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DOI

Cloud-based tutorials on biomolecules of Colombia's biodiversity

Department of Biological Science, Universidad de los Andes, Bogotá, Colombia.

Product and Process Design Group, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia.

Introduction

This is a set of eight tutorials on the structure, function and interaction of biomolecules with some important receptors for distance learning using the Google Colab. In addition, this series of tutorials highlight and make visible the value-added biomolecules present in Colombia's plant biodiversity.

These tutorials were created between February to August 2023 as part of the open repository project for cloud-based hands-on computer labs for STEM education. Each tutorial was developed for use in a 16-week undergraduate course called molecular biology within the Department of Biological Sciences, and in a graduate course titled artificial intelligence in biocatalysis as part of the Master' program in Biological Sciences and the undergraduate programme in chemical and food engineering at Universidad de los Andes.

The tutorials integrated into the courses consist of four main sections. The initial section provides an introduction that highlights the significance of the molecule and its prevalence in Colombia’s biodiversity. The second section focuses on the characterization of the chemical structure of the molecule of interest. This is followed by a detailed description of the receptor to which the molecule binds, including the individual components of its structure. The final section features an activity designed to reinforce the learning acquired from the tutorial by applying it to another molecule that interacts with the same receptor as the studied molecule.

Description of the tutorials

The following is a brief of each tutorial, along with the receptor used for each biomolecule.

Tutorials Title Receptor
Tutorial_00 Open In Colab Google Colab warm-up tutorial
Tutorial_01 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule galantamine Acetylcholinesterase [1]
Tutorial_02 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule kaempferol DAPK1 [2]
Tutorial_03 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule quercetin DAPK1 [2]
Tutorial_04 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule resveratrol QR2 [5]
Tutorial_05 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule luteolin Tankyrase 2 [3]
Tutorial_06 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule apigenin Tankyrase 2 [3]
Tutorial_07 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule epicatechin Ara h8 [4]
Tutorial_08 Open In Colab Exploring Colombia's rich biodiversity: A closer look at the biomolecule cannabidiol CA14 [6]

Authors

Juan Fernando Meza, Cielo Leon Ramos, Francisco Bohorquez Martinez, Wilson Rodriguez Escucha, Adriana Bernal Giraldo, María Domínguez Cuenca, César Ramírez Sarmiento, María Francisca Villegas and Andrés Gonzalez Barrios.

Cite us!

If you use these tutorials in your research/teaching, please cite us!:

Meza J, Leon C, Bohorquez F, Rodriguez W, Bernal A, Domínguez M, Ramírez C, Villegas F, Gonzalez A (2024) Development and implementation of cloud-based tutorials on biomolecules of Colombia’s biodiversity.Unpublished.

Contributions and Code of Conduct

Please read our rules on Contributions and Code of Conduct before making any changes.

References

  1. Cheung, J., Rudolph, M. J., Burshteyn, F., Cassidy, M. S., Gary, E. N., Love, J., ... & Height, J. J. Structures of human acetylcholinesterase in complex with pharmacologically important ligands. Journal of medicinal chemistry. 2012; 55(22), 10282-10286.
  2. Yokoyama, T., Kosaka, Y., & Mizuguchi, M. Structural insight into the interactions between death-associated protein kinase 1 and natural flavonoids. Journal of medicinal chemistry. 2015; 58(18), 7400-7408.
  3. Narwal, M., Haikarainen, T., Fallarero, A., Vuorela, P. M., & Lehtiö, L. (2013). Screening and structural analysis of flavones inhibiting tankyrases. Journal of medicinal chemistry, 56(9), 3507-3517.
  4. Offermann, L.R., Yarbrough, J., McBride, J., Hurlburt, B.K., Maleki, S.J., Pote, S.S., Chruszcz, M. Structure of PR-10 Allergen Ara h 8.01. Protein Data Bank. 2024. 6AWV. https://www.rcsb.org/structure/6AWV.
  5. Buryanovskyy, L., Fu, Y., Boyd, M., Ma, Y., Hsieh, T. C., Wu, J. M., & Zhang, Z. Crystal structure of quinone reductase 2 in complex with resveratrol. Biochemistry. 2004; 43(36), 11417-11426.
  6. Cao, S., Kang, S., Mao, H., Yao, J., Gu, L., & Zheng, N. (2022). Defining molecular glues with a dual-nanobody cannabidiol sensor. Nature communications, 13(1), 815.