New publication is out: “Unimolecular FRET Sensors: Simple Linker Designs and Properties”


A new publication by researchers at University College Dublin and Boston University including E-CAM funded corresponding author Dr. Donal MacKernan was published in Nano Communication Networks. The measurement of biomarkers and ligands are increasingly used to study transport, signaling, and communication in cells, and as diagnostics/prognostics of disease, or the presence of pathogens, allergens and pollutants in foods, and the environment. Accurate measurement in assays or cellular environments is important, and protein-based biosensors can be used in this context. Using simple Coarse-Grained models of unimolecular fusion protein based FRET sensors of target ligands, the authors address four main questions. Can simple CG models reproduce qualitatively experimental results? Is there an advantage in replacing flexible protein linkers with hinge-like peptides? To enhance the precision of measurement, is it  better to increase or decrease the Föster radius of fluorescent proteins? Is precision enhanced or reduced if the binding energy of the ligand and sensor domains is attractive or repulsive in the absence of the target ligand? The answers are disclosed in the paper.

The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher’s version can be found at

This work is a particular part of  E-CAM Pilot Project on Food and Pharmaceutical Proteins focused on the development of protein-based sensors and therapeutics. The software used in the publication will soon be published in the E-CAM software library. Industry partners of the Pilot Project include Kerry GroupAPC and others.


Title: Unimolecular FRET Sensors: Simple Linker Designs and Properties

Authors: Shourjya Sanyal, David F. Coker, Donal MacKernan

Abstract: Protein activation and deactivation is central to a variety of biological mechanisms, including cellular signaling and transport. Unimolecular fluorescent resonance energy transfer (FRET) probes are a class of fusion protein sensors that allow biologists to visualize using an optical microscope whether specific proteins are activated due to the presence nearby of small drug-like signaling molecules, ligands or analytes. Often such probes comprise a donor fluorescent protein attached to a ligand binding domain, a sensor or reporter domain attached to the acceptor fluorescent protein, with these ligand binding and sensor domains connected by a protein linker. Various choices of linker type are possible ranging from highly flexible proteins to hinge-like proteins. It is also possible to select donor and acceptor pairs according to their corresponding Föster radius, or even to mutate binding and sensor domains so as to change their binding energy in the activated or inactivated states. The focus of the present work is the exploration through simulation of the impact of such choices on sensor performance.