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! 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.

Jan 9, 2019
BiochemAR

As anyone who has attempted to assemble furniture using only a set of drawings for instructions can attest, the use of only 2D images to navigate a 3D object can be tricky and problematic. In the classroom, this problem becomes particularly relevant when trying to teach students about the importance of 3D shape in dictating the function of biological molecules, such as proteins and nucleic acids. However, the tools to visualize 3D renderings of biological molecules remains limited to a subset of programs with varying ranges of usability. AR technology, on the other hand, has the potential to change the way instructors and students show and interact with virtual 3D models of biological macromolecules. In AR, a video display shows an overlay of a virtual 3D object projected over the real world-- in the case of Pokemon, a Pikachu can pop up in the middle of the road that one can walk around and "catch." But what about having 3D visualizations of important biological molecules pop up in class that one can rotate and zoom in on? Dr. Rou-Jia Sung, an assistant professor in Biology at Carleton College, has been working in collaboration with Dr. Andrew Wilson at Academic Technologies to develop BiochemAR, an AR-based app containing different 3D visualizations with accompanying classroom learning materials for 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.

Below are the learning modules that are ready for use and modules the team is interested in developing further:

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!

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.

Interested in using the potassium module for your course or developing new module ideas? Rou-Jia and Andrew are always interested in how the app is used/gathering feedback for improvement on future versions of the app. Please feel free to email Rou-Jia with any questions/thoughts/ideas for how to share the beauty of the 3D world these molecules live in!"