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Study of the interaction between the amyloid b peptide and the S100B protein using computational techniques
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Resumo(s)
Amyloid beta peptides (Ab) are associated with several neurodegenerative diseases, notoriously with Alzheimer’s disease (AD). In the AD brain, Ab peptides are produced as result of misprocessing of APP which results in the production of the variants with multiple lengths, including the highly amyloidogenic Ab42. The latter aggregates extracellularly, forming the so called amyloid plaques, which constitute one of AD’s landmarks. The formation of these aggregates, which are neurotoxic, leads to an inflammatory response releasing several inflammatory citokynes, among which is S100B. S100B is a small homodimeric protein from the S100 protein family that binds four Ca2+ per dimer in EF-hands motifs and which also comprises an interfacial metal binding site for Cu2+ and Zn2+. It has signaling and pro-inflammatory functions in late AD stages but recent findings implicate this protein as a regulator of proteostasis and metallostasis in the brain. S100B was described to act as an extracellular chaperone counteracting Ab42 aggregation in a Ca2+ dependent manner. Binding of Ca2+ to S100B induces conformational changes which result in the exposure of a binding cleft within the dimer interface that is able to mediate protein:protein interactions. Experimental data from structural NMR experiments revealed that Ab42 interacts with S100B through this region, involving Lys28 and Ile31. However, the atomic details of this interaction are not well known. The main goal of this thesis is therefore to elucidate these details, through the use of computational techniques, namely docking calculations and molecular dynamics simulations, guided by experimental evidence. Initially, quantum mechanics calculations were performed to parametrize the metal coordination centers of S100B. At the start of this work, we used molecular docking calculations to obtain starting configurations of the complex for molecular dynamics simulations. As such, we used HADDOCK, a docking tool developed to handle protein-protein interactions. After obtaining and selecting promising structures of the complex, we used them as starting configurations of long (1 ms) molecular dynamics simulations. Most simulations converged and the conformational space obtained for the different binding modes (BMs) was explored using several analysis. We focused our attention at the interfaces formed by the a-helix rich region of Ab42, what we named the head group, where we identified hotspot interactions. We quantified the hydrophobic/hydrophilic nature of the interactions, using a newly devised SAShydro index property, and calculated the binding affinities between S100B and the Ab42 head region using molecular mechanics energies combined with Poisson-Boltzmann and solvation surface area (MM/PBSA). Two BMs (BM1 and 2) showed very stable interfaces, where the two key residues were packed inside the S100B interface and with Lys28 stabilized by neighboring acidic residues, which provided an increase in the Coulombic contribution to the binding energy. The main difference between BM1 and BM2 came from a the topological arrangement of the Ab42 tail region, where in BM1 it was mostly unstructured, while in BM2, it retained a large meta-stable a-helix. The fact that the peptide is only partially folded in solution creates a huge challenge to model its conformational space which is inaccessible to most computational techniques. However, with the help of all experimental evidence available, we were able to devise a protocol to direct both the conformational space of the peptide and the geometry of the final complex configurations. Altogether, we were able to explore successful binding modes which providedatomistic information about the specific interactions that are stabilizing the complex.
Descrição
Tese de mestrado, Bioquímica (Bioquímica) Universidade de Lisboa, Faculdade de Ciências, 2020
Palavras-chave
Ab S100B HADDOCK Dinâmica Molecular Configuração de ligação Teses de mestrado - 2020