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Publications

Publications (since 1999)


       1999

  • Mendes, J., Soares, C.M., Carrondo, M.A. (1999) "Improvement of side-chain modelling in proteins with the Self-Consistent Mean Field Theory method based on an analysis of the factors influencing prediction",Biopolymers, 50, 111-131 DOI
  • Petukhov, M., Cregut, D., Soares, C.M., Serrano, L. (1999) "Local water bridges and protein conformational stability", Prot.Sci.,8, 1982-1989 Abstract
  • 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.", JBIC, 4, 73-86 Abstract
  • 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 Abstract
  • Cunha, C.A., Romão, M.J., Sadeghi, S.J., Valetti, F., Gilardi, G., Soares, C.M. (1999) "Modelling of electron transfer complexes between flavodoxin and c-type cytochromes", JBIC, 4, 360-374 Abstract
  • Mendes, J., Baptista, A. M. and 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 Abstract
  • Pereira, M.M., Santana, M., Soares, C.M., Mendes, J., Carita, J.N., Saraste, M., Carrondo, M.A., Teixeira, M. (1999) "The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus ", BBA, 1413, 1-13 Abstract
  • Burke, D.F., Deane, C.M., Nagarajaram, H.A., Campillo, N., Martin-Martinez, M., Mendes, J., Molina, F., Perry, J., Reddy, B.V.B., Soares, C.M., Steward, R.E., Williams, M., Carrondo, M.A., Blundell, T.L., Mizuguchi, K. (1999)"An iterative structure-assisted approach to sequence alignment and comparative modelling", Proteins, Suppl 3, 55-60 Abstract
  • Matias, P.M., Saraiva, L.M., Soares, C.M., Coelho, A.V., LeGall, J., Carrondo, M.A. (1999) "Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774: primary sequence determination, crystallographic refinement at 1.8Å and modelling studies of its interaction with the tetrahaem cytochrome c3 from the same organism", JBIC, 4, 478-494 Abstract
  • Frazão, C., Bento, I., Costa, J., Soares, C.M., Veríssimo, P., Faro, C., Pires, E., Cooper, J., Carrondo, M.A. (1999) "Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp containing aspartic proteinase from the flowers of Cynaracardunculus L.", J.Biol. Chem., 274, 27694-27701 Abstract



       2000

  • Power, D. M., Elias, N. P., Richardson, S.J., Mendes, J., Soares, C. M., & Santos, C.R.A. (2000) "Evolution of the Thyroid Hormone Binding Protein, Transthyretin", Gen. Comp. Endocrinol., 119, 241-255  DOI
  • Sadeghi, S. J., Valetti, F., Cunha, C. A., Romão, M. J., Soares, C. M. and Gilardi, G. (2000) "Ionic strength dependence of the non-physiological electron transfer between flavodoxin and cytochrome c553 from D. vulgaris.", JBIC, 5, 730-737 Abstract



       2001

  • Matias, P.M., Soares, C.M., Saraiva, L.M., Coelho, R., Morais, J.,LeGall, J., Carrondo, M.A. (2001) "[NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: primary sequence determination, crystallographic refinement at 1.8 Å and modelling studies of its interaction with the tetra-haem cytochrome c3", JBIC, 6, 63-81 Abstract
  • 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 DOI
  • Santana, M., Pereira, M.M., Elias, N.P., Soares, C.M., Teixeira, M. (2001) "The genes encoding Rhodothermus marinus HiPiP:oxygen oxidoreductase, a caa3-type oxidase belonging to the superfamily of membrane heme-copper oxidases", J. Bacteriology, 183, 687-699 Abstract
  • Carrondo, M.A., Soares, C.M., Matias, P.M. (2001) "Nine-heme cytochrome c" in Handbook of Metalloproteins
  • Mendes, J., Nagarajaram, H.A., Soares, C.M., Blundell, T.L.,Carrondo, M.A. (2001) "Incorporing a knowledge-based bias into an energy-based side-chain modelling method: application to comparative modelling of protein structure", Biopolymers, 59, 72-86 Abstract
  • Mendes, J., Baptista, A.M, Carrondo, M.A., Soares, C.M. (2001) "Implicit solvation in the Self-Consistent Mean Field Theory method: side-chain modelling and prediction of folding free energies of protein mutants", J.Comp.Aid.Mol.Des. , 15, 721-740 Abstract
  • Abreu, I.A., Saraiva, L.M., Soares, C.M., Teixeira, M., Cabelli, D.E. (2001) "The mechanism of superoxide scavenging by Archaeoglobus fulgidus neelaredoxin", J.Biol.Chem., 276, 38995-39001 Abstract
  • 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 DOI



          2002

  • Teixeira, V.H., Soares, C.M., Baptista, A.M. (2002) "Studies of the reduction and protonation behaviour of tetrahaem cytochromes using atomic detail", JBIC, 7, 200-216 DOI
  • Martins, L.O., Soares, C.M., Pereira, M.M., Teixeira, M., Costa, T., Jones, G.H., Henriques, A.O. (2002) "Molecular and biochemical characterization of a highly stable bacterial laccase which occurs as a structural component of the Bacillus subtilis endospore coat", J.Biol.Chem., 277, 18849-18859 DOI
  • Baptista, A.M., Teixeira, V.H., Soares, C.M. (2002) "Constant-pH molecular dynamics using stochastic titration", J.Chem.Phys., 117, 4184-4200 DOI



       2003

  • 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
  • Victor, B.L., Vicente, J.B., Rodrigues, R., Oliveira, S., Rodrigues-Pousada, C., Frazão, C., Gomes, C.M., Teixeira, M., Soares, C.M. (2003) "Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase", JBIC, 8, 475-488 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
  • Price, N.J., Pinheiro, C., Soares, C.M., Ashford, D.A., Ricardo, C.P., Jackson, P.A. (2003) "A biochemical and molecular characterization of LEP1, an extensin peroxidase from lupin", J.Biol.Chem., 278, 41389-41399 DOI



       2004

  • Vidinha, P., Harper, N., Micaelo, N.M., Lourenço, N.M., da Silva, M.D., Cabral, J.M., Afonso, C.A., Soares, C.M., Barreiros, S. (2004) "Effects of immobilization support, water activity, and enzyme ionization state on cutinase activity and enantioselectivity in organic media", Biotechnol Bioeng., 85, 442-449 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 modeling studies of oxidised and reduced high-resolution structures at pH 7.6", Proteins, 54, 135-152 DOI
  • Soares, C.M., Baptista, A.M., Pereira, M.M., Teixeira, M.(2004) "Investigation of protonatable residues in Rhodothermus marinus caa(3) haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa(3) haem-copper oxygen reductase", JBIC, 9, 124-134 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
  • Serrano, M., Neves, A., Soares, C.M., Moran, C.P., Henriques, A.O. (2004) "Role of the anti-sigma factor SpoIIAB in the regulation of sigmaG during Bacillus subtilis sporulation", J.Bacteriology, 186, 4000-4013 DOI
  • Victor, B.L., Baptista, A.M, Soares, C.M. (2004) "Theoretical identification of proton channels in the Quinol Oxidase aa3 from Acidianus ambivalens", Biophys.J., 87, 4316-4325 DOI



       2005

  • 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 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies.", Biophys. J., 88, 4188-4199 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
  • Matias, P.M., Pereira, I.A., Soares, C.M., Carrondo, M.A. (2005) "Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview.", Prog. Biophys. Mol. Biol., 89, 292-329 DOI
  • Kirichenko, A.V., Pfitzner, U., Ludwig, B., Soares, C.M., Vygodina, T.V., Konstantinov, A.A. (2005) "Cytochrome c Oxidase as a Calcium Binding Protein. Studies on the Role of a Conserved Aspartate in Helices XI-XII Cytoplasmic Loop in Cation Binding.", Biochemistry, 44, 12391-12401 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 DOI
  • Oliveira, A.S., 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
  • Valente, F.M.A., Oliveira, A.S.F., Gnadt, N., Pacheco, I., Coelho, A.V., Xavier, A.V., Teixeira, M., Soares, C.M., Pereira, I.A.C. (2005) "Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase", JBIC, 10, 667-682 DOI



       2006

  • Lopes, S.C.N.D., Soares, C.M., Baptista, A.M., Goormaghtigh, E., Cabral, B.J.C., Castanho, M.A.R.B. (2006) "Conformational and Orientational Guidance of the Analgesic Dipeptide Kyotorphin Induced by Lipidic Membranes: Putative Correlation toward Receptor Docking", J. Phys. Chem. B, 110, 3385-3394 DOI
  • Franco, I.S., Mota, L.J., Soares, C.M., Sá-Nogueira, I. (2006) "Funtional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector-binding". J.Bact., 188, 3024-3036 DOI
  • Teixeira, V.H., Baptista, A.M., Soares, C.M. (2006) "Pathways of H2 towards the active site of [NiFE]-hydrogenase", Biophys.J., 91, 2035-45 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
  • 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 a zinc-lacking ferredoxin isoform shows that a hydrophobic core efficiently replaces the structural metal site", Biochemistry, 45, 10376-10384 DOI
  • Roxo-Rosa, Xu, Z., M., Schmidt, Neto, M.F., Cai, Z., Soares, C.M., D., Sheppard, D.N., Amaral, M.D. (2006) "Rescue of cystic fibrosis mutations in the first nucleotide-binding domain of G550E and 4RK", PNAS, 103, 17891-17896 DOI


    2007

     

  • Araújo, R., Silva, C., O´Neill, A., Micaelo, N., Guebitz, G., Soares, C.M., Casal, M., Cavaco-Paulo, A. (2007) “Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6.6 fibers”, J. Biotechnol., 128, 849-857 DOI
  • Micaelo, N., Soares, C.M. (2007) “ Hydration mechanisms of enzymes in nonpolar and polar organic solvents”, FEBS J., 274, 2424-2436 DOI
  • Fernandes, A.T., Soares, C.M., Pereira, M.M., Huber, R., Grass, G., Martins, L.O. (2007) “A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus”, FEBS J., 274, 2683-2694 DOI
  • Teixeira, V.H., Soares, C.M., Baptista, A.M. (2007) “Proton Pathways in a [NiFe]-Hydrogenase: A Theoretical Study", Proteins, 70, 1010-1022 DOI
  • Franco, I, Mota, LJ, Soares, CM, Sá-Nogueira, I (2007) “Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon”, Nucleic Acids Res., 35, 4755-4766 DOI
  • Broco, M, Soares, CM, Oliveira, S, Mayhew, SG, Rodrigues-Pousada, C (2007) “Identification of FMN binding sites in the flavoprotein Flavoredoxin from Desulfovibrio gigas”, FEBS Lett., 581, 4397-4402 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

 

       2008

  • Rodrigues, J.V., Victor, B.L., Huber, H., Saraiva, L.M., Soares, C.M., Cabelli, D.E., Teixeira, M. (2008) ">Superoxide reduction by Nanoarchaeum equitans neelaredoxin, a “natural mutant” lacking the ferric sixth ligand glutamate”, JBIC, 13, 219-228 DOI
  • Micaelo, N.M., Victor, B.L., Soares, C.M. (2008) "Protein thermal stabilization by charged compatible solutes. Computtaional studies in rubredoxin from Desulfovibrio gigas" , Proteins, 72, 580-588 DOI
  • Micaelo, N.M., Soares, C.M. (2008) "Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies". J. Phys. Chem. B, 112, 2566-2572 DOI
  • Durão, P., Chen, Z., Silva, C.S., Soares, C.M., Pereira, M.M., Todorovic, S., Hildebrandt, P., Bento, I., Lindley, P.F., Martins, L.O. (2008) "Proximal mutations at the type 1 copper site of CotA-laccase; spectroscopic, redox, kinetic and structural characterization of the ILE469A and L386A mutants", Biochemical J., 412, 339-346, DOI
  • Escrevente, C., Morais, V.A., Keller, S., Soares, C.M., Altevogt, P., Costa, J. (2008) "Functional role of N-glycosylation from ADAM10 in processing, activity, stability and localization of the enzyme", BBA, 1780, 905-91 DOI

 

       2009

  • Fonseca, B.M., Saraiva, I.H., Paquete, C.M., Soares, C.M., Pacheco, I., Salgueiro, C.A., Louro, R.O. (2009) “The small tetrahaem cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the different haems”, JBIC, 14, 375-385 DOI
  • Victor, BL, Baptista, AM, Soares, CM (2009) “Dioxygen and nitric oxide pathways and affinity to the catalytic site of ROO from Desulfovibrio gigas”, JBIC, 14, 853-862 DOI

 

       2010

  • Gonçalves, S, Borges, N, Esteves, AM, Victor, B, Soares, CM, Santos, H, Matias, PM (2010) “Structural Analysis of Thermus thermophilus HB27 Mannosyl-3-phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight into the Retaining Mechanism of Glycosyltransferases “, JBC, 285, 17857-17868 DOI
  • Oliveira, ASF, Baptista, AM, Soares, CM (2010) “Insights into the ATP-hydrolysis mechanism of an ABC-transporter: conformational changes in the NBD dimer of MJ0796”, J Phys Chem B, 114, 5486-5496 DOI
  • Fernandes, AT, Damas, JM, Todorovic, S, Huber, R, Pogni, R, Soares, CM, Martins, LO (2010) “The Multicopper Oxidase from the Archaeon Pyrobaculum aerophilum Shows Nitrous Oxide Reductase Activity”, FEBS J., 277, 3176-3189 DOI
  • Bento, I, Silva, C, Chen, Z, Martins, LO, Lindley, PF, Soares, CM (2010) “Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies.”, BMC Struct. Biol., 2010, 10:28 DOI
  • Machuqueiro, M, Campos, SRR, Soares, CM, Baptista, AM (2010) “Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations”, J Phys Chem B, 114, 11659–11667 DOI

 

       2011

  • Lousa, D, Baptista, AM, Soares, CM (2010) “Structural determinants of ligand imprinting: a molecular dynamics simulation study of subtilisin in aqueous and apolar solvents”, Prot.Sci., 20, 379-86
  •  Baltazar, C, Marques, MC, Soares, CM, DeLacey, AM, Pereira, IAC, Matias, PM (2011) “Nickel-Iron-Selenium Hydrogenases - An Overview”, Eur.J.Inor.Chem., 2011, 948-962.
  • Oliveira, ASF, Baptista, AM, Soares, CM (2011) “Conformational changes induced by ATP-hydrolysis in an ABC transporter: a molecular dynamics study of the Sav1866 exporter”, Proteins, 79, 1977-1990
  • Bento, I, Louro, RO, Soares, CM, Carrondo, MA (2011) “Tetraheme cytochromes c3”, Handbook of Metalloproteins, vol: 4 & 5 edited by Albrecht Messerschmidt. Chichester, UK: John Wiley & Sons, Ltd, pp 5-15
  • Damas, JM, Oliveira, ASF, Baptista, AM, Soares, CM (2011) “Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB”, Prot.Sci., 20, 1220-1230
  • Varanda, C, Felix, MR, Soares, CM, Oliveira, S, Clara, MI (2011) “Specific amino acids of Olive mild mosaic virus coat protein are involved on transmission by Olpidium brassicae”, J. Gen.Virol., 92, 2209-2213
  • Oliveira, ASF, Baptista, AM, Soares, CM (2011) “Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex”, PLoS Comp.Biol., 7(8), e1002128

 

   2012

  • Soares, CM, Baptista, AM (2012) “Simulation of multihaem cytochromes”, FEBS Lett., 586, 510-518 (joint corresponding author).
  • Silva, CS, Damas, JM, Chen, Z., Brissos, V, Martins, LO, Soares, CM, Lindley, PF, Bento, I (2012) “The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: assistance during the proton transfer mechanism”, Acta Crys D, D68,186-193. (joint corresponding author).
  • Azoia, NG, Fernandes, MM, Micaelo, NM, Soares, CM, Cavaco-Paulo, A (2012) “Molecular modeling of hair keratin/peptide complex: using MM-PBSA calculations to describe experimental binding results”, Proteins, 80, 1409-1417
  • Baltazar, CSA, Teixeira, VH, Soares, CM (2012) “Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach”, JBIC, 17, 543-555
  • Lousa, D, Baptista, AM, Soares, CM (2012) “Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations”, J.Chem.Infor.Model., 52: 465-473
  • Lousa, D, Cianci, M, Helliwell, JR, Halling, PJ, Baptista, AM, Soares, CM (2012) “Interaction of counterions with subtilisin in acetonitrile: Insights from molecular dynamics simulations”, J.Phys.Chem.B, 116, 5838–5848
     
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