Teaching Enzyme Catalysis Using Interactive Molecular Dynamics in Virtual Reality
Teaching Enzyme Catalysis Using Interactive Molecular Dynamics in Virtual Reality
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DOI：
10.1021/acs.jchemed.9b00181
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发表时间：
2019-11-01
影响因子：
3
通讯作者：
Glowacki, David R.
中科院分区：
文献类型：
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作者：
Bennie, Simon J.;Ranaghan, Kara E.;Glowacki, David R.
在过去的几年里，虚拟现实（VR）的重新出现导致了价格实惠，高质量的商品硬件，可以提供新的方式来教学，交流和参与复杂的概念。在高等教育环境中，这些沉浸式技术可以帮助甚至取代传统的方法，如分子模型、教科书图像和传统的基于屏幕的计算环境，来教授复杂的分子主题。在这项工作中，我们描述了一项涉及22名英国三年级本科化学学生的研究，他们参加了传统的计算化学课程，并辅以我们设计的额外组件，利用VR （iMD-VR）中的实时交互分子动力学模拟。利用我们最近描述的开源iMD-VR框架的灵活性，学生们被要求在iMD-VR中完成三个简短的任务：(1)利用密度泛函数理论计算得到的力对choris酸分子进行交互重排以预苯；(2)利用实时计算的分子力学力使choris酸与活性位点choris酸突变酶解结；(3)利用实时分子力学力实现choris酸与choris酸突变酶的对接。一项学生调查显示，大多数学生发现iMD-VR组件比传统方法更吸引人，而且它还提高了他们对教育成果的感知，并提高了他们在计算科学领域继续学习的兴趣。
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.