António M. Baptista

PhD, Research Scientist (Investigador Principal)

Head of the Molecular Simulation Laboratory at ITQB.


Address

António M. Baptista
Instituto de Tecnologia Química e Biológica
Av. da República, EAN
2780-157 Oeiras
Portugal

Phone : +351-21-4469619
Fax : +351-21-4411277
E-mail :
WWW : http://www.itqb.unl.pt/~baptista

ORCID: http://orcid.org/0000-0002-7044-1210
ResearcherID: http://www.researcherid.com/rid/C-7246-2012
Scopus: http://www.scopus.com/authid/detail.url?authorId=7007078918
ResearchGate: https://www.researchgate.net/profile/Antonio_Baptista2
GoogleScholar: https://scholar.google.com/citations?user=qV4DT_UAAAAJ


Research interests

Current research


Refereeing


Publications

  1. Pires, M. J., Martel, P., Baptista, A., Petersen, S. B., Willson, R., Cabral, J. M. S. (1994) Improving protein extraction yield in reversed micellar systems through surface charge engineering. Biotechnol. Bioeng. 44:773-780.
  2. Anthonsen, H. W., Baptista, A., Drabløs, F., Martel, P., Petersen, S. B. (1994) The blind watchmaker and rational protein engineering. J. Biotechnol. 36:185-220.
  3. Anthonsen, H. W., Baptista, A., Drabløs, F., Martel, P., Petersen, S. B., Sebastião, M., Vaz, L. (1995) Lipases and esterases - a review of their sequences, structure and evolution. In Biotechnology Annual Review, vol. 1; El-Gewely, M. R. (Ed.), Elsevier, Amsterdam, pp. 315-371.
  4. Baptista, A., Brautaseth, T., Drabløs, F., Martel, P., Valla, S., Petersen, S. B. (1995) Electrostatic studies of carbohydrate active enzymes. In Progress in Biotechnology, vol. 10, "Carbohydrate Bioengineering". Petersen, S. B., Svensson, B., Pedersen, S. (Eds.), Elsevier, Amsterdam, pp. 181-204.
  5. Jones, R. A., Müller, T. B., Haraldseth, O., Baptista, A. M., Øksendal, A. N. (1996) Cerebrovascular changes in rats during ischemia and reperfusion: a comparison of BOLD and first pass bolus tracking techniques. Magn. Reson. Med. 35:489-496.
  6. Jones, R. A., Haraldseth, O., Baptista, A. M., Müller, T. B., Øksendal, A. N. (1997) A study of the contribution of changes in the cerebral blood volume to the haemodynamic response to anoxia in rat brain. NMR Biomed. 9:233-240.
  7. Martel, P. J., Baptista, A., Petersen, S. B. (1996) Protein electrostatics. In Biotechnology Annual Review, vol. 2; El-Gewely, M. R. (Ed.), Elsevier, Amsterdam, pp. 315-372.
  8. Sebastião, M. J., Martel, P., Baptista, A., Petersen, S. B., Cabral, J. M. S., Aires-Barros, M. R. (1997) Predicting the partition coefficients of a recombinant cutinase in polyethylene glycol/phosphate aqueous two-phase systems. Biotechnol. Bioeng. 56:248-257.
  9. Baptista, A.M., Martel, P.J., Petersen, S.B. (1997) Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins, 27:523-544.
  10. Jones, R. A., Haraldseth, O., Baptista, A. M., Müller, T. B., Øksendal, A. N. (1997) A study of the contribution of changes in the cerebral blood volume to the haemodynamic response to anoxia in rat brain. NMR Biomed. 10:59-66.
  11. Baptista, A.M., Jonson, P.H., Hough, E., Petersen, S.B. (1998) The origin of trypsin: evidence for multiple gene duplications in trypsins. J. Mol. Evol. 47:353-362.
  12. Martel, P.J., Soares, C.M., Baptista, A.M., Fuxreiter, M., Náray-Szabó;, G., Louro, R.O., Carrondo, M.A. (1999) Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods. J. Biol. Inorg. Chem. 4:73-86.
  13. Baptista, A.M., Martel, P.J., Soares, C.M. (1999) Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics. Biophys. J. 76:2978-2998.
  14. Mendes, J., Baptista, A.M., Carrondo, M.A., Soares, C.M. (1999) Improved modelling of side-chains in proteins with rotamer-based methods: a flexible rotamer model. Proteins, 37:530-543.
  15. Baptista, A.M., Soares, C.M. (2001) Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. J. Phys. Chem. B, 105:293-309.
  16. Mendes, J., Baptista, A.M., Carrondo, M.A., Soares, C.M. (2001) Incorporating implicit solvation in the self-consistent mean field theory method: application to sidechain modelling and prediction of folding free energies of protein mutants. J. Comp.-Aided Mol. Design, 15:721-740.
  17. Louro, R.O., Bento, I., Matias, P.M., Catarino, T., Baptista, A.M., Soares, C.M., Carrondo, M.A., Turner, D.L., Xavier, A.V. (2001) Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetrahaem cytochrome. J. Biol. Chem. 276:44044-44051.
  18. Teixeira, V.H., Soares, C.M., Baptista, A.M. (2002) Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail. J. Biol. Inorg. Chem. 7:200-216.
  19. Baptista, A. M. (2002) Comment on "Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines". J. Chem. Phys. 116:7766-7768.
  20. Baptista, A. M., Teixeira, V. H., Soares, C. M. (2002) Constant-pH molecular dynamics using stochastic titration. J. Chem. Phys. 117:4184-4200.
  21. Soares, C. M., Teixeira, V. H., Baptista, A. M. (2003) Protein structure and dynamics in nonaqueous solvents. Insights from molecular dynamics simulation studies. Biophys. J. 84:1628-1641.
  22. Bento, I., Teixeira, V. H., Baptista, A. M., Soares, C. M., Matias, P. M., Carrondo, M. A. (2003) Redox-Bohr and other cooperativity effects in the nine-heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies. J. Biol. Chem. 278:36455-36469.
  23. Bento, I., Matias, P. M., Baptista, A. M., da Costa, P. N., van Dongen, W. M. A. M., Saraiva, L. M., Schneider, T. R., Soares, C. M., Carrondo, M. A. (2004) Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modelling studies of oxidised and reduced high-resolution structures at pH 7.6. Proteins, 54:135-152.
  24. Eberini, I., Baptista, A. M., Gianazza, E., Fraternali, F., Beringhelli, T. (2004) Reorganization in apo- and holo-β-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations. Proteins, 54:744-758.
  25. Soares, C. M., Baptista, A. M., Pereira, M. M., Teixeira, M. (2004) Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase. Comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase. J. Biol. Inorg. Chem. 9:124-134.
  26. Teixeira, V. H., Baptista, A. M., Soares, C. M. (2004) Modelling electron transfer thermodynamics in protein complexes: Interaction between two cytochromes c3. Biophys. J. 86:2773-2785.
  27. Victor, B. L., Baptista, A. M., Soares, C. M. (2004) Theoretical identification of of proton channels in the quinol oxidase aa3 of Acidianus ambivalens. Biophys. J. 87:4316-4325.
  28. Rivas, L., Soares, C. M., Baptista, A. M., Simaan, J., Di Paolo, R. E., Murgida, D. H., Hildebrandt, P. (2005) Electric-field induced redox potential shifts of tetraheme cytochromes c3 immobilised on self-assembled monolayers. Surface enhanced resonance Raman spectroscopy and simulation studies. Biophys. J. 88:4188-4199.
  29. Micaelo, N. M., Teixeira, V. H., Baptista, A. M., Soares, C. M. (2005) Water dependent properties of cutinase in nonaqueous solvents. A computational study of enantioselectivity. Biophys. J. 89:999-1008.
  30. Teixeira, V. H., Cunha, C. A., Machuqueiro, M., Oliveira, A. S. F., Victor, B. L., Soares, C. M., Baptista, A. M. (2005) On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium. J. Phys. Chem. B, 109:14691-14706.
  31. Oliveira, A. S. F., Teixeira, V. H., Baptista, A. M., Soares, C. M. (2005) Reorganization and conformational changes in the reduction of tetraheme cytochromes. Biophys. J. 89:3919-3930.
  32. Machuqueiro, M., Baptista, A. M. (2006) Constant-pH molecular dynamics with ionic strength effects: the protonation-conformation coupling in decalysine. J. Phys. Chem. B, 110:2927-2933.
  33. Lopes, S. C. D. N., Soares, C. M., Baptista, A. M., Goormaghtigh, E., Costa Cabral, B. J., Castanho, M. A. R. B. (2006) Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes. Putative correlation towards receptor docking. J. Phys. Chem. B, 110:3385-3394.
  34. Teixeira, V. H., Baptista, A. M., Soares, C. M. (2006) Pathways of H2 towards the active site of [NiFe]-hydrogenase. Biophys. J. 91:2035-2045.
  35. Micaelo, N. M., Baptista, A. M., Soares, C. M. (2006) Parameterization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field. J. Phys. Chem. B, 110:14444-14451.
  36. Rocha, R., Leal, S. S., Teixeira, V. H., Regalla, M., Huber, H., Baptista, A. M., Soares, C. M., Gomes, C. M. (2006) Natural domain design: enhanced thermal stability of zinc lacking ferredoxin isoforms shows that a hydrophobic core efficiently replaces the structural metal site. Biochemistry, 45:10376-10384.
  37. Machuqueiro, M., Baptista, A. M. (2006) The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study. Biophys. J. 92:1836-1845.
  38. Gaspar, P., Neves, A. R., Shearman, C. A., Gasson, M. J., Baptista, A. M., Turner, D. L., Soares, C. M., Santos, H. (2007) The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties: comparative modelling to probe the molecular basis. FEBS J. 274:5924-5936.
  39. Veríssimo, A. F., Sousa, F. L., Baptista, A. M., Teixeira, M., Pereira. M. M. (2007) Thermodynamic redox behavior of the heme centers of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum? Biochemistry, 46:13245-13253.
  40. Teixeira, V. H., Soares, C. M., Baptista, A. M. (2008) Proton pathways in a [NiFe]-hydrogenase: A Theoretical Study. Proteins, 70:1010-1022.
  41. Sousa, F. L., Veríssimo, A. F., Baptista, A. M., Soulimane, T., Teixeira, M., Pereira, M. M. (2008) Redox properties of Thermus thermophilus ba3: different electron-proton coupling in oxygen reductases? Biophys. J. 94:2434-2441.
  42. Rocco, A. G., Mollica, L., Ricchiuto, P., Baptista, A. M., Gianazza, E., Eberini, I. (2008) Characterization of the protein unfolding process induced by urea and temperature. Biophys. J. 94:2241-2251.
  43. Eberini, I., Rocco, A. G., Ientile, A. R., Baptista, A. M., Gianazza, E., Tomaselli, S., Molinari, H., Ragona, L. (2008) Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein. Proteins, 71:1889-1898.
  44. Machuqueiro, M., Baptista, A. M. (2008) Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins, 72:289-298.
  45. Veríssimo, A. F., Sousa, F. L., Baptista, A. M., Teixeira, M., Pereira. M. M. (2008) Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies. Biophys. J. 95:4448-4455.
  46. Machuqueiro, M., Baptista, A. M. (2009) Molecular Dynamics at Constant pH and Reduction Potential: Application to Cytochrome c3. J. Am. Chem. Soc. 131:12586-12594. http://dx.doi.org/10.1021/ja808463e
  47. Victor, B. L., Baptista, A. M., Soares, C. M. (2009) Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas. J. Biol. Inorg. Chem. 14:853-862. http://dx.doi.org/10.1007/s00775-009-0497-5
  48. Campos, S. R. R., Baptista, A. M. (2009) Conformational analysis in a multidimensional energy landscape: study of an arginylglutamate repeat. J. Phys. Chem. B, 113:15989-16001. http://dx.doi.org/10.1021/jp902991u
  49. Oliveira, A. S. F., Baptista, A. M., Soares, C. M. (2010) Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796. J. Phys. Chem. B, 114:5486-5496. http://dx.doi.org/10.1021/jp905735y
  50. Machuqueiro, M., Campos, S. R. R., Soares, C. M., Baptista, A. M. (2010) Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations. J. Phys. Chem. B, 114:11659-11667. http://dx.doi.org/10.1021/jp104418g
  51. Campos, S. R. R., Machuqueiro, M., Baptista, A. M. (2010) Constant-pH molecular dynamics simulations reveal a β-rich form of the human prion protein. J. Phys. Chem. B, 114:12692-12700. http://dx.doi.org/10.1021/jp104753t
  52. Oliveira, A. S. F., Baptista, A. M., Soares, C. M. (2011) Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter. Proteins, 79:1977-1990. http://dx.doi.org/10.1002/prot.23023
  53. Lousa, D., Baptista, A. M., Soares, C. M. (2011) Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents. Prot. Sci, 20:379-386. http://dx.doi.org/10.1002/pro.569
  54. Filipe, L. C. S., Machuqueiro, M., Baptista, A. M. (2011) Unfolding the Conformational Behavior of Peptide Dendrimers: Insights from Molecular Dynamics Simulations. J. Am. Chem. Soc. 133:5042-5052. http://dx.doi.org/10.1021/ja111001v
  55. Damas, J. M., Oliveira, A. S. F., Baptista, A. M., Soares, C. M. (2011) Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: Molecular dynamics studies of HlyB. Prot. Sci. 20:1220-1230. http://dx.doi.org/10.1002/pro.650
  56. Oliveira, A. S. F., Baptista, A. M., Soares, C. M. (2011) Exploring the inter-domain communication mechanisms in an ABC importer: A molecular dynamics study of the MBP-MalFGK2 complex. PLoS Comput. Biol., 7:e1002128. http://dx.doi.org/10.1371/journal.pcbi.1002128
  57. Machuqueiro, M., Baptista, A. M. (2011) Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems? Proteins, 79:3437-3447. http://dx.doi.org/10.1002/prot.23115
  58. Alexov, E., Mehler, E. L., Baker, N., Baptista, A. M., Huang, Y., Milletti, F., Nielsen, J. E., Farrell, D., Carstensen, T., Olsson, M. H. M., Shen, J. K., Warwicker, J., Williams, S., Word, J. M. (2011) Progress in the prediction of pKa values in proteins. Proteins, 79:3260-3275. http://dx.doi.org/10.1002/prot.23189
  59. Soares, C. M., Baptista, A. M. (2012) Simulation of multihaem cytochromes. FEBS Lett. 586:510-518. http://dx.doi.org/10.1016/j.febslet.2011.10.019
  60. Lousa, D., Baptista, A. M., Soares, C. M. (2011) Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations. J. Chem. Inf. Model. 52:465-473. http://dx.doi.org/10.1021/ci200455z
  61. Vila-Viçosa, D., Campos, S. R. R., Baptista, A. M., Machuqueiro, M. (2012) Reversibility of prion misfolding: insights from constant-pH molecular dynamics Simulations. J. Phys. Chem. B, 116:8812-8821. http://dx.doi.org/10.1021/jp3034837
  62. Mateus, P., Delgado, R., Groves, P., Campos, S. R. R., Baptista, A. M., Brandão, P., Felix, V. (2012) Water encapsulation in a polyoxapolyaza macrobicyclic compound. J. Org. Chem. B, 77:6816-6824. http://dx.doi.org/10.1021/jo300799s
  63. Victor, B. L., Baptista, A. M., Soares, C. M. (2012) Structural determinants for the membrane insertion of the transmembrane peptide of hemagglutinin from influenza virus. J. Chem. Inf. Model. 52: 3001-3012. http://dx.doi.org/10.1021/ci3003396
  64. Lousa, D., Cianci, M., Helliwell, J. R., Halling, P. J., Baptista, A. M., Soares C. M. (2012) Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations, J. Phys. Chem. B, 116:5838-5848. http://dx.doi.org/10.1021/jp303008g
  65. Lousa, D., Cianci, M., Helliwel, Baptista, A. M., Soares C. M. (2013) A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies. Phys. Chem. Chem. Phys. 15:13723-13736. http://dx.doi.org/10.1039/C3CP51761F
  66. Damas, J. M., Filipe, L. C. S., Campos, S. R. R., Lousa, D., Victor, B. L., Baptista, A. M., Soares (2013) Predicting the thermodynamics and kinetics of helix formation in a cyclic peptide model. J. Chem. Theory Comput. 9:5148-5157. http://dx.doi.org/10.1021/ct400529k
  67. Carvalheda, C. A., Campos, S. R. R., Machuqueiro, M., Baptista, A. M. (2013) Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study. J. Chem. Inf. Model. 53:2979-2989. http://dx.doi.org/10.1021/ci400479c
  68. Filipe, L. C. S., Machuqueiro, M., Darbre, T., Baptista, A. M. (2013) Unraveling the conformational determinants of peptide dendrimers using molecular dynamics simulations. Macromolecules, 46:9427-9436. http://dx.doi.org/10.1021/ma401574b
  69. Barros, D. P. C., Campos, S. R. R., Madeira, P. P., Azevedo, A. M., Baptista, A. M., Aires-Barros, M. R. (2014) Modelling the partitioning of amino acids in aqueous two phase systems. J. Chromatogr. A, 1329: 52-60. http://dx.doi.org/10.1016/j.chroma.2013.12.015
  70. Teixeira, V. H., Vila-Viçosa, D., Baptista, A. M., Machuqueiro, M. (2014) Protonation of DMPC in a bilayer environment using a linear response approximation. J. Chem. Theory Comput. 10:2176-2184. http://dx.doi.org/10.1021/ct5000082
  71. Damas, J. M., Baptista, A. M., Soares, C. M. (2014) The pathway for O2 diffusion inside CotA laccase and possible implications on the multicopper oxidases family. J. Chem. Theory Comput. 10:3525-3531. http://dx.doi.org/10.1021/ct500196e
  72. Oliveira, A. S. F., Damas, J. M., Baptista, A. M., Soares, C. M. (2014) Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site. PLoS Comput. Biol. 10: e1004010. http://dx.doi.org/10.1371/journal.pcbi.1004010
  73. Vila-Viçosa, D., Teixeira, V. H., Santos, H. A. F., Baptista, A. M., Machuqueiro, M. (2014) Treatment of ionic strength in biomolecular simulations of charged lipid bilayers. J. Chem. Theory Comput. 10: 5483-5492. http://dx.doi.org/10.1021/ct500680q
  74. Correia, M., Snabe, T., Thiagarajan, V., Petersen, S. B., Campos, S. R. R., Baptista, A. M., Neves-Petersen, M. T. (2015) Photonic Activation of Plasminogen induced by low dose UVB. PLOS ONE, 10: e0116737. http://dx.doi.org/10.1371/journal.pone.0116737
  75. Magalhães, P. R., Machuqueiro, M., Baptista, A. M. (2015) Constant-pH molecular dynamics study of kyotorphin in an explicit bilayer. Biophys. J. 108: 2282. http://dx.doi.org/10.1016/j.bpj.2015.03.052
  76. Vila-Viçosa, D., Teixeira, V. H., Baptista, A. M., Machuqueiro, M. (2015) Constant-pH MD simulations of an oleic acid bilayer. J. Chem. Theory Comput. 11: 2367. http://dx.doi.org/10.1021/acs.jctc.5b00095
  77. Carvalheda, C. A., Campos, S. R. R., Baptista, A. M. (2015) Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study. J. Chem. Inf. Model. 55: 2206. http://dx.doi.org/10.1021/acs.jcim.5b00076
  78. Santos, H. A. F., Vila-Viçosa, D., Teixeira, V. H., Baptista, A. M., Machuqueiro, M. (2015) Constant-pH MD simulations of DMPA/DMPC bilayers. J. Chem. Theory Comput. 11: 5973. http://dx.doi.org/10.1021/acs.jctc.5b00956
  79. Conceição, K., Magalhães, P. R., Campos, S. R. R., Domingues, M. M., Ramu, V. G., Michalek, M., Bertani, P., Baptista, A. M., Heras, M., Bardaji, E. R., Bechinger, B., Lopes Ferreira, M., Castanho, M. A. R. B. (2015) The anti-inflammatory action of the analgesic kyotorphin neuropeptide derivatives: insights of a lipid-mediated mechanism. Amino Acids, 48: 307. http://dx.doi.org/10.1007/s00726-015-2088-9
  80. Campos, S. R. R., Iranzo, O., Baptista, A. M. (2016) Constant-pH MD simulations portray the protonation and structural behavior of four decapeptides designed to coordinate Cu2+. J. Phys. Chem. 120: 1080. http://dx.doi.org/10.1021/acs.jpcb.5b12052
  81. Oliveira, A. S. F., Campos, S. R. R., Baptista, A. M., Soares, C. M. (2016) Coupling between protonation and conformation in cytochrome c oxidase: insights from constant-pH MD simulations. Biochim. Biophys. Acta - Bioenerg., 1857: 759-771. http://dx.doi.org/10.1016/j.bbabio.2016.03.024