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Structural and functional studies of proteins involved in neurodegenerative diseases using normal mode analysis and molecular dynamics

Abstract

Despite the great number of research in neurodegenerative diseases, these pathologies and their molecular mechanisms are not well understood nowadays. The better understanding of the molecular mechanisms involved in neurodegenerative diseases (as Parkinson's, AD, ALS, Huntington's Disease (HD), Spinal muscular atrophy (SMA)) can help the development of new drugs and treatments. Knowledge of the 3D structure of proteins is very important in order to decipher their function and to find other macromolecular partners with whom they may interact. In this context, we aim to investigate these diseases from the molecular focus (involved proteins), studing them from several aspects: structure, dynamic, aggregation, function and interaction. We intend to study different aspects: evolution, patterns searching (bioinformatics), folding and aggregates studies, protein-ligand and protein-protein interaction and drug design. This hierarchical investigation allows a better understanding and a deep study of the molecular process of these disorders. This research project has the following main objectives: i) to understand the molecular interactions involved in the formation of aggregates of proteins involved in neurodegenerative diseases, ii) to identify patterns (as flexibility and the solvent accessible surface) in proteins and their respective mutants that are related with different neurodegenerative diseases, iii) to identify possible allosteric binding sites through global conformational changes (movements) of the proteins involved in neurodegenerative diseases, iv) to investigate the docking of these proteins with compound candidates for allosteric inhibitors. The research project will be developed in the Laboratory of Computational Biology and Bioinformatics UFAB. The study of mechanisms and proteins involved in pathologies can assist in understanding them and in the development of new drugs and treatments. (AU)

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