| TAZ-TFM-2025-086 |
Desarrollo de algoritmos para el análisis de datos experimentales obtenidos mediante espectroscopía de absorción en equilibrio y resuelta en el tiempo
Asensio Franco, Mario
Medina Trullenque, María Milagros (dir.) ; Ciria Cosculluela, José Carlos (dir.)
Universidad de Zaragoza,
CIEN,
2025
Máster Universitario en Biofísica y Biotecnología Cuantitativa / Master in Biophysics and Quantitative Biotechnology
Abstract: Proteins in general, and enzymes in particular, are indispensable for supporting the development and reproduction of all forms of living beings. In addition to their key roles as biomolecules of life, scientists also investigate how to enhance their potential in biotechnological synthesis, bioremediation, or food industries as well as their biomedical applicability. Nonetheless, their rational use for those applications can only happen after a deep knowledge about their interplay with other molecules and the reactions occurring as a consequence of such interactions.
In this line, the main objective of this project is to develop software capable of analyzing experimental data generated by differential spectroscopy and multiwavelength time-resolved absorption spectroscopy using stopped-flow. Differential spectroscopy is useful for studying proteins because it captures subtle changes in absorbance of particular chromophores due to structural or environmental changes, allowing monitoring ligand binding and conformational changes. Multiwavelength time-resolved absorption spectroscopy using stopped-flow provides real-time kinetic data across multiple wavelengths, enabling researchers to study rapid reactions, identify intermediates and understand processes such as enzyme catalysis and ligand interactions. They offer information about protein/enzyme behavior and particular reaction mechanisms.
Currently, most of the software used to analyze results obtained from these techniques is mainly proprietary. This poses some issues: there is a license fee (which hinders their use in teaching), it is linked to the equipment manufacturer (generates dependence), the software is not open-source (it cannot be adapted to particular or evolving necessities) and tend to be not user-friendly.
Therefore, as an open-source alternative, three different software were here developed: DAIPProLi (Determination of Affinity of Interaction Parameters between Protein and Ligand), KiPaD (Kinetic Parameters Determination) and AKiPa (Analysis of Kinetic Parameters). DAIPProLi is aimed to analyze data from differential spectroscopy, whereas KiPaD and AKiPa are both aimed to analyze data from multiwavelength time-resolved absorption spectroscopy using stopped-flow. They are openly accessible to the community through the unizar-flav GitHub repository (https://github.com/unizar-flav).
All these tools display similar performance to that of proprietary software and solve the issues aforementioned. Furthermore, as they are open-source software, they allow students and young researchers to familiarize themselves with the numerical methods of analysis employed in the particular studied methodologies. The software produced here will be immediately used in practicums for students in the Informatics and Biophysics courses of the Biotechnology degree program at the University of Zaragoza in the coming years.
In this line, the main objective of this project is to develop software capable of analyzing experimental data generated by differential spectroscopy and multiwavelength time-resolved absorption spectroscopy using stopped-flow. Differential spectroscopy is useful for studying proteins because it captures subtle changes in absorbance of particular chromophores due to structural or environmental changes, allowing monitoring ligand binding and conformational changes. Multiwavelength time-resolved absorption spectroscopy using stopped-flow provides real-time kinetic data across multiple wavelengths, enabling researchers to study rapid reactions, identify intermediates and understand processes such as enzyme catalysis and ligand interactions. They offer information about protein/enzyme behavior and particular reaction mechanisms.
Currently, most of the software used to analyze results obtained from these techniques is mainly proprietary. This poses some issues: there is a license fee (which hinders their use in teaching), it is linked to the equipment manufacturer (generates dependence), the software is not open-source (it cannot be adapted to particular or evolving necessities) and tend to be not user-friendly.
Therefore, as an open-source alternative, three different software were here developed: DAIPProLi (Determination of Affinity of Interaction Parameters between Protein and Ligand), KiPaD (Kinetic Parameters Determination) and AKiPa (Analysis of Kinetic Parameters). DAIPProLi is aimed to analyze data from differential spectroscopy, whereas KiPaD and AKiPa are both aimed to analyze data from multiwavelength time-resolved absorption spectroscopy using stopped-flow. They are openly accessible to the community through the unizar-flav GitHub repository (https://github.com/unizar-flav).
All these tools display similar performance to that of proprietary software and solve the issues aforementioned. Furthermore, as they are open-source software, they allow students and young researchers to familiarize themselves with the numerical methods of analysis employed in the particular studied methodologies. The software produced here will be immediately used in practicums for students in the Informatics and Biophysics courses of the Biotechnology degree program at the University of Zaragoza in the coming years.
Tipo de Trabajo Académico: Trabajo Fin de Master
Permalink:
El registro pertenece a las siguientes colecciones:
Academic Works > Trabajos Académicos por Centro > facultad-de-ciencias
Academic Works > End-of-master works