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Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality


 
 The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer
new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D
motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach
complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models,
textbook images, and traditional screen-based computational environments. In this work we describe a study involving
24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class
complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR
(iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building
on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory
in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement
of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations;
(2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces
calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics
forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional
approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field
of computational sciences.

