ITQB: MS - MA Dissertations
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- Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulationsPublication . Vitória, Sara Moreno Jorge; Baptista, António"Photosystem II subunit S (PsbS) plays a central role in non-photochemical quenching (NPQ), a key photoprotective mechanism that allows plants to dissipate excess absorbed energy under fluctuating light. Acting as a pH sensor, PsbS undergoes protonation-dependent conformational changes triggered by lumen acidification, but the molecular determinants of its activation and dimerization remain still not fully understood. In this study, we employ constant pH molecular dynamics (CpHMD) simulations to investigate the protonation behaviour, conformational dynamics, and pH-dependent dimerization free energies of PsbS. Protonation states of titratable residues were sampled across a range of pH values (3-8), allowing to construct titration curves and estimate residue p𝐾a shifts. These revealed positively shifted p𝐾a values for several lumen-exposed glutamates, which can act as pH sensors in the physiological window of pH 5–6. Protonation correlation analysis further indicated the presence of complex networks encompassing both lumenal and stromal residues, suggesting long-range communication across the membrane in both monomeric and dimeric states.(...)"
- Molecular modeling study of β-lactoglobulin dimerization: a first step to hypoallergen design for immunotherapyPublication . Rocha, Lucie da; Baptista, António; Campos, Sara"Milk and its derivatives are important worldwide food sources, particularly for infant nutrition, but face a major health complication: some of their proteins are allergens, especially β-lactoglobulin (BLG), a major component of bovine milk. The fate of BLG upon ingestion remains unsettled, being unclear how extensive BLG proteolysis is and how it affects allergenicity. The fact that proteolytic resistance and antigenic response remain related even for non-oral administration suggests that they are not causally related but rather reflect an underlying common feature.(...)"