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Applied Protein Engineering Lab

Institute of Biomaterials and Biomedical Engineering

Department of Electrical and Computer Engineering

University of Toronto

Introduction

Cells are continuously processing and reacting to external signals that elicit various responses including cell division, migration, differentiation and death. Decades of research in cell biology has revealed these responses are controlled by cellular signaling pathways that resemble computer networks and electrical circuits.  These cellular signaling pathways are composed of a network of interacting proteins.  As a result, the malfunction of proteins often causes human illnesses such as Alzheimer’s disease, heart disease and cancer.  For example, many cancers have a malfunction in the p53 protein, which impairs the cell’s ability to undergo apoptosis – a cell suicide mechanism that kills errant cells.  By evasion of apoptosis, cancer cells can grow longer than otherwise possible.

The field of protein engineering focuses on designing proteins with desired biological functions and accordingly, offers opportunities of designing proteins to repair malfunctioning signaling pathways.  The long term vision of our research is to make possible the treatment of a variety of diseases using engineered proteins.  To achieve that vision, we need to first, observe signaling events in living cells so we can identify the hallmarks of disease and second, repair signaling when these hallmarks are discovered.  Engineered proteins are an attractive approach because they allow a natural connection to the biological networks and also, they allow us to use Nature’s own protein designs as the basis of our synthetic designs.

Our long term vision is realized by biological and computational methods applied to two synergistic protein engineering themes: Protein Biosensors and Protein Switches. 

Protein Biosensors

Protein biosensors allow us to image cellular events of signaling pathways within living cells and organisms.  Using proteins found in Nature that detect cellular events, these biosensors are designed to transduce the occurrence of a cellular event into a measurable fluorescence intensity or spectral change.  Unlike common methods for measuring signaling changes based on western blots of cell lysate, these types of biosensors allow  imaging of a cellular event as it occurs in a living cell.  Furthermore, unlike synthetic dyes, protein biosensors are encoded in DNA and accordingly, can be targeted to subcellular organelles within cells or tissues within organisms.  This real-time measurement and targeting ability are the key advantages of protein biosensors that enable a unique insight into cellular signaling.  Our long term aim is to use protein biosensors to identify changes in the patterns of signaling that are the hallmarks of disease.

Protein Switches

Using protein biosensors, we can observe cellular events as they occur in living cells and identify signaling abnormalities that are the hallmarks of disease.  Once these hallmarks are discovered, treatment could involve repairing the signaling abnormality.  Engineered proteins are an attractive approach because they can naturally interact with signaling pathways and furthermore, we can use Nature’s own protein design as the basis of our synthetic designs.  Our long term aim is to use engineered protein switches to repair signaling abnormalities that are the hallmarks of disease.  In the short term, we can use engineered protein switches to better understand signaling in living cells by intervening with cellular signaling as we are imaging it with our protein biosensor.  The design of protein switches can be rational if the protein structure is available as we can splice the regulatory elements of the switch near the active site of the protein to create a synthetic allosteric effect.  Lastly, designing protein switches leverages on our protein biosensor work because these biosensors are essentially switches themselves.

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