![]() ![]() A conversion of residues to toxic beta-sheets is observed in the optimized misfolded complex. The binding free energy and interactions in a complex of a misfolded prion with a native prion are first analyzed by MD and compared to a complex of two native conformers. The example of the prion - an intrinsically disordered protein - is studied, but the models can be generalized to other misfolding diseases. Protein misfolding is characterized by the formation of highly reactive beta-sheets oligomers leading to fibrillar macroscopic aggregates, which are studied with the models given herein that can be useful for the development of new immunotherapies against the Alzheimer's disease and prion, e.g. Outdated hypotheses on protein folding must be revised: More realistic molecular models, focusing not only on classical molecular dynamics (MD) but also on ab initio quantum mechanics (QM) at the molecular orbitals (MOs) scale, which is not experimentally achievable, are presented to improve our understanding of the thermodynamics of the protein-protein interactions leading to misfolding and neurodegenerative diseases for future drug design. A misfolded protein compared with its native state lacks its biological function resulting in cell dysregulations and often death. ![]()
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