this is a draft
Papeco: An In Silico Design Project for a Second-Generation Genetically Encoded Carbon Monoxide Biosensor SECTION 1: ABSTRACT Papeco is a in silico synthetic biology project focused on designing a second-generation genetically encoded biosensor for carbon monoxide (CO). The project addresses an important problem in chemical biology and biosensing: CO has real biological relevance in heme metabolism, stress signaling, and disease, but the available fluorescent tools are dominated by small-molecule probes rather than programmable protein-based systems. This matters because genetically encoded sensors can, in principle, be targeted to defined cells or compartments, redesigned by DNA sequence alone, and improved iteratively through structure-guided engineering. Natural heme-based CO sensor proteins such as CooA and RcoM provide a strong biological starting point because they already recognize CO through ligand-dependent conformational changes. The broad objective of Papeco is therefore to computationally design and prioritize new fluorescent CO biosensor architectures built from these natural sensing domains.