Visualizing different models for molecular binding and interactions
This project is part of my Master's Thesis and consists of a 3D animation aimed at helping students clarify misconceptions about the principles of molecular binding and interactions.
"Mental models", such as Lock and Key, Induced Fit or Conformational Populations, are used to explain how protein conformational change drives binding and interactions. These models have been created over more than a century of research and introduce the concepts of complementarity, changes in conformation during binding and the exploration of multiple conformations in unbound proteins. However, they are still too simple to reflect all protein interactions. New discoveries in proteins science, such as Intrinsically Disordered Proteins (IDPs), have changed the way in what we envision these mental models. This animation will explore these different mental models and dive into the fascinating world of IDPs!
Directed primarily to first and second-year undergraduate students of any Biological field.
Adobe After Effects
Adobe Premiere Pro
BA, MScBMC, PhD, FAMI
Director & Associate Professor
University of Toronto
BFA, BA, Hons BSc, MScBMC, CMI
Associate Director & Associate Professor
University of Toronto
Director of Molecular Visualization and Founder & CEO of Digizyme Inc.
Hardvard Medical School
Professor of Teaching
University of California Davis
Proteins are involved in all molecular processes in living cells including metabolic, signaling, catalysis, viral entry, and regulation. Molecular recognition is essential for their interaction and protein dynamics and flexibility are key in this process. Many protein-protein interactions (PPIs) are involved in disease pathways where therapeutic intervention could bring widespread benefit. Understanding how protein interactions work is essential to elucidate disease mechanisms, and discover compelling targets for drug design and discovery (Kuzu et al., 2012).
BEHIND THE STORY
In first and second year of Biological Science Undergraduate courses, students are taught about protein interactions through three mental models that represent different aspects of this complex process: Lock & Key, Induced Fit and Conformational Selection. These models are depicted through static images that aim to communicate important conformational changes and sequences of events through time. However, these static images oversimplify the complexity of the binding events, failing to communicate some important concepts such as the dynamic nature of proteins, the randomness of the encounter, the inevitable unsuccessful binding events or the influence of the environment. Thus, learners infer molecular interactions as straightforward, highly efficient mechanistic systems (Chi, 2013), which can lead to the formation of misconceptions and difficult the acquisition of further complex knowledge in protein science.
The main goal is to bridge the knowledge gap in undergraduate Biological Science students’ understanding of key concepts in molecular binding and interactions.
Intramolecular and intermolecular dynamics.
Conformational selection, intermediate states, population ensambles.