Molecular Biology Meets the Learning Sciences: Visualizations in Education and Outreach

A Concise Review of Biomolecule Visualization

The structural characteristics of biomolecules are a major focus in the field of structural biology. Molecular visualization plays a crucial role in displaying structural information in an intuitive manner, aiding in the understanding of molecular properties. This paper provides a comprehensive overview of core concepts, key techniques, and tools in molecular visualization. Additionally, it presents the latest research findings to uncover emerging trends and highlights the challenges and potential directions for the development of the field.

The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern

Due to the COVID-19 pandemic the virus responsible, SARS-CoV-2, became a source of intense interest for non-expert audiences. The viral spike protein gained particular public interest as the main target for protective immune responses, including those elicited by vaccines. The rapid evolution of SARS-CoV-2 resulted in variations in the spike that enhanced transmissibility or weakened vaccine protection. This created new variants of concern (VOCs). The emergence of VOCs was studied using viral sequence data which was shared through portals such as the online Mutation Explorer of the COVID-19 Genomics UK consortium (COG-UK/ME). This was designed for an expert audience, but the information it contained could be of general interest if suitably communicated. Visualisations, interactivity and animation can improve engagement and understanding of molecular biology topics, and so we developed a graphical educational resource, the SARS-CoV-2 Spike Protein Mutation Explorer (SSPME), which used interactive 3D molecular models and animations to explain the molecular biology underpinning VOCs. User testing showed that the SSPME had better usability and improved participant knowledge confidence and knowledge acquisition compared to COG-UK/ME. This demonstrates how interactive visualisations can be used for effective molecular biology communication, as well as improving the public understanding of SARS-CoV-2 VOCs.

Using Molecular Visualisation Techniques to Explain the Molecular Biology of SARS-CoV-2 Spike Protein Mutations to a General Audience

Since the COVID-19 pandemic started in 2019, the virus responsible for the outbreak-SARS-CoV-2-has continued to evolve. Mutations of the virus' spike protein, the main protein driving infectivity and transmissibility, are especially concerning as they may allow the virus to improve its infectivity, transmissibility, and ability to evade the immune system. Understanding how specific molecular changes can alter the behaviour of a virus is challenging for non-experts, but this information helps us to understand the pandemic we are living through and the public health measures and interventions needed to bring it under control. In response to communication challenges arising from the COVID-19 pandemic, we recently developed an online educational application to explain the molecular biology of SARS-CoV-2 spike protein mutations to the general public. We used visualisation techniques such as 3D modelling and animation, which have been shown to be highly effective teaching tools in molecular biology, allowing the viewer to better understand protein structure, function, and dynamics. We also included interactive elements for users to learn actively by engaging with the digital content, and consequently improve information retention.This chapter presents the methodological and technological framework which we used to create this resource, the 'SARS-CoV-2 Spike Protein Mutation Explorer' (SSPME). It explains how molecular visualisation and 3D modelling software were used to develop accurate models of relevant proteins; how 3D animation software was used to accurately visualise the dynamic molecular processes of SARS-CoV-2 infection, transmission, and antibody evasion; and how game development software was used to compile the 3D models and animations into a comprehensive, informative interactive application on SARS-CoV-2 spike protein mutations. This chapter indicates how cutting-edge visualisation techniques and technologies can be used to improve science communication about complex topics in molecular biology and infection biology to the general public, something that is critical to gaining control of the continuing COVID-19 pandemic.

Development and use of augmented reality models to teach medicinal chemistry

BACKGROUND AND PURPOSE

Students in the doctor of pharmacy curriculum have varied backgrounds in their chemical training and also their ability to make mental conversions from two-dimensional chemical representations, on lecture slides or textbook images, to three-dimensional cognitive understanding. In order to bridge the gap, augmented reality (AR) models were developed to provide an alternative learning medium for the students. AR was selected to take advantage of the ubiquitous presence of smartphones, without incurring the expense of Virtual Reality hardware.

EDUCATIONAL ACTIVITY AND SETTING

AR models were developed and introduced in the classroom in three phases. Student survey responses were used to improve the utility of the models in between phases. Active learning exercises were developed that required both individual and group interactions to complete.

FINDINGS

An optimized AR model creation workflow was developed that allowed each AR model to be created and posted in about 30 min. Depending on the phase of the study, 69% to 88% of the students found the AR models easy to use and 58% to 83% wanted to see more AR models used in future lectures. A majority (76%) of the students viewed the AR models on their smartphones.

SUMMARY

Augmented reality modules were created for use in medicinal chemistry courses in the pharmacy curriculum. Models were introduced in phases and included iterative improvements based on student feedback. The AR exercises provided active learning opportunities and were well received. The majority of students would like additional AR modules used in the course.

Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships

Ensuring undergraduate students become proficient in relating protein structure to biological function has important implications. With current two-dimensional (2D) methods of teaching, students frequently develop misconceptions, including that proteins contain a lot of empty space, that bond angles for different amino acids can rotate equally, and that product inhibition is equivalent to allostery. To help students translate 2D images to 3D molecules and assign biochemical meaning to physical structures, we designed three 3D learning modules consisting of interactive activities with 3D printed models for amino acids, proteins, and allosteric regulation with coordinating pre- and post-assessments. Module implementation resulted in normalized learning gains on module-based assessments of 30% compared to 17% in a no-module course and normalized learning gains on a comprehensive assessment of 19% compared to 3% in a no-module course. This suggests that interacting with these modules helps students develop an improved ability to visualize and retain molecular structure and function.

Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.

Student Understanding of DNA Structure-Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure-function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure-function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA supercoiling dynamics. We also designed accompanying assessments to gauge student learning. Students responded favorably to the modules and showed normalized learning gains of 49% with respect to their ability to understand and relate molecular structures to biochemical functions. By incorporating accurate 3D printed structures, these modules represent a novel advance in instructional design for biomolecular visualization. We provide instructors with the materials necessary to incorporate each module in the classroom, including instructions for acquiring and distributing the models, activities, and assessments. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):303-317, 2019.

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.