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Author Ferreiro García, Miguel |
Abstract One of the challenges of structural bioinformatics is the comparative analysis of protein families. Currently there are robust software for aligning three-dimensional protein structures, however, the same does not happen when it comes to analyzing these overlaps. The objective of this project is to develop a tool capable of generating a comprehensible representation, and analyzable by the user, of a superposition of protein structures of the same family. In this way, the family can be analyzed, allowing a greater understanding and providing a new approach to the structure-function relationship of enzymes. To create these representations, the celestial coordinate system used in star maps has been used as inspiration, with which it is intended to approach the problem from a new perspective that allows increasing the resources available in the field of protein engineering. The result has been a computer tool, called EASiMap, capable of extracting the spherical coordinates of a superposition of protein structures using as a reference the position of the substrate in the catalytic center of the enzymes. For the representation of these coordinates, a web server has been created in which "maps" of the protein families can be viewed, offering a new representation system that helps in the comparative analysis of the different families. From the tests of this new system, patterns of structural motifs have been discovered in the family of Glycosyl Hydrolases 1 that may mark the starting point for future research. In addition, the program has generated other results beyond those originally sought that can contribute more information to the research in this field, it is about the structural conservation of the different positions of the protein, a property that may help define the importance of each position in relation to the function of the enzyme. On the other hand, although the system was designed to study the environment of the active center of the enzyme, it has been seen that by observing the complete structure of the overlapping family, structural patterns can be detected that deserve to be studied in order to better understand the protein folding and enzyme – substrate interactions. In short, it is a new representation system for protein families, which offers a different perspective, and allows a greater level of understanding of protein structures and their relationship with function. |
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Director Biarnés Fontal, Xavier |
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Degree IQS SE - Master’s Degree in Bioengineering |
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Date 2020-07-15
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