsky.social
Our latest collaborative paper with David Baker's lab is now live in Cell Biomaterials (@cp-cellbiomat.bsky.social, Cell Press)! Check out "Stimuli-triggered Formation of De Novo-designed Protein Biomaterials"!

🔓 : www.cell.com/cell-biomate...
Protein-based biomaterials have risen in popularity in recent years owing to their genetic encodability, sequence specificity, monodispersity, and ability to interface with biological systems in comparison with synthetic polymer-based materials. Though naturally derived and minimally engineered proteins have been at the forefront of these efforts, recent advances in computational protein design offer exciting opportunities for next-generation biomaterial development. In this work, we employ de novo protein design methodologies to generate a suite of self-assembling multimeric proteins, whose step-growth heteropolymerization into bulk hydrogels and condensates can be exogenously triggered through small-molecule addition. Our results highlight how changes in programmed multimer valency and their triggered assembly yield materials with varying structures and viscoelasticity. We anticipate that these approaches will prove useful in rapidly generating large libraries of stimuli-responsive biomaterials that are precisely tailored to specific applications in the biosciences and beyond.
October 20, 2025 at 10:46 PM
coledeforest.bsky.social
Our new paper entitled “Boolean Logic-gated Protein Presentation through Autonomously Compiled Molecular Topology” is now live at Nature Chemical Biology (@natchembio.nature.com)! Check it out!

📜: www.nature.com/articles/s41...

@uwnews.uw.edu feature write-up: www.washington.edu/news/2025/10...
Stimulus-responsive materials have enabled advanced applications in biosensing, tissue engineering and therapeutic delivery. Although controlled molecular topology has been demonstrated as an effective route toward creating materials that respond to prespecified input combinations, prior efforts suffer from a reliance on complicated and low-yielding multistep organic syntheses that dramatically limit their utility. Harnessing the power of recombinant expression, we integrate emerging chemical biology tools to create topologically specified protein cargos that can be site-specifically tethered to and conditionally released from biomaterials following user-programmable Boolean logic. Critically, construct topology is autonomously compiled during expression through spontaneous intramolecular ligations, enabling direct and scalable synthesis of advanced operators. Using this framework, we specify protein release from biomaterials following all 17 possible YES/OR/AND logic outputs from input combinations of three orthogonal protease actuators, multiplexed delivery of three distinct biomacromolecules from hydrogels, five-input-based conditional cargo liberation and logically defined protein localization on or within living mammalian cells.
October 13, 2025 at 4:22 PM
coledeforest.bsky.social
Happy Holidays from the DeForest Lab!

What fun to celebrate the group’s 2024 achievements, especially in the baking sector. Our annual dessert bake-off competition was a tasty success!
December 12, 2024 at 8:41 PM
coledeforest.bsky.social
Professors often tell graduate students that “Your PhD is a #marathon, not a sprint”.

Having now run the 2024 Seattle Marathon (many years after finishing a PhD), I now actually feel qualified to make such a statement.

@uwmedicine.bsky.social
December 2, 2024 at 9:16 PM