Visualizing different models for molecular binding and interactions
3D animation
PROJECT
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!
Adobe Photoshop
Adobe Illustrator
Chimera
Molecular Maya
AUDIENCE
Directed primarily to first and second-year undergraduate students of any Biological field.
software
Autodesk Maya
Pizologic Zbrush
Adobe After Effects
Adobe Premiere Pro
Format
3D animation
COmmittee MEMBERS
Jodie Jenkinson
BA, MScBMC, PhD, FAMI
Director & Associate Professor
University of Toronto
Michael Corrin
BFA, BA, Hons BSc, MScBMC, CMI
Associate Director & Associate Professor
University of Toronto
Gaël McGill
PhD
Director of Molecular Visualization and Founder & CEO of Digizyme Inc.
Hardvard Medical School
Susan Keen
MSc, PhD
Professor of Teaching
University of California Davis
FUNDING
RESEARCH BACKGROUND
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.
COMMUNICATION GAP
PRIMARY GOALS
The main goal is to bridge the knowledge gap in undergraduate Biological Science students’ understanding of key concepts in molecular binding and interactions.
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Intramolecular and intermolecular dynamics.
Conformational selection, intermediate states, population ensambles.
Structure drives function.
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PRE-PRODUCTION
PROPOSAL
Before diving in to the project, I carried out literature review, research on existing media audit and need of assessment. In this proposal I determine the communication gaps to address and justify why animation is an effective medium to bridge them. Moreover, I explore the most important principles when animating molecules and have a look at how to measure the project's success.
STORYBOARD
The storyboard is a planning document that served to visualize the scenes accompanying the script. It started as a series of rough black and white sketches and later on I found the use of color very helpful to identify the different molecules and to better depict the scenes. It was very useful to share this document with my committee to make sure we were all in the same page with the visuals representations (specially those of the "mental models").
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SCRIPT
Writing the script was an important step in figuring out the real scope of the project, the story development and the tone I wanted to use. This script underwent many revisions in order to make sure as little changes as possible would be needed later during the production process.
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