Estudio de la interacción de la proteína albumina sérica humana con diversos ligandos utilizando dinámica molecular

Abstract

The aim of this research project was to study the complex system between human serum albumin (HSA) protein and different ligands using molecular dynamics to analyse conformational changes in the protein-ligand interaction. Molecular files were obtained from a database and a Python algorithm was used to preprocess the structures through mutagenesis. Then, software was used to visualise the best model generated and molecular dynamics was run with GROMACS. The complexes were modelled with the CHARMMm36 and CGenFF force field. For the sample preparation, physiological aspects were applied such as: inclusion of protons into the system, creation of a unit cell, establishing the contour properties and the inclusion of water molecules. The dynamic properties of the complex interacting with constant temperature and constant pressure assemblies were established. For each phase, modelling was configured through mdp files where time integration parameters and coupling algorithms are assigned. The simulation was run for 10 nanoseconds and at the end the results were extracted through data files. Physical results describing each system were obtained. Also, RMSD and radius of gyration values describing the dynamics, showing differences in the values that occur during the interaction of the protein with each type of ligand. Very different values were shown for those measurements describing the structure and elasticity of the protein-ligand interaction. It was concluded that HSA has structural changes depending on the ligand with which it interacts that can increase or decrease its physical properties and it is recommended to make an extension of the analysis of the ligands in the binding sites.