| Neurodegenerative diseases including Alzheimer's, Parkinson's disease, mad cow disease are among the most stubborn diseases. Its breakout in Europe caused a great loss and society turbulence and there have been intensive researches on prion about its origin and effective therapy in life science in recent years. It was found that prion which is made up of proteins exclusively is the main cause and it has two forms, i. e , normal form PrPc and abnormal one PrPsc. PrPc and PrPsc have great difference in secondary structure although the primary structure, namely, their amino acid sequence, is identical. The former has 40% a-helix and almost no B-sheet and the latter has 43%β-sheet and 30%a-helix. The transformation from PrPc to PrPsc caused by part of its a-helix changed into β-sheet is the direct cause of the neurodegenerative diseases. There are many theories and hypotheses on the mechanism of the transformation from PrPc to PrPsc, such as seed model, refolding model, protein X hypothesis, free radical theory, and so on. All kinds of theories cannot perfectly interpret the pathological mechanism of prion for no one of these theories can elucidate the infectious, hereditary and sporadic characteristics of prion.In this thesis we explored prion's pathological mechanism by quantum chemical calculation combined with bioinformation and proposed our hypothesis.Free radical theory assumes that some strongly active free radicals produced by respiration can probably attack proteins and cause oxidative damage in vivo. Prion has several Tyr residues, whose phenolic hydroxyl hydrogen is easily abstracted and forms free radical by the specially active hydroxyl group (.OH) in body. The Tyr. can link with Tyr, thus results in prion's aggregation with the extension of the reaction chain. By calculations, we find that the reaction between Tyr. and Tyr cannot occur because of its Gibbs free energy AG>0, which testify the defect of the free radical theory. But this hypothesis has some reasonable part because protein's damage caused by free radicals is common in vivo. Therefore, based on the hypothesis and physical organic chemistry, we propose our own mechanical hypothesis that the hydrogens of residues are abstracted by free radicals and theproteins become protein radicals, and this alters the conformation of peptide chain and results in the transformation from PrPc to PrPsc. By calculations we found that BDE of Ca-H is low and Ca-H is easily abstracted. The formed Ca-H radicals lead to the variations of the dihedral angles Φ and Ψ. Thus verified our own hypothesis.As for the calculation of small molecule's C-H BDE, density functional theory (DFT) B3LYP is employed. As for the calculation of macromolecule's C-H BDE, we adopt semiempirical AMI to optimize geometry and density functional theory (DFT) B3LYP to calculate single point energy because AMI has advantage of optimizing geometry and is economic in time, so AM1//B3LYP method is reliable to study C-H BDE of peptide.C-H BDE is a parameter for the strength of bond, whose value indicates the easiness of free radical formation. In order to investigate the effects of side chains and environment to C-H BDE, quantum chemical calculation was again used we found that the property of substituents , dihedral angles Φ and Ψ and temperature can all affect C-H BDE. In the secondary structure of peptide, dihedral angles Φ and Ψ are the essential factors of C-H BDE. Each pair of ( Φ , Ψ ) has unique BDE value which varies with the different combination of Φ and Ψ. Therefore, in the secondary structure of polypeptide, different conformations adopted by the protein are the main cause for their vulnerability against oxidative stress, and this could be used as a theoretical evidence to find the sites for protein radical.In brief, in this thesis we testified protein radical theory and proposed our own theory. This has great inspiring significance to elucidate the pathological mechanism and sporadicalness of prion protein. |
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