Dataset Information

Peppy: A virtual reality environment for exploring the principles of polypeptide structure.

ABSTRACT: A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone ?/? angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.

SUBMITTER: Doak DG

PROVIDER: S-EPMC6933844 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Peppy: A virtual reality environment for exploring the principles of polypeptide structure.

Doak David G DG Denyer Gareth S GS Gerrard Juliet A JA Mackay Joel P JP Allison Jane R JR

Protein science : a publication of the Protein Society 20191111 1

A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structu ...[more]

PMID: 31622516

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Project description:Spatial navigation is influenced by landmarks, which are prominent visual features in the environment. Although previous research has focused on finding advantages of landmarks on wayfinding via experimentation; however, less attention has been given to identifying the key attributes of landmarks that facilitate wayfinding, including the study of neural correlates (involving electroencephalogram, EEG analyses). In this paper, we combine behavioral measures, virtual environment, and EEG signal-processing to provide a holistic investigation about the influence of landmarks on performance during navigation in a maze-like environment. In an experiment, participants were randomly divided into two conditions, Landmark-enriched (LM+; N = 17) and Landmark-devoid (LM-; N = 18), and asked to navigate from an initial location to a goal location in a maze. In the LM+ condition, there were landmarks placed at certain locations, which participants could use for wayfinding in the maze. However, in the LM- condition, such landmarks were not present. Beyond behavioral analyses of data, analyses were carried out of the EEG data collected using a 64-channel device. Results revealed that participants took less time and committed fewer errors in navigating the maze in the LM+ condition compared to the LM- condition. EEG analyses of the data revealed that the left-hemispheric activation was more prominent in the LM+ condition compared to the LM- condition. The event-related desynchronization/synchronization (ERD/ERS) of the theta frequency band, revealed activation in the left posterior inferior and superior regions in the LM+ condition compared to the LM- condition, suggesting an occurrence of an object-location binding in the LM+ condition along with spatial transformation between representations. Moreover, directed transfer function method, which measures information flow between two regions, showed a higher number of active channels in the LM- condition compared to the LM+ condition, exhibiting additional wiring cost associated with the cognitive demands when no landmark was available. These findings reveal pivotal role of the left-hemispheric region (especially, parietal cortex), which indicates the integration of available sensory cues and current memory requirements to encode contextual information of landmarks. Overall, this research helps to understand the role of brain regions and processes that are utilized when people use landmarks in navigating maze-like environments.

Dataset Information

Peppy: A virtual reality environment for exploring the principles of polypeptide structure.

Publications

Peppy: A virtual reality environment for exploring the principles of polypeptide structure.

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