Tools for molecular visualization

Understanding the relationship between macromolecular structure and function is a critical learning outcome for many biology courses; however, instructors are largely limited to using 2D images in order to teach students about 3D molecules (imagine trying to describe a car to someone who has never seen a car before, using only pictures!). This creates limitations on communicating key elements of 3D molecular structures, including depth perception, sense of scale, and the effects of conformational changes on both local and macromolecular levels.

We aim to develop new teaching tools to help address these limitations and increase the accessibility of the beautiful 3D world of macromolecules for both instructors and students.

Ongoing research projects:

BiochemAR: an augmented reality app for easy visualization of virtual 3D molecular models

Have you played Pokemon Go? Then you've used Augmented Reality (AR) technology! In AR, a video display shows an overlay of a virtual 3D object projected over the real world. AR technology holds substantial promise and potential for providing a low-cost, easy to use digital platform for the manipulation of virtual 3D objects, including 3D models of biological macromolecules. In collaboration with Andrew Wilson at Academic Technologies, the goal of this project is to develop 3D visualizations with accompanying classroom learning materials for integration into our BiochemAR app that can be broadly used in a variety of courses.

BiochemAR is currently freely available for iOS on iPad and iPhone from the Apple store and for Android from Google Play. BiochemAR has been featured on The Scientist and Carleton Now.

Below are the learning modules we have developed/are interested in developing:

Membrane transport: the potassium channel

The role of membranes as an impermeable barrier, resulting in unique chemical environments on either side of the barrier, is a fundamental concept in biology. Equally important is the role of transmembrane macromolecules in facilitating the active or passive transport of solutes across the membrane barrier. Our understanding of the molecular mechanisms of transport has been vastly improved by the increasing availability of 3D structures of these remarkable molecules. The KscA potassium channel structure (PDB ID: 1BL8) is a seminal and enduringly elegant example of how knowledge of macromolecular structure significantly furthered our understanding of protein function.

This learning module shows two views of the KscA channel: one of the entire channel (Model 1) as well as a zoomed-in view of only the selectivity filter (Model 2). Certain features of the channel (potassium ions, important functional groups, etc) are deliberately highlighted using different colors/representations. In order to use the module:

1) Download and install BiochemAR onto either your mobile or tablet device.

2) Download and print the QR code and instructions. If you would like to customize the size of the QR code, here is the QR code image file (PNG).

3) Start up the app and point your device camera at the QR code to quickly load up two different representations of the KscA channel!

Interested in using this module for your course? We are always interested in how the app is used/gathering feedback for improvement on future versions of the app. Please feel free to email me with any questions/thoughts!

Allosteric regulation of protein function: hemoglobin (under development)

This module will use structures of hemoglobin to illustrate the role of allostery in the regulation of protein function.

Role of active site architecture in catalysis: GTP hydrolysis by G-proteins (under development)

This module will use the active site of a heterotrimeric G-protein as a model for illustrating how the precise arrangement of different amino acid functional groups within the 3D space of an enzyme active site is critical for facilitating reaction catalysis.

Holding a molecule in your hand: 3D printed models as tangible representations of protein structure

Protein molecules are the invisible machines of our molecular world-- beyond than simply being tasty, they are critical for biological function (and life!). However, much of how we study and interact with protein molecules tends to be in the digital world, by using different software visualization tools to manipulate the 3D object. Imagine being able to hold a protein in your hand-- turn it around, poke at it, examine its intricacies to understand how it works. The goal of this project is to utilize 3D printing technology to design 3D models and associated learning materials for teaching the following topics:

Active site architecture

Understanding how the unique 3D arrangement of chemical functionalities (be it amino acids or nucleic acids) within an active site results in catalysis is a fundamental part of biochemistry. This project aims to take advantage of examples of proteins and catalytic RNAs that can execute similar chemistries using vastly different active sites/functional groups. This provides an amazing opportunity to examine how the 3D arrangement of functional groups (even from different macromolecules!) in an active site is critical for its function! This project aims to:

  • design and fabricate models of catalytically similar but structurally distinct active sites
  • develop an in-class activity (with guiding questions for discussion) around these models
  • assess the impact of these models on student understanding of active site architecture and catalysis