Teaching Enzyme Catalysis Using Interactive Molecular Dynamics in Virtual Reality

• Published in: Journal of chemical education Vol. 96; no. 11; pp. 2488 - 2496
• Main Authors: Bennie, Simon J, Ranaghan, Kara E, Deeks, Helen, Goldsmith, Heather E, O’Connor, Michael B, Mulholland, Adrian J, Glowacki, David R
• Format: Journal Article
• Language: English
• Published: Easton American Chemical Society and Division of Chemical Education, Inc 12.11.2019; Division of Chemical Education, Inc; American Chemical Society
• Subjects: Biochemistry; Catalysis; College students; Computation; Computational chemistry; Computer Simulation; Density functional theory; Education; Educational Objectives; Enzymes; Foreign Countries; Learner Engagement; Mechanics (physics); Molecular Biology; Molecular dynamics; Organic chemistry; Outcomes of Education; Preferences; Real time; Science education; Science Instruction; Student Attitudes; Student Surveys; Students; Teaching Methods; Time; Undergraduate Students; Virtual reality; United Kingdom; Graduate Education/Research; Enzymes; Molecular Biology; Theoretical Chemistry; Biochemistry; Computer-Based Learning; Undergraduate Research; Nanotechnology; Computational Chemistry
• ISSN: 0021-9584; 1938-1328
• DOI: 10.1021/acs.jchemed.9b00181

The reemergence of virtual reality (VR) in the past few years has led to affordable, high-quality commodity hardware that can offer new ways to teach, communicate, and engage with complex concepts. 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 22 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented by an additional component which we designed to utilize real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described, the students were given three short tasks to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from 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 student 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.