Diogo Ruivo dos Santos Vila Viçosa

    Ongoing Projects


  • Inclusion of pH effects in molecular modelling of lipid bilayers


  • membrane

    The lipid bilayer is the basic structural component of biological membranes. Membrane protein function is often strongly affected by the chemical and physical properties of the bilayer, which in turn depend on the composition of lipids and their complex interactions at the molecular level. A detailed description of a lipid bilayer at the atomic level has to take in consideration all important factors that affect in some way the membrane behavior and stability. pH is recognizably one of these factors even though it is usually forgotten due to the high complexity in terms of modeling. Changes in pH are usually associated with (de)protonation in key titrable groups present in the polar head of some phospholipids that constitute the bilayer. The resulting changes in the electrostatic environment will influence strongly the very structure of the bilayer allowing for the appearance of certain phenomena, like lipid phase transition and microdomain formation. Our objective is to apply the stochastic titration constant-pH MD methodology to the study of lipid protonation in bilayers.





    CV

  • Diploma in Biochemistry, Faculdade de Ciêcias da Universidade de Lisboa - 2005-2008

  • MSc in Biochemistry, Faculdade de Ciêcias da Universidade de Lisboa - 2008-2010


  • Publications

  • Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers, Santos, H. A. F., Vila-Viçosa, D., Teixeira, V. H., Baptista, A. M., Machuqueiro, M. J. Chem. Theory Comput., 2015, 11, 5973-5979.

  • Wittig Reaction: Domino Olefination and Stereoselectivity DFT Study. Synthesis of the Miharamycins’ Bicyclic Sugar Moiety Cachatra, V., Almeida, A., Sardinha, J., Lucas, S. D., Gomes, A., Vaz, P. D., Florêncio, M. H., Nunes, R., Vila-Viçosa, D., Calhorda, M. J., Rauter, A. P. Org. Lett., 2015, 17:5622-5625.

  • Luminescent Di- and Trinuclear Boron Complexes Based on Aromatic Iminopyrrolyl Spacer Ligands: Synthesis, Characterization, and Application in OLEDs Suresh, D., Gomes, C. S. B., Lopes, P. S., Figueira, C. A., Ferreira, B., Gomes, P. T., Di Paolo, R. E., Maçanita, A. L., Duarte, M. T., Charas, A., Morgado, J., Vila-Viçosa, D., Calhorda, M. J. Chem. Eur. J., 2015, 21: 9133–9149.

  • Constant-pH MD Simulations of an Oleic Acid Bilayer Vila-Viçosa, D., Teixeira, V. H., Baptista, A. M., Machuqueiro, M. J. Chem. Theory Comput., 2015, 11, 2367-2376.

  • Treatment of ionic strength in biomolecular simulations of charged lipid bilayers Vila-Viçosa, D., Teixeira, V. H., Santos, H. A. F., Baptista, A. M., Machuqueiro, M. J. Chem. Theory Comput., 2014, 10, 5483-5492.

  • Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?, D. Vila-Viçosa, O. Francesconi, M. Machuqueiro, Beilstein J. Org. Chem., 2014 , 10, 1513-1523.

  • Protonation of DMPC in a bilayer environment using a linear response approximation, V. H. Teixeira, D. Vila-Viçosa, A. M. Baptista, M. Machuqueiro, J. Chem. Theory Comput., 2014, 10, 2176-2184.

  • A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior, S. G. Estácio, H. Krobath, D. Vila-Viçosa, M. Machuqueiro, E.I. Shakhnovich, P.F.N. Faísca, PLoS Comput. Biol., 2014, 10, 1-17.

  • Dinuclear Zinc N-heterocyclic Carbene Complexes for either the Controlled ROP of lactide or the Controlled Degradation of Polylactide Under Mild Conditions, C. Fliedel, D. Vila-Viçosa, M. J. Calhorda, S.l Dagorne, T. Avilés, ChemCatChem, 2014, 6, 1357-1367.

  • Conformational Study of GSH and GSSG Using Constant-pH Molecular Dynamics Simulations, D. Vila-Viçosa, V. H. Teixeira, H. A. F. Santos, M. Machuqueiro, J. Phys Chem. B, 2013, 117, 7507-7517.

  • Can self-assembly of copper(II) picolinamide building blocks be controlled?, M. Đakovic, D. Vila-Viçosa, N. A. G. Bandeira, M. J. Calhorda, B. Kozlevcar, Z. Jaglicic, Z. Popovic, CrystEngComm, 2013, 15, 8074-8087.

  • Reversibility of Prion Misfolding: Insights from Constant-pH Molecular Dynamics Simulations, D. Vila-Viçosa, S.R.R. Campos, A.M. Baptista, M. Machuqueiro, J. Phys. Chem. B, 2012, 116, 8812-8821.

  • Coordination-driven self-assembly of thiocyanate complexes of Co(II), Ni(II) and Cu(II) with picolinamide: a structural and DFT study, M. Đakovic, D. Vila-Viçosa, M. J. Calhorda, Z. Popovic, Cryst. Eng. Comm., 2011, 13, 5863-5871.