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Publications

Publications (since the Lab formation)

  • da Rocha, L., Baptista, A. M., Campos, S. R. R. (2022) Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin. J. Phys. Chem. B, 126:9123. https://doi.org/10.1021/acs.jpcb.2c03797

  • Baptista, A. M., Campos, da Rocha, L., S. R. R. (2022) FixBox: A General Algorithm to Fix Molecular Systems in Periodic Boxes. J. Chem. Inf. Model. 62:4435. https://doi.org/10.1021/acs.jcim.2c00823

  • da Rocha, L., Baptista, A. M., Campos, S. R. R. (2022) Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin. J. Chem. Theory Comput. 18:1982. https://doi.org/10.1021/acs.jctc.1c01187

 

  • Lousa, D., Pinto, A. R. T. , Campos, S. R. R., Baptista, A. M., Veiga, A. S., Castanho,  M. A. R. B., Soares, C. M. (2020) Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment. Sci. Rep., 10:20082. https://doi.org/10.1038/s41598-020-77040-y

 

  • Liguori, N., Campos, S. R. R., Baptista, A. M., Croce, R. (2019) Molecular Anatomy of Plant Photoprotective Switches: the Sensitivity of PsbS to the Environment, Residue by Residue. J. Phys. Chem. Lett., 10: 1737–1742. http://dx.doi.org/10.1021/acs.jpclett.9b00437
  • Vila-Viçosa, D., Reis, P. B. P. S., Baptista, A. M., Oostenbrink, C., Machuqueiro, M. (2019) A pH Replica Exchange scheme in the Stochastic Titration constant-pH MD method. J. Chem. Theory Comput. 15:3108–3116. http://dx.doi.org/10.1021/acs.jctc.9b00030

 

  • Reis, P. B. P. S., Vila-Viçosa, D., Campos, S. R. R., Baptista, A. M., Machuqueiro, M. (2018) Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers. ACS Omega, 3: 2001. http://dx.doi.org/10.1021/acsomega.7b01708

 

  • Magalhães, P. R., Oliveira, A. S. F., Campos, S. R. R., Soares, C. M., Baptista, A. M. (2017) Effect of a pH Gradient on the Protonation States of Cytochrome Oxidase: A Continuum Electrostatics Study. J. Chem. Inf. Model., 57: 256–266. http://dx.doi.org/10.1021/acs.jcim.6b00575

 

  • Filipe, L. C. S., Machuqueiro, M., Darbre, T., Baptista, A. M. (2016) Exploring the Structural Properties of Positively Charged Peptide Dendrimers. J. Phys. Chem. B. 120: 11323–11330. http://dx.doi.org/10.1021/acs.jpcb.6b09156

  • Barros, D. P. C., Campos, S. R. R., Azevedo, A. M., Baptista, A. M., Aires-Barros, M. R. (2016) Predicting protein partition coefficients in aqueous two phase system. J. Chromatogr. A. 1470: 50–58. http://dx.doi.org/10.1016/j.chroma.2016.09.072

  • Filipe, L. C. S., Campos, S. R. R., Machuqueiro, M., Darbre, T., Baptista, A. M. (2016) Structuring Peptide Dendrimers Through pH Modulation and Substrate Binding. J. Phys. Chem. B. 120: 10138–10152. http://dx.doi.org/10.1021/acs.jpcb.6b05905

  • 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
  • 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., Ferreira, M. L., Castanho, M. A. R. (2016) The anti-inflammatory action of the analgesic kyotorphin neuropeptide derivatives: insights of a lipid-mediated mechanism. Amino Acids. 48: 307-318. http://dx.doi.org/10.1007/s00726-015-2088-9

  • 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. B. 120: 1080. http://dx.doi.org/10.1021/acs.jpcb.5b12052

 

  • Santos, H. A. F., Vila-Viçosa, D., Teixeira, V. H., Baptista, A. M., Machuqueiro, M. (2015) Constant-pH MD simulations of DMPA/DMPC lipid bilayers. J. Chem. Theory Comput. 11: 5973. http://dx.doi.org/10.1021/acs.jctc.5b00956

  • Carvalheda, C. A., Campos, S. R. R., Baptista, A. M. (2015) The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics. J. Chem. Inf. Model. 55: 2206. http://dx.doi.org/10.1021/acs.jcim.5b00076

  • 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
  • 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
  • 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

 

  • 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
  • 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
  • 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. http://dx.doi.org/10.1021/ct500196e
  • 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
  • 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

 

  • 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
  • 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
  • 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
  • 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

 

  • 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
  • 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
  • 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. 77:6816–6824. http://dx.doi.org/10.1021/jo300799s
  • 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
  • Lousa, D., Baptista, A. M., Soares, C. M. (2012) 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
  • 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

 

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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

 

  • 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.[doi]
  • 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.[doi]
  • 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.[doi]

 

  • 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.[doi]
  • 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.[doi]
  • 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.[doi]

 

  • 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.[doi]
  • Machuqueiro, M., Baptista, A. M. (2008) Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins, 72:289-298.[doi]
  • 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.[doi]
  • 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.[doi]
  • 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.[doi]
  • Teixeira, V. H., Soares, C. M., Baptista, A. M. (2008) Proton pathways in a [NiFe]-hydrogenase: A Theoretical Study. Proteins, 70:1010-1022.[doi]

 

  • 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.[doi]
  • 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.[doi]
  • Machuqueiro, M., Baptista, A. M. (2007) The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study. Biophys. J. 92:1836-1845.[doi]

 

  • 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.[doi]
  • 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.[doi]
  • 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.[doi]
  • 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.[doi]
  • 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.[doi]

 

  • 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.[doi]
  • 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.[doi]
  • 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.[doi]
  • 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.[doi]

 

  • Victor, B. L., Baptista, A. M., Soares, C. M. (2004) Theoretical identification of proton channels in the quinol oxidase aa3 of Acidianus ambivalens. Biophys. J. 87:4316-4325.[doi]
  • 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.[doi]
  • 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.[doi]
  • 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.[doi]
  • 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.[doi]

 

  • 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.[doi]
  • 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.[doi]

 

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