António M. Baptista

Head of the Molecular Simulation Laboratory at ITQB.

Address

Research interests

• Molecular simulation of proteins using computational methods, with emphasis on the study of electrostatic processes.
• Development of theoretical methods for molecular simulation.
• Application of statistical mechanics to the study of chemical and biochemical systems.

Current research

• Inclusion of pH and electrostatic potential effects in molecular dynamics simulations.
• Simulation of peptide- and protein-membrane interactions.
• Simulation of pH-induced protein misfolding.
• Simulation of peptide dendrimers.
• Simulation of redox and protonation equilibria by Monte Carlo methods.
• Characterization of low-dimensional energy landscapes.
• Simulation of proteins in non-aqueous media.

Refereeing

• Biophysical Journal
• BMC Structural Biology
• Chemical Physics
• Extremophiles
• FEBS Letters
• Journal of the American Chemical Society
• Journal of Biological Inorganic Chemistry
• Journal of Chemical Physics
• Journal of Computational Chemistry
• Journal of Physical Chemistry B
• Molecular Simulation
• Proteins: Structure, Function and Bioinformatics

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 pK_a 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 pK_a 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
57. Machuqueiro, M., Baptista, A. M. (2011) Is the prediction of pK_a values by constant-pH molecular dynamics being hindered by inherited problems? Proteins, 79:3437-3447.
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 pK_a values in proteins. Proteins, 79:3260-3275.
59. Soares, C. M., Baptista, A. M. (2012) Simulation of multihaem cytochromes. FEBS Lett. 586:510-518.
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.