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Undergraduate research experiences are increasingly important in biology education with efforts underway to provide more projects by embedded them in a course. The shift to online learning at the beginning of the pandemic presented a challenge. How could biology instructors provide research experiences to students who were unable to attend in-person labs? During the 2021 ISMB (Intelligent Systems for Molecular Biology) iCn3D Hackathon–Collaborative Tools for Protein Analysis–we learned about new capabilities in iCn3D for analyzing the interactions between amino acids in the paratopes of antibodies with amino acids in the epitopes of antigens and predicting the effects of mutations on binding. Additionally, new sequence alignment tools in iCn3D support aligning protein sequences with sequences in structure models. We used these methods to create a new undergraduate research project, that students could perform online as part of a course, by combining the use of new features in iCn3D with analysis tools in NextStrain, and a data set of anti-SARS-CoV-2 antibodies. We present results from an example project to illustrate how students would investigate the likelihood of SARS-CoV-2 variants escaping from commercial antibodies and use chemical interaction data to support their hypotheses. We also demonstrate that online tools (iCn3D, NextStrain, and the NCBI databases) can be used to carry out the necessary steps and that this work satisfies the requirements for course-based undergraduate research. This project reinforces major concepts in undergraduate biology–evolution and the relationship between the sequence of a protein, its three-dimensional structure, and its function.
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Combining 3D-Printed Models and Open Source Molecular Modeling of p53 To Engage Students with Concepts in Cell Biology
While understanding macromolecular structural elements and their roles in dictating cellular function is critical to grasp basic concepts in biology, it can be challenging for students to master this content—these elements naturally exist at the nanoscale and are not observable with the naked eye. Oftentimes this understanding is catalyzed by impactful illustrations and animations found online and in textbooks. In recent years, 3D printing technology has become readily accessible as an additional way to generate models and visualize entities of interest. In this report, we describe and discuss the efficacy of an approach using 3D-printed models in combination with online open-source molecular modeling analyses of the macromolecular structure of p53 to engage students with molecular concepts in cancer cell biology and human health. This pedagogy strategy has been successfully integrated into an upper-level undergraduate course at a primarily undergraduate institution and a graduate biology course at a public research university. We describe the potential benefits while providing tools for others to integrate this strategy into their teaching.
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- PAR ID:
- 10281341
- Date Published:
- Journal Name:
- Journal of Microbiology & Biology Education
- Volume:
- 21
- Issue:
- 3
- ISSN:
- 1935-7877
- Page Range / eLocation ID:
- 10
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1128/jmbe.v21i3.2161
