António M. Baptista

PhD, Research Scientist (Investigador Auxiliar)

Leader of the Molecular Simulation Laboratory at ITQB.

Address

António M. Baptista
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Av. da República, EAN, ITQB II, Apartado 127
2781-901 Oeiras
Portugal

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

Research interests

Current research

Software

Classes

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. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. Baptista, A. M., Teixeira, V. H., Soares, C. M. (2002) Constant-pH molecular dynamics using stochastic titration. J. Chem. Phys. 117:4184-4200.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. Machuqueiro, M., Baptista, A. M. (2006) The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study. Biophys. J. 92:1836-1845.
  37. 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.
  38. 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.
  39. Teixeira, V. H., Soares, C. M., Baptista, A. M. (2008) Proton pathways in a [NiFe]-hydrogenase: A Theoretical Study. Proteins, 70:1010-1022.
  40. 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.
  41. 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.
  42. 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.
  43. Machuqueiro, M., Baptista, A. M. (2008) Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins, 72:289-298.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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, in press.