Crystal structure of Circadian Clock Protein KaiC (source: PDB)
Created with Midjourney: A timepiece made of circadian clock proteins
The aim of this project is to develop a proof-of-concept timepiece utilizing nature’s biological timekeeping mechanism, the circadian clock protein. In this early phase, the project focused on using the circadian clock protein from cyanobacteria, fused with a visible reporter for visualization. Circadian rhythms are fundamental biological processes that regulate various physiological functions, and their visualization can provide insights into biological timing mechanisms. Cyanobacteria possess an endogenous circadian clock system, making them an ideal candidate for engineering a timepiece.
Circadian clock proteins have been extensively studied for their role in regulating physiological processes, primarily in clinical or academic settings. This project seeks to explore the potential of integrating these biological timekeeping mechanisms into everyday objects
The project involves two main objectives: (1) Engineering cyanobacteria to express a fusion protein consisting of the circadian clock protein (e.g., KaiC) fused with a visible reporter (e.g., fluorescent protein) for real-time visualization, and (2) Integrating the engineered cyanobacteria into a physical medium (e.g., hydrogel or microfluidic device) for sustained protein expression and visualization.
Cyanobacteria - KaiC protein
An organism's circadian clock mechanism is a system that typically includes various types of clock proteins to create a feedback loop or oscillation. As I learn more about the clock protein, I realize that, as a baby step, I need to identify the simplest model to manipulate.
Human’s circadian clock system
The human internal clock involves a network of genes and proteins, including a master pacemaker (SCN) that regulates the timing of biological processes through clock genes like PER and CRY in a feedback loop. This complexity led me to explore other models with similar rhythmic patterns. [12]
Cyanobacterial clock system
Cyanobacteria (strain: Synechococcus elongatus PCC 7942) are the only known prokaryotes to exhibit circadian rhythms similar to those in eukaryotes, making them well-studied model organisms for circadian rhythm. [12]
Focusing on expressing the KaiC protein
KaiC, in particular, undergoes rhythmic phosphorylation and dephosphorylation cycles that drive the core circadian oscillations. I decided to target KaiC to express the circadian pattern. [13][14]
The aim of this phase is to develop observable clock proteins in prokaryotes by fusing them with visible reporters using established protocols. The second part of this phase involves exploring the possibility of integrating visible proteins into physical materials by utilizing current fabrication methods for biomaterials, such as engineered living material (ELM) or microfluidic devices.
Taking the learning from phase 1, the goal of this phase is to apply the knowledge to create observable clock proteins in eukaryote cells, specifically mammalian proteins. Since the eukaryote cell has a more complex machinery that requires post-translational modification, one of the aims of this phase is to investigate techniques and suitable chassis for expressing these proteins
Develop a proof-of-concept timepiece with a person’s clock protein. In this phase, the project will explore a workflow and prototyping process for extracting a person’s clock protein and turning it into a personalized wearable piece, applying the technique learned from experimenting with mammalian clock protein.