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THE USE OF 3D ENVIRONMENT TO TEACH LIGAND-PROTEIN INTERACTIONS

C. Rius-Alonso, Y. González Quezada

Universidad Nacional Autónoma de México (MEXICO)
The use of 3D visualization is a powerful tool for teaching chemistry. At the Faculty of Chemistry, (Universidad Nacional Autónoma de México) UNAM, we have implemented several courses with the aid of 3D visualization with videos, to teach the interaction of ligands with proteins.

Influenza is one of the most abundant acute respiratory diseases affecting people worldwide of all age groups and social backgrounds. Frequent seasonal epidemics lead to increased morbidity and, in more severe cases, mortality on a global scale. Annually, up to 10% among the world population is affected by symptomatic influenza infection.

Binding of the influenza virus to the host cell is primarily attributed to the hemagglutinin (HA) glycoprotein. HA receptor-binding properties are a critical determinant of influenza evolution and are influenced by several factors such as glycosylation, also the neuraminidase is very important to release the virus from the infected cell, neutralizing antibodies, and inter-residue atomic interactions.

The availability of protein's structural models found at the Research Collaboratory for Structural Bioinformatics (RCSB) and the Protein Data Bank (PDB), is a key element to understand the biological processes at the molecular level. In generating homology models from amino acid sequences, it is important to establish the fidelity and quality of each model. In producing experimental or theoretical models of protein structures, it is always relevant to assess template accuracy and reliability before proceeding to further analyses.

During our course, we teach students to perform the docking of the ligand, inside the active site of the neuraminidase, and simulate mutations of the amino acids at the active sites in different positions, to evaluate the efficiency of the antiviral drugs in mutated influenza virus. Saving the information of the docking dynamics in video, allow students to retrieve the information in a visual way, helping them in the process of learning complex interactions intuitively. The visualization and modeling together with the information about the proteins are employed in an active learning strategy to assist students in the understanding of enzyme structural features and the molecular basis of ligand-protein interaction.

This work was partially supported by a grant from Dirección General de Asuntos del Personal Académico (DGAPA) Universidad Nacional Autónoma de México PE205313 and IOCD (International Organization for Chemical Science in Development).