ITQB: MM-Master Thesis
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- Parameterization of bacterial peptidoglycan for state-of-the-art molecular dynamics coarse-grain force fieldsPublication . Reis Catarino, João Filipe; Melo, Manuel"The cellwallisoneofthemostdefiningcharacteristicsofbacteria.Itplaysacrucialrole in cellintegritywhileregulatingthepassivetransportofmanynutrientsandproteins.The main culpritbehindthecellwallpropertiesisthepeptidoglycanpolymer.Itiscomposed of abackboneoftwoalternatingsugars(NAGandNAM)andapentapeptidelinkedto everyNAMsugar.Thispentapeptideiscapableofcross-linkingwithotherpeptidesto create largemeshes.(...)"
- Poking holes in membranes with coarse-grained simulationsPublication . Araújo, Ana CarolinaThe lipid membrane is a crucial structure as it plays many roles in the cell,such as regulation of metabolite transport.Ion fluxis typically controlled by membrane transporters but they can also leak through transient lipidpores.This regulation is essential for the maintenance of cell life.
- Ceramide in the Outer Mitochondrial Membrane and its Role in ApoptosisPublication . Vieira, Gonçalo Miguel Pinto Batista e Sá"Ceramides constitute a class of lipids found in different locations such as the outer mitochondrial membrane (OMM), whose permeabilization is a point-of-no-return in apoptosis. This phenomenon has been linked to the Voltage Dependent Anion Channel (VDAC), with which Ceramides can interact via a membrane-buried Glutamate residue in isoforms 1 and 2. To study the role of Ceramides in apoptosis, a Coarse Grain (CG) model of this lipid was created and subsequently optimized in terms of Solvent Accessible Surface Area and topology parameters. The latter were developed through a trial-and-error approach until the CG behavior resembled the atomistic references. The obtained parameters were further tested but results were inconclusive, probably due to the method used. Nevertheless, preliminary data demonstrated the model to properly interact with the Glutamate of VDAC."
- Simulating substrate binding sites in the S. aureus Type II NADH DehydrogenasePublication . Barriga, Rodrigo; Melo, Manuel"Type II NADH Oxidoreductase (NDH-2) from Staphylococcus aureus was established as a therapeutic target against the virulency of this bacterium and an alternative to treat Complex I-derived diseases. To accurately model interactions of NDH-2 with its substrates such as menaquinones and NADH, Coarse-Grain (CG) simulations were employed. "