Facilitating student learning using a virtual protein studio

Executive summary

In contrast to “traditional” 2D-PowerPoint slides, emerging technology platforms built on computer game engines successfully capture the true 3D-nature of biomolecules. This project proposes that the incorporation of interactive 3D-models of complex molecular architectures in education enhances student learning by providing a unique hands-on experience of how the structure and dynamics of proteins govern their function. The tools discussed herein could favorable be incorporated in education programs within biotechnology, chemistry and medicine.

Figure 1. A protein structure used in the present project. To reach beyond this flat 2D-representation, a pilot virtual protein studio was set up for which the students could interact with the model in high-resolution 3D.

Course and context

The present project constitutes a pilot study that took place at KTH 2016-12-02. The outcome will be used as a foundation to develop my own teaching in the near future.

Aim

The main purpose of this project was to evaluate the impact on student learning when implementing emerging interactive 3D-technologies in education, using proteins of relevance for disease as a case study.

Material and Methods

Test group

A test group of a total of nine students with different backgrounds (6 from KTH and 3 from KI/SciLifeLab) was assembled. Two of the students were first-year PhD-students, whereas the remaining students were on an educational level corresponding to MSc-studies.
For reference, a 20 min PowerPoint presentation centered on how the structure and dynamics of proteins control their function was prepared.
A pilot virtual protein studio was created in close collaboration with the KTH Visualization Studio. Specifically, interactive 3D-prototypes of the same proteins discussed in the presentation above were prepared by downloading the corresponding structural files containing the atomic coordinates from the protein data bank (PDB) and through visualization in the interactive molecular modeling software YASARA.  3D-VR movies of aquaporin proteins were downloaded from YouTube and were made available to students by a mobile-VR solution (Figure 2b). Furthermore, protein structures were displayed using YASARA linked to a 4K stereoscopics system by JVC D-ILA 4K projectors  powered by a 2x Quadro FX 5800 graphical processor (referred to as “screen model”, Figure 2c). An interactive surface (referred to as “touch table”, Figure 2d) was generated by linking the software YASARA to a Microsoft PixelSense system. The virtual reality platform (Figure 2e) was achieved by the Unity computer game engine linked to a VR-HTC Vive system configured by the KTH Visualization Studio. The students were divided into four groups that alternated between different stations representing the different technologies implemented in the pilot (Figure 2b-e).

Figure 2. Implementing a virtual protein studio in teaching. Pictures from the pilot that took place at KTH 2016-12-02.

Evaluation

The impact on student learning was assessed by the following questionnaire:

Question 1 (Q1). Satisfaction

Q2. The teaching methodology helped my understanding of protein dynamics and engineering.

Q3A. How did the screen model help your learning?

Q3B. How did the touch-screen model help your learning?

Q4. Do you think the teaching tools should be implemented in a course?

Q5. Other comments

The students were specifically asked to evaluate the VR HTC-vive technology (Figure 2e) in question 5.

Results

  • A pilot for a virtual protein studio was successfully performed during a 2h lecture and with a time effort corresponding roughly to one man week (40 hours)
  • Utilizing emerging and interactive 3D-technological tools leads to enhanced student stimulation (Figure 3)
  • The investigated tools got different feedback (Figure 3)
  • VR-movies (Figure 2b) constitute valuable assets in teaching
  • The touch screen technology (Figure 2d) is suitable for project works in smaller groups
  • The VR-HTC vive technology represents the largest satisfaction in terms of experience – but requires the most effort from the teacher as structural coordinates currently have to be manually remodeled to fit the prerequisites of the Unity computer game engine
  • High-resolution 3D-interactive models (screen model, Figure 2c) represents an excellent trade-off between preparation effort and enhanced understanding and facilitated student learning (Figure 3)

Figure 3. Results from student survey.

Discussion

Simulations have been acknowledged as an important tool in medicinal education to facilitate complex learning processes such as dissection and surgery.1 The “anatomy” of chemistry and biotechnology would correspond to the detailed study of how the assembled building blocks of molecules dictate their function. However, representing and “dissecting” the 3D-nature of complex molecular architectures by traditional teaching tools is inherently difficult. Here, the ultimate experience would be represented by Virtual Reality environments, which have attracted a significant interest recently2 for a number of teaching subjects ranging from social sciences and mathematics to physics.

It could perhaps be expected that incorporating 3D-models of proteins and other molecules in chemistry and biotechnology education would be beneficial for student learning. The study herein corroborates this hypothesis by showing that a virtual protein studio may lead to enhanced student satisfaction (Figure 3a) and learning (Figure 3b-c). The potential to enhance motivation is emphasized by the following comments from the students:

“It felt like the molecules came out of the screen”

“I could touch parts at different depths inside the structure with my hands”

“Great lecture, very entertaining!”

“Really fun!”

“FUN!”

“I really look forward to the implementation of these teaching tools within education, even in chemistry classes.”

“It was a wonderful experience!”

Some challenges associated with the technologies are illuminated by the spread of the student opinions on the touch screen model (Figure 3). Here, some students experienced difficulties in interacting with the protein surface using their hands.

The VR HTC-vive technology was a preferred platform by the students:

“The VR was the best one!”

“The VR was awesome!”

However, the preparation of molecules for a “virtual world experience” requires manual programming in Unity, which constitutes a bottleneck. Thus, incorporation of interactive models in full 3D on high resolution screens represents an excellent tradeoff between effort and learning outcome.

Conclusion

The incorporation of true 3D-models of protein structures in teaching is associated with a positive impact on student understanding and learning, which could have important implications for education in chemistry, biotechnology and medicine.

Practice Points

Implementing 3D interactive models in teaching is greatly facilitated by the availability of university educational staff with technical expertise (e.g. KTH Visualization studio).
Preparation of lectures and exercises that incorporate VR-tools and 3D-models requires significantly more time and effort compared to “traditional” PowerPoint.
Careful planning is a prerequisite of unleashing the full potential of the technologies discussed herein; merely showing structures of proteins in 3D is not sufficient.

References

1. Nesbitt, C.I., Birdi, N., Mafeld, S. et al. The role of simulation in the development of endovascular surgical skills. Perspect Med Educ (2016) 5, 8-14.

2. Mikropoulos, T. A., Natsis, A. Educational virtual environments: A ten-year review of empirical research (1999–2009). Computers & Education (2011) 56, 769–780.

Contact

Per-Olof Syrén, Associate Professor in Chemistry for Life Sciences, KTH/Science for Life Laboratory
per-olof.syren@biotech.kth.se