Personal tools
You are here: Home / Labs / Protein Modelling / Publications
 

Publications

 

2023

  • Hanko, E. K. R., Correia, J., Souza, C. S., Green, A., Chromy, J., Stoney, R., Yan, C., Takano, E., Lousa, D., Soares, C. M., & Breitling, R. (2023). Microbial production of the plant flavanone hesperetin from caffeic acid. BMC Research Notes, 16(1). DOI

 

2022

  • Galocha, M., Viana, R., Pais, P., Silva-Dias, A., Cavalheiro, M., Miranda, I. M., van Ende, M., Souza, C. S., Costa, C., Branco, J., Soares, C. M., van Dijck, P., Rodrigues, A. G., & Teixeira, M. C. (2022). Genomic evolution towards azole resistance in Candida glabrata clinical isolates unveils the importance of CgHxt4/6/7 in azole accumulation. Communications Biology, 5(1). DOI
  • Valério, M., Borges-Araújo, L., Melo, M. N., Lousa, D., & Soares, C. M. (2022). SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. Frontiers in Medical Technology, 4. DOI
  • Valério, M., Mendonça, D. A., Morais, J., Buga, C. C., Cruz, C. H., Castanho, M. A. R. B., Melo, M. N., Soares, C. M., Veiga, A. S., & Lousa, D. (2022). Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures. ACS Chemical Biology, 17(7), 1831–1843. DOI
  • Sequeira, A. M., Lousa, D., & Rocha, M. (2022). ProPythia: A Python package for protein classification based on machine and deep learning. Neurocomputing, 484, 172–182. DOI
  • Marques, M. C., Lousa, D., Silva, P. M., Faustino, A. F., Soares, C. M., & Santos, N. C. (2022). The Importance of Lipid Conjugation on Anti-Fusion Peptides against Nipah Virus. Biomedicines, 10(3). DOI
  • Lousa, D., Soares, C. M., & Barroso da Silva, F. L. (2022). Editorial: Computational Approaches to Foster Innovation in the Treatment and Diagnosis of Infectious Diseases. Frontiers in Medical Technology, 4. DOI
  • Saramago, M., Costa, V. G., Souza, C. S., Bárria, C., Domingues, S., Viegas, S. C., Lousa, D., Soares, C. M., Arraiano, C. M., & Matos, R. G. (2022). The nsp15 Nuclease as a Good Target to Combat SARS‐CoV‐2: Mechanism of Action and Its Inactivation with FDA‐Approved Drugs. Microorganisms, 10(2). DOI

​

2021

  • Lousa, D., & Soares, C. M. (2021). Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies. FEBS Open Bio, 11(12), 3253–3261. DOI
  • Moreira, P., Sequeira, A. M., Pereira, S., Rodrigues, R., Rocha, M., & Lousa, D. (2021). ViralFP: A Web Application of Viral Fusion Proteins. Frontiers in Medical Technology, 3. DOI
  • Alenquer, M., Ferreira, F., Lousa, D., Valério, M., Medina-Lopes, M., Bergman, M.-L., Gonçalves, J., Demengeot, J., Leite, R. B., Lilue, J., Ning, Z., Penha-Gonçalves, C., Soares, H., Soares, C. M., & Amorim, M. J. (2021). Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. PLoS Pathogens, 17(8). DOI
  • Martins, M. C., Fernandes, S. F., Salgueiro, B. A., Soares, J. C., Romão, C. v, Soares, C. M., Lousa, D., Folgosa, F., & Teixeira, M. (2021). The amino acids motif-32GSSYN36-in the catalytic domain of E. coli flavorubredoxin NO reductase is essential for its activity. Catalysts, 11(8). DOI
  • Abreu, B., Cruz, C., Oliveira, A. S. F., & Soares, C. M. (2021). ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer. Scientific Reports, 11(1). DOI
  • Pavlu-Pereira, H., Lousa, D., Tomé, C. S., Florindo, C., Silva, M. J., de Almeida, I. T., Leandro, P., Rivera, I., & Vicente, J. B. (2021). Structural and functional impact of clinically relevant E1α variants causing pyruvate dehydrogenase complex deficiency. Biochimie, 183, 78–88. DOI
  • Saramago, M., Bárria, C., Costa, V. G., Souza, C. S., Viegas, S. C., Domingues, S., Lousa, D., Soares, C. M., Arraiano, C. M., & Matos, R. G. (2021). New targets for drug design: importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2. FEBS Journal, 288(17), 5130–5147. DOI
  • Faustino, M. M., Fonseca, B. M., Costa, N. L., Lousa, D., Louro, R. O., & Paquete, C. M. (2021). Crossing the wall: Characterization of the multiheme cytochromes involved in the extracellular electron transfer pathway of Thermincola ferriacetica. Microorganisms, 9(2), 1–14. DOI
  • Sequeira, A. M., Lousa, D., & Rocha, M. (2021). ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning. Advances in Intelligent Systems and Computing, 1240 AISC, 32–41. DOI

​

2020

  • 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. Scientific Reports, 10(1). DOI
  • da Silva, J. A., Meneghetti, M. R., & Soares, C. M. (2020). Molecular dynamics simulations suggest a possible role for no in the polyol synthesis of silver nanostructures. Journal of Physical Chemistry C, 124(44), 24279–24288. DOI
  • Abreu, B., Lopes, E. F., Oliveira, A. S. F., & Soares, C. M. (2020). F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis. Proteins: Structure, Function and Bioinformatics, 88(1), 113–126. DOI
  • Barbosa, T. M., Baltazar, C. S. A., Cruz, D. R., Lousa, D., & Soares, C. M. (2020). Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases. Scientific Reports, 10(1). DOI
  • Orengo, C., Velankar, S., Wodak, S., Zoete, V., Bonvin, A. M. J. J., Elofsson, A., Feenstra, K. A., Gerloff, D. L., Hamelryck, T., Hancock, J. M., Helmer-Citterich, M., Hospital, A., Orozco, M., Perrakis, A., Rarey, M., Soares, C., Sussman, J. L., Thornton, J. M., Tuffery, P., Schneider, B. (2020). A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Research, 9. DOI
  • Rebelo, B. A., Santos, R. B., Ascenso, O. S., Nogueira, A. C., Lousa, D., Abranches, R., & Ventura, M. R. (2020). Synthesis and biological effects of small molecule enhancers for improved recombinant protein production in plant cell cultures. Bioorganic Chemistry, 94. DOI

 

2019

  • Pereira, F. C., Nunes, F., Cruz, F., Fernandes, C., Isidro, A. L., Lousa, D., Soares, C. M., Moran, C. P., Henriques, A. O., & Serrano, M. (2019). A LysM Domain intervenes in sequential protein-protein and protein-peptidoglycan interactions important for spore coat assembly in bacillus subtilis. Journal of Bacteriology, 201(4). DOI

 

2018

  • Duarte, A. G., Catarino, T., White, G. F., Lousa, D., Neukirchen, S., Soares, C. M., Sousa, F. L., Clarke, T. A., & Pereira, I. A. C. (2018). An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation. Nature Communications, 9(1). DOI
  • Velada, I., Grzebelus, D., Lousa, D., Soares, C. M., Macedo, E. S., Peixe, A., Arnholdt-Schmitt, B., & Cardoso, H. G. (2018). AOX1-subfamily gene members in olea europaea cv. “Galega vulgar”—gene characterization and expression of transcripts during IBA-induced in vitro adventitious rooting. International Journal of Molecular Sciences, 19(2). DOI
  • Kaur, H., Abreu, B., Akhmetzyanov, D., Lakatos-Karoly, A., Soares, Cláudio M., Prisner, T., & Glaubitz, C. (2018). Unexplored Nucleotide Binding Modes for the ABC Exporter MsbA. Journal of the American Chemical Society, 140(43), 14112–14125. DOI
  • Jeremias, H. F., Lousa, D., Hollmann, A., Coelho, A. C., Baltazar, C. S., Seixas, J. D., Marques, A. R., Santos, N. C., Romão, C. C., & Soares, C. M. (2018). Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods. PLoS ONE, 13(9). DOI
  • Sena, F. V., Sousa, F. M., Oliveira, A. S. F., Soares, C. M., Catarino, T., & Pereira, M. M. (2018). Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus. Redox Biology, 16, 209–214. DOI
  • Almadanim, M. C., Gonçalves, N. M., Rosa, M. T. G., Alexandre, B. M., Cordeiro, A. M., Rodrigues, M., Saibo, N. J. M., Soares, C. M., Romão, C. v, Oliveira, M. M., & Abreu, I. A. (2018). The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications. Biochimica et Biophysica Acta - Molecular Cell Research, 1865(2), 231–246. DOI

 

2017

  • Sousa, F. M., Sena, F. v, Batista, A. P., Athayde, D., Brito, J. A., Archer, M., Oliveira, A. S. F., Soares, C. M., Catarino, T., & Pereira, M. M. (2017). The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus. Biochimica et Biophysica Acta - Bioenergetics, 1858(10), 823–832. DOI
  • Pereira, L., Saraiva, I. H., Oliveira, A. S. F., Soares, C. M., Louro, R. O., & Frazão, C. (2017). Molecular structure of FoxE, the putative iron oxidase of Rhodobacter ferrooxidans SW2. Biochimica et Biophysica Acta - Bioenergetics, 1858(10), 847–853. DOI
  • Marreiros, B. C., Sena, F. v, Sousa, F. M., Oliveira, A. S. F., Soares, C. M., Batista, A. P., & Pereira, M. M. (2017). Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family. Scientific Reports, 7. DOI
  • 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 c Oxidase: A Continuum Electrostatics Study. Journal of Chemical Information and Modeling, 57(2), 256–266. DOI

 

2016

  • Romão, C. v, Vicente, J. B., Borges, P. T., Victor, B. L., Lamosa, P., Silva, E., Pereira, L., Bandeiras, T. M., Soares, C. M., Carrondo, M. A., Turner, D., Teixeira, M., & Frazão, C. (2016). Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase. Journal of Molecular Biology, 428(23), 4686–4707. DOI
  • 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. Biochimica et Biophysica Acta - Bioenergetics, 1857(6), 759–771. DOI
  • Lousa, D., Pinto, A. R. T., Victor, B. L., Laio, A., Veiga, A. S., Castanho, M. A. R. B., & Soares, C. M. (2016). Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide. Scientific Reports, 6. DOI
  • Lousa, D., Baptista, A. M., & Soares, C. M. (2016). Hydration effects on enzyme properties in nonaqueous media analyzed by MD simulations. In Understanding Enzymes: Function, Design, Engineering and Analysis (pp. 501–521). DOI

​

2015

  • Fernandes, C. G., Plácido, D., Lousa, D., Brito, J. A., Isidro, A., Soares, C. M., Pohl, J., Carrondo, M. A., Archer, M., & Henriques, A. O. (2015). Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking. Biochemistry, 54(37), 5723–5734. DOI
  • Alves, M. N., Neto, S. E., Alves, A. S., Fonseca, B. M., Carrêlo, A., Pacheco, I., Paquete, C. M., Soares, C. M., & Louro, R. O. (2015). Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1. Frontiers in Microbiology, 6(JUN). DOI
  • Victor, B. L., Lousa, D., Antunes, J. M., & Soares, C. M. (2015). Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion peptide with a membrane bilayer. Journal of Chemical Information and Modeling, 55(4), 795–805. DOI
  • Nobre, L. S., Lousa, D., Pacheco, I., Soares, C. M., Teixeira, M., & Saraiva, L. M. (2015). Insights into the structure of the diiron site of RIC from Escherichia coli. FEBS Letters, 589(4), 426–431. DOI

 

2014

  • Paquete, C. M., Fonseca, B. M., Cruz, D. R., Pereira, T. M., Pacheco, I., Soares, C. M., & Louro, R. O. (2014). Exploring the molecular mechanisms of electron shuttling across the microbe/metal space. Frontiers in Microbiology, 5(JUN). DOI
  • Oliveira, A. S. F., Damas, J. M., Baptista, A. M., & Soares, C. M. (2014). Exploring O2Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site. PLoS Computational Biology, 10(12). DOI
  • 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. Journal of Chemical Theory and Computation, 10(8), 3525–3531. DOI
  • McVey, C. E., Ferreira, M. J., Correia, B., Lahiri, S., de Sanctis, D., Carrondo, M. A., Lindley, P. F., de Sá Nogueira, I., Soares, C. M., & Bento, I. (2014). The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis Topical Issue in honor of Ivano Bertini. Guest editors: Lucia Banci, Claudio Luchinat. Journal of Biological Inorganic Chemistry, 19(4–5), 505–513. DOI
     

2013

  • Volkers, G., Damas, J. M., Palm, G. J., Panjikar, S., Soares, C. M., & Hinrichs, W. (2013). Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX. Acta Crystallographica Section D: Biological Crystallography, 69(9), 1758–1767. DOI
  • Damas, J. M., Filipe, L. C. S., Campos, S. R. R., Lousa, D., Victor, B. L., Baptista, A. M., & Soares, C. M. (2013). Predicting the thermodynamics and kinetics of helix formation in a cyclic peptide model. Journal of Chemical Theory and Computation, 9(11), 5148–5157. DOI
  • Lousa, D., Baptista, A. M., & Soares, C. M. (2013). A molecular perspective on nonaqueous biocatalysis: Contributions from simulation studies. Physical Chemistry Chemical Physics, 15(33), 13723–13736. DOI
  • Fonseca, B. M., Paquete, C. M., Neto, S. E., Pacheco, I., Soares, C. M., & Louro, R. O. (2013). Erratum: Mind the gap: Cytochrome interactions reveal electron pathways across the periplasm of shewanella oneidensis MR-1 (Biochemical Journal (2013) 449 (101-108)). Biochemical Journal, 451(2), 343. DOI
  • Gutiérrez-Sanz, O., Marques, M. C., Baltazar, C. S. A., Fernández, V. M., Soares, C. M., Pereira, I. A. C., & de Lacey, A. L. (2013). Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases. Journal of Biological Inorganic Chemistry, 18(4), 419–427. DOI
  • Fonseca, B. M., Paquete, C. M., Neto, S. E., Pacheco, I., Soares, C. M., & Louro, R. O. (2013). Mind the gap: Cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1. Biochemical Journal, 449(1), 101–108. DOI
     

2012

  • Silva, C. S., Damas, J. M., Chen, Z., Brissos, V., Martins, L. O., Soares, C. M., Lindley, P. F., & 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 Crystallographica Section D: Biological Crystallography, 68(2), 186–193. DOI
  • 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. Journal of Chemical Information and Modeling, 52(11), 3001–3012. DOI
  • Soares, C. M., & Baptista, A. M. (2012). Simulation of multihaem cytochromes. FEBS Letters, 586(5), 510–518. DOI
  • Pires, S., Habjanič, J., Sezer, M., Soares, C. M., Hemmingsen, L., & Iranzo, O. (2012). Design of a peptidic turn with high affinity for HgII. Inorganic Chemistry, 51(21), 11339–11348. DOI
  • Campos, E., Asandei, A., McVey, C. E., Dias, J. C., Oliveira, A. S. F., Soares, C. M., Luchian, T., & Astier, Y. (2012). The role of lys147 in the interaction between MPSA-gold nanoparticles and the α-hemolysin nanopore. Langmuir, 28(44), 15643–15650. DOI
  • 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. Journal of Physical Chemistry B, 116(20), 5838–5848. DOI
  • Baltazar, C. S. A., Teixeira, V. H., & Soares, C. M. (2012). Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: A computational approach. Journal of Biological Inorganic Chemistry, 17(4), 543–555. DOI
  • Azoia, N. G., Fernandes, M. M., Micaêlo, N. M., Soares, C. M., & Cavaco-Paulo, A. (2012). Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results. Proteins: Structure, Function and Bioinformatics, 80(5), 1409–1417. DOI
  • Lousa, D., Baptista, A. M., & Soares, C. M. (2012). Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations. Journal of Chemical Information and Modeling, 52(2), 465–473. DOI

 

2011

  • 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. Protein Science, 20(2), 379–386. DOI
  • Varanda, C., Félix, M. R., Soares, C. M., Oliveira, S., & Clara, M. I. (2011). Specific amino acids of Olive mild mosaic virus coat protein are involved in transmission by Olpidium brassicae. Journal of General Virology, 92(9), 2209–2213. DOI
  • Oliveira, A. S. F., Baptista, A. M., & Soares, C. M. (2011). Inter-domain communication mechanisms in an ABC importer: A molecular dynamics study of the MalFGK2E complex. PLoS Computational Biology, 7(8). DOI
  • 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. Protein Science, 20(7), 1220–1230. DOI
  • Oliveira, A. S., 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: Structure, Function and Bioinformatics, 79(6), 1977–1990. DOI
  • Baltazar, C. S. A., Marques, M. C., Soares, C. M., DeLacey, A. M., Pereira, I. A. C., & Matias, P. M. (2011). Nickel-iron-selenium hydrogenases - An overview. European Journal of Inorganic Chemistry, 7, 948–962. DOI

 

2010

  • Bento, I., Silva, C. S., Chen, Z., Martins, L. O., Lindley, P. F., & Soares, C. M. (2010). Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer. BMC Structural Biology, 10. 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. Journal of Physical Chemistry B, 114(35), 11659–11667. DOI
  • Gonçalves, S., Borges, N., Esteves, A. M., Victor, B. L., Soares, C. M., Santos, H., & Matias, P. M. (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. Journal of Biological Chemistry, 285(23), 17857–17868. DOI
  • Fernandes, A. T., Damas, J. M., Todorovic, S., Huber, R., Baratto, M. C., Pogni, R., Soares, C. M., & Martins, L. O. (2010). The multicopper oxidase from the archaeon Pyrobaculum aerophilum shows nitrous oxide reductase activity. FEBS Journal, 277(15), 3176–3189. 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. Journal of Physical Chemistry B, 114(16), 5486–5496. 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. Journal of Biological Inorganic Chemistry, 14(6), 853–862. DOI
     

2009

  • Fonseca, B. M., Saraiva, I. H., Paquete, C. M., Soares, C. M., Pacheco, I., Salgueiro, C. A., & Louro, R. O. (2009). The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes. Journal of Biological Inorganic Chemistry, 14(3), 375–385. 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. Journal of Biological Inorganic Chemistry, 14(6), 853–862. 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, an enzyme lacking the highly conserved glutamate iron ligand. Journal of Biological Inorganic Chemistry, 13(2), 219–228. 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, localization and activity of the enzyme. Biochimica et Biophysica Acta - General Subjects, 1780(6), 905–913. 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 I494A and L386A mutants. Biochemical Journal, 412(2), 339–346. DOI
  • Micaelo, N. M., Victor, B. L., & Soares, C. M. (2008). Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas. Proteins: Structure, Function and Genetics, 72(2), 580–588. DOI
  • Micaêlo, N. M., & Soares, C. M. (2008). Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies. Journal of Physical Chemistry B, 112(9), 2566–2572. DOI
  • Teixeira, V. H., Soares, C. M., & Baptista, A. M. (2008). Proton pathways in a [NiFe]-hydrogenase: A theoretical study. Proteins: Structure, Function and Genetics, 70(3), 1010–1022. DOI

 

2007

  • 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 modeling to probe the molecular basis. FEBS Journal, 274(22), 5924–5936. DOI
  • Broco, M., Soares, C. M., Oliveira, S., Mayhew, S. G., & Rodrigues-Pousada, C. (2007). Molecular determinants for FMN-binding in Desulfovibrio gigas flavoredoxin. FEBS Letters, 581(23), 4397–4402. DOI
  • Franco, I. S., Mota, L. J., Soares, C. M., & de Sá-Nogueira, I. (2007). Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon. Nucleic Acids Research, 35(14), 4755–4766. 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 Journal, 274(11), 2683–2694. DOI
  • Micaêlo, N. M., & Soares, C. M. (2007). Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS Journal, 274(9), 2424–2436. DOI
  • 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. Journal of Biotechnology, 128(4), 849–857. DOI

 

2006

  • Roxo-Rosa, M., Xu, Z., Schmidt, A., Neto, M., Cai, Z., Soares, C. M., Sheppard, D. H., & Amaral, M. D. (2006). Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms. Proceedings of the National Academy of Sciences of the United States of America, 103(47), 17891–17896. DOI
  • Teixeira, V. H., Baptista, A. M., & Soares, C. M. (2006). Pathways of H2 toward the active site of [NiFe]-hydrogenase. Biophysical Journal, 91(6), 2035–2045. 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(34), 10376–10384. DOI
  • Micaelo, N. M., Baptists, A. M., & Soares, C. M. (2006). Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field. Journal of Physical Chemistry B, 110(29), 14444–14451. DOI
  • Iley, J., Moreira, R., Martins, L., Guedes, R. C., & Soares, C. M. (2006). The Bsmoc group as a novel scaffold for the design of irreversible inhibitors of cysteine proteases. Bioorganic and Medicinal Chemistry Letters, 16(10), 2738–2741. DOI
  • Franco, I. S., Mota, L. J., Soares, C. M., & de Sá-Nogueira, I. (2006). Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding. Journal of Bacteriology, 188(8), 3024–3036. DOI
  • Lopes, S. C. D. N., 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. Journal of Physical Chemistry B, 110(7), 3385–3394. DOI

 

2005

  • Oliveira, A. S. F., Teixeira, V. H., Baptista, A. M., & Soares, C. M. (2005). Reorganization and conformational changes in the reduction of tetraheme cytochromes. Biophysical Journal, 89(6), 3919–3930. DOI
  • Matias, P. M., Pereira, I. A. C., Soares, C. M., & Carrondo, M. A. (2005). Sulphate respiration from hydrogen in Desulfovibrio bacteria: A structural biology overview. Progress in Biophysics and Molecular Biology, 89(3), 292–329. 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. Journal of Biological Inorganic Chemistry, 10(6), 667–682. 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. Biophysical Journal, 89(2), 999–1008. 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(37), 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. Journal of Physical Chemistry B, 109(30), 14691–14706. 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 immobilized on self-assembled monolayers: Surface-enhanced resonance raman spectroscopy and simulation studies. Biophysical Journal, 88(6), 4188–4199. DOI

 

2004

  • 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: Comparism with Paracoccus denitrificans aa3 haem-copper oxygen reductase. Journal of Biological Inorganic Chemistry, 9(2), 124–134. DOI
  • Victor, B. L., Baptista, A. M., & Soares, C. M. (2004). Theoretical identification of proton channels in the quinol oxidase aa 3 from Acidianus ambivalens. Biophysical Journal, 87(6), 4316–4325. 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 c 3 from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High-Resolution Structures at pH 7.6. Proteins: Structure, Function and Genetics, 54(1), 135–152. DOI
  • Garcia, S., Lourenço, N. M. T., Lousa, D., Sequeira, A. F., Mimoso, P., Cabral, J. M. S., Afonso, C. A. M., & Barreiros, S. (2004). A comparative study of biocatalysis in non-conventional solvents: Ionic liquids, supercritical fluids and organic media. Green Chemistry, 6(9), 466–470. DOI
  • Serrano, M., Neves, A., Soares, C. M., Moran Jr., C. P., & Henriques, A. O. (2004). Role of the anti-sigma factor SpoIIAB in regulation of σG during Bacillus subtilis sporulation. Journal of Bacteriology, 186(12), 4000–4013. DOI
  • Teixeira, V. H., Baptista, A. M., & Soares, C. M. (2004). Modeling Electron Transfer Thermodynamics in Protein Complexes: Interaction between Two Cytochromes c3. Biophysical Journal, 86(5), 2773–2785. DOI
  • Vidinha, P., Harper, N., Micaelo, N. M., Lourenco, N. M. T., Gomes Da Silva, M. D. R., Cabral, J., Afonso, C. A. M., Soares, C. M., & Barreiros, S. (2004). Effect of Immobilization Support, Water Activity, and Enzyme Ionization State on Cutinase Activity and Enantioselectivity in Organic Media. Biotechnology and Bioengineering, 85(4), 442–449. DOI
     

2003

  • 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. Journal of Biological Chemistry, 278(42), 41389–41399. DOI
  • Soares, C. M., Teixeira, V. H., & Baptista, A. M. (2003). Protein structure and dynamics in nonaqueous solvents: Insights from molecular dynamics simulation studies. Biophysical Journal, 84(3), 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. Journal of Biological Inorganic Chemistry, 8(4), 475–488. DOI
     

2002

  • Teixeira, V. H., Soares, C. M., & Baptista, A. M. (2002). Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail. Journal of Biological Inorganic Chemistry, 7(1–2), 200–216. DOI
  • Baptista, A. M., Teixeira, V. H., & Soares, C. M. (2002). Constant-pH molecular dynamics using stochastic titration. Journal of Chemical Physics, 117(9), 4184–4200. 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 that occurs as a structural component of the Bacillus subtilis endospore coat. Journal of Biological Chemistry, 277(21), 18849–18859. DOI

 

2001

  • 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 Tetraheme Cytochrome. Journal of Biological Chemistry, 276(47), 44044–44051. DOI
  • Abreu, I. A., Saraiva, L. M., Soares, C. M., Teixeira, M., & Cabelli, D. E. (2001). The Mechanism of Superoxide Scavenging by Archaeoglobus fulgidus Neelaredoxin. Journal of Biological Chemistry, 276(42), 38995–39001. DOI
  • Mendes, J., Baptista, A. M., Carrondo, M. A., & Soares, C. M. (2001). Implicit solvation in the self-consistent mean field theory method: Sidechain modelling and prediction of folding free energies of protein mutants. Journal of Computer-Aided Molecular Design, 15(8), 721–740. DOI
  • Mendes, J., Nagarajaram, H. A., Soares, C. M., Blundell, T. L., & Carrondo, M. A. (2001). Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure. Biopolymers, 59(2), 72–86. DOI
  • Matias, P. M., Soares, C. M., Saraiva, L. M., Coelho, R., Morais, J., le Gall, J., & Carrondo, M. A. (2001). [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: Gene sequencing, three-dimensional structure determination and refinement at 1.8 Å and modelling studies of its interaction with the tetrahaem cytochrome c3. Journal of Biological Inorganic Chemistry, 6(1), 63–81. DOI
  • Santana, M., Pereira, M. M., Elias, N. P., Soares, C. M., & Teixeira, M. (2001). Gene cluster of Rhodothermus marinus high-potential iron-sulfur protein:oxygen oxidoreductase, a caa3-type oxidase belonging to the superfamily of heme-copper oxidases. Journal of Bacteriology, 183(2), 687–699. DOI
  • Baptista, A. M., & Scares, C. M. (2001). Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. Journal of Physical Chemistry B, 105(1), 293–309. DOI
     

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. General and Comparative Endocrinology, 119(3), 241–255. DOI
  • Sadeghi, S. J., Valetti, F., Cunha, C. A., Romão, M. J., Soares, C. M., & Gilardi, G. (2000). Ionic strength dependence of the non-physiological electron transfer between flavodoxin and cytochrome C553 from D. vulgaris. Journal of Biological Inorganic Chemistry, 5(6), 730–737. DOI

 

1999

  • Mendes, J., Baptista, A. M., Carrondo, M. A., & Soares, C. M. (1999). Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model. Proteins: Structure, Function and Genetics, 37(4), 530–543. DOI
  • 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 modeling. Proteins: Structure, Function and Genetics, 37(SUPPL. 3), 55–60. DOI
  • Mendes, J., Soares, C. M., & Carrondo, M. A. (1999). Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. Biopolymers, 50(2), 111–131. DOI
  • Pereira, M. M., Santana, M., Soares, C. M., Mendes, J., Carita, J. N., Fernandes, A. S., Saraste, M., Carrondo, M. A., & Teixeira, M. (1999). The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: A HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel. Biochimica et Biophysica Acta - Bioenergetics, 1413(1), 1–13. DOI
  • 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 Cynara cardunculus L. Journal of Biological Chemistry, 274(39), 27694–27701. DOI
  • 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 1.8 and modelling studies of its interaction with the tetrahaem cytochrome c3. Journal of Biological Inorganic Chemistry, 4(4), 478–494. DOI
  • Cunha, C. A., Romão, M. J., Sadeghi, S. J., Valetti, F., Gilardi, G., & Soares, C. M. (1999). Effects of protein-protein interactions on electron transfer: Docking and electron transfer calculations for complexes between flavodoxin and c- type cytochromes. Journal of Biological Inorganic Chemistry, 4(3), 360–374. DOI
  • 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. Biophysical Journal, 76(6), 2978–2998. DOI
  • 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. Journal of Biological Inorganic Chemistry, 4(1), 73–86. DOI
  • Petukhov, M., Cregut, D., Soares, C. M., & Serrano, L. (1999). Local water bridges and protein conformational stability. Protein Science, 8(10), 1982–1989. DOI


1998

  • Fontes, N., Almeida, M. C., Garcia, S., Peres, C., Grave, J., Aires-Barros, M. R., Soares, C. M., Cabral, J. M. S., Maycock, C. D., & Barreiros, S. (1998). Cutinase activity and enantioselectivity in supercritical fluids. In Progress in Biotechnology (Vol. 15, Issue C, pp. 483–486). DOI
  • Fontes, N., Conceição Almeida, M., Peres, C., Garcia, S., Grave, J., Aires-Barros, M. R., Soares, C. M., Cabral, J. M. S., Maycock, C. D., & Barreiros, S. (1998). Cutinase activity and enantioselectivity in supercritical fluids. Industrial and Engineering Chemistry Research, 37(8), 3189–3194. DOI
  • Soares, C. M., Martel, P. J., Mendes, J., & Carrondo, M. A. (1998). Molecular dynamics simulation of cytochrome c3: Studying the reduction processes using free energy calculations. Biophysical Journal, 74(4), 1708–1721. DOI
     

1997

  • Soares, C. M., Martel, P. J., & Carrondo, M. A. (1997). Theoretical studies on the redox-Bohr effect in cytochrome c3 from Desulfovibrio vulgaris Hildenborough. Journal of Biological Inorganic Chemistry, 2(6), 714–727. DOI

 

1995

  • Stamato, F. M. L. G., Paulino, M., Garratt, R., Soares, C. M., & Tapia, O. (1995). Computer assisted simulations and molecular graphics methods in molecular design 2. Proteinases and receptor and transport proteins. Molecular Engineering, 4(4), 375–414. DOI
  • Soares, C. M., & Tapia, O. (1995). Computer assisted simulations and molecular graphics methods in molecular design - 3. Methods based on statistical mechanics procedures. Molecular Engineering, 4(4), 415–430. DOI
  • Frazão, C., Soares, C. M., Carrondo, M. A., Pohl, E., Dauter, Z., Wilson, K. S., Hervés, M., Navarro, J. A., de la Rosa, M. A., & Sheldrick, G. M. (1995). Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin. Structure, 3(11), 1159–1169. DOI
     

1994

  • Björkstén, J., Soares, C. M., Nilsson, O., & Tapia, O. (1994). On the stability and plastic properties of the interior l3 loop in R.capsulatus porin. A molecular dynamics study. Protein Engineering, Design and Selection, 7(4), 487–493. DOI
Document Actions