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Publications

2024

  • Pires, C., Marques, I.J., Valério, M., Saramago, A., Santo, P.E., Santos, S., Silva, M., Moura, M.M., Matos, J., Pereira, T., Cabrera, R., Lousa, D., Leite, V., Bandeiras, T.M., Vicente, J.B., Cavaco, B.M. (2024) CHEK2 germline variants identified in familial nonmedullary thyroid cancer lead to impaired protein structure and function. Journal of Biological Chemistry,300(3). DOI 
  • da Silva Pinto, L., Junior, R.S.A., Lopes, B.R.P., da Silva, G.S., de Lima Menezes, G., Moreira, P., de Oliveira, J., da Silva, R.A., Lousa, D., Toledo, K.A. (2024) MPO interacts with hRSV particles, contributing to the virucidal effects of NETs against clinical and laboratory hRSV isolates. International Journal of Biological Macromolecules,283. DOI
  • Mendonça, D.A., Cadima-Couto, I., Buga, C.C., Arnaut, Z.A., Schaberle, F.A., Arnaut, L.G., Castanho, M.A.R.B., Cruz-Oliveira, C. (2024) Repurposing anti-cancer porphyrin derivative drugs to target SARS-CoV-2 envelope. Biomedicine and Pharmacotherapy,176. DOI 
  • Ferreira, S., Balola, A., Sveshnikova, A., Hatzimanikatis, V., Vilaça, P., Maia, P., Carreira, R., Stoney, R., Carbonell, P., Souza, C.S., Correia, J., Lousa, D., Soares, C.M., Rocha, I. (2024) Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli. Frontiers in Bioengineering and Biotechnology,12. DOI

 

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

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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

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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

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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
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