Publications

Representative publications

Peskin, A. V., Meotti, F. C., Magon, N. J., de Souza, L. F. , Salvador, A.*, Winterbourn, C. C.* (2025). “Mechanism of Glutathionylation of the Active Site Thiols of Peroxiredoxin 2.” Journal of Biological Chemistry, 108503. doi: 10.1016/j.jbc.2025.108503

Zimmermann, J., Lang, L., Malo Pueyo, J., Riedel,  M., Wahni, K., Stobbe, D., Lux, C., Janvier, S., Vertommen, D., Lenhard, S., Hannemann, F., Castro, H., Tomas, A. M., Herrmann, J. M., Salvador, A., Mühlhaus, T., Riemer, J., Messens, J., Deponte, M., Morgan, B. (2025). “Heterooligomerization Drives Structural Plasticity of Eukaryotic Peroxiredoxins.” BioRxiv. doi: 10.1101/2025.03.03.641172.

Griffith, M., Araújo, A.*, Travasso, R.*, Salvador, A.* (2024). The architecture of redox microdomains: Cascading gradients and peroxiredoxins’ redox-oligomeric coupling integrate redox signaling and antioxidant protection. Redox Biology, 103000. doi: 10.1016/j.redox.2023.103000

Salvador, A. (2024). Pillars of theoretical biology: “Biochemical systems analysis, I, II and III,” Journal of Theoretical Biology 576:111655. doi:10.1016/j.jtbi.2023.111655.

Antunes, F., Salvador, A. (2023). How Gradients and Microdomains Determine H2O2 Redox Signaling. In I. Medraño-Fernández, G. P. Bienert, & R. Sitia (Eds.), Peroxiporins (pp. 5–20). Boca Raton: CRC Press. doi: 10.1201/9781003160649-2

Ferreira, M. J., Rodrigues, T. A., Pedrosa, A. G., Gales, L., Salvador, A., Francisco, T., Azevedo, J. E. (2023). The mammalian peroxisomal membrane is permeable to both GSH and GSSG – Implications for intraperoxisomal redox homeostasis. Redox Biology, 102764. doi: 10.1016/j.redox.2023.102764

Moreno, M. J.*, & Salvador, A. (2023). Ligand’s Partition to the Lipid Bilayer Should Be Accounted for When Estimating Their Affinity to Proteins. Molecules, 28(7), 3136. doi: 10.3390/molecules28073136

Oliveira, A. C., Filipe, H. A. L.*, & Loura, L. M. S.* (2023). Fluorescent Probes cis- and trans-Parinaric Acids in Fluid and Gel Lipid Bilayers: A Molecular Dynamics Study. Molecules, 28, 2241. doi: 10.3390/MOLECULES28052241

Sousa, T., Gouveia, M., Travasso, R. D. M.*, & Salvador, A.* (2022). How abundant are superoxide and hydrogen peroxide in the vasculature lumen, how far can they reach? Redox Biology, 102527. doi: 10.1016/j.redox.2022.102527 (SPBf Young Biophysicist 2023 prize)

Moreno, M. J.*, Loura, L. M. S., Martins, J., Salvador, A., Velazquez-Campoy, A. (2022). Analysis of the Equilibrium Distribution of Ligands in Heterogeneous Media: Approaches and Pitfalls. International Journal of Molecular Sciences, 23(17), 9757. doi: 10.3390/IJMS23179757

Oliveira, A. C., Filipe, H. A. L., Ramalho, J. P. P., Salvador, A., Geraldes, C. F. G. C., Moreno, M. J.*, Loura, L. M. S.* (2022). Modeling Gd 3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of MRI Contrast Agents. Inorganic Chemistry, 61(30), 11837–11858. doi: 10.1021/acs.inorgchem.2c01597

Lee, H. Y., Ithnin, A., Azma, R. Z., Othman, A., Salvador, A., Cheah, F. C. (2022). Glucose-6-Phosphate Dehydrogenase Deficiency and Neonatal Hyperbilirubinemia: Insights on Pathophysiology, Diagnosis, and Gene Variants in Disease Heterogeneity. Frontiers in Pediatrics, 10, 795. DOI: 10.3389/fped.2022.875877

Cordeiro, M.M., Salvador, A.*, Moreno, M.J.* (2022). Calculation of Permeability Coefficients from Solute Equilibration Dynamics: An Assessment of Various Methods. Membranes, 12, 254. DOI: 10.3390/membranes12030254

Magalhães, N., Simões, G. M., Ramos, C., Samelo, J., Oliveira, A. C., Filipe, H. A. L., Ramalho, J. P. P., Moreno, M. J.,  Loura, L. M. S.* (2022). Interactions between Rhodamine Dyes and Model Membrane Systems-Insights from Molecular Dynamics Simulations. Molecules (Basel, Switzerland), 27(4), 1420. DOI: 10.3390/MOLECULES27041420

Ledo, A., Fernandes, E., Salvador, A., Laranjinha, J., Barbosa, R.M. (2022). "In vivo hydrogen peroxide diffusivity in brain tissue supports volume signaling activity". Redox Biology, 50, 102250 DOI:10.1016/j.redox.2022.102250.

Peskin, A.V., Meotti, F.C.; Sousa, L.F., Anderson, R.F., Winterbourn, C.C.*, Salvador, A.* (2020). "Intra-dimer cooperativity between the active site cysteines during the oxidation of peroxiredoxin 2". Free Radical Biology and Medicine 158:115-125. DOI:10.1016/j.freeradbiomed.2020.07.007 [Full text][Formatted full text]

Neves, M.C., Filipe, H.A.L., Reis, R.L., Prates Ramalho, J.P., Coreta-Gomes, F., Moreno, M.J., Loura, L.M.S. (2019). "Interaction of Bile Salts With Lipid Bilayers: An Atomistic Molecular Dynamics Study". Frontiers in Physiology, 10 (393). DOI: 10.3389/fphys.2019.00393. [Full text]

Granada-Flor, A., Sousa, C., Filipe, H. A. L., Santos, M.S.C.S., Almeida, R.F.M. (2019). “Quercetin Dual Interaction at the Membrane Level”. Chemical Communications 55 (12): 1750–53. DOI: 10.1039/C8CC09656B. [Full text]

Filipe, H. A. L.; Pokorná, Š.; Hof, M.; Amaro, M.; Loura, L. M. S. (2019). “Orientation of nitro-group governs the fluorescence lifetime of nitrobenzoxadiazole (NBD)-labeled lipids in lipid bilayers”. Physical Chemistry Chemical Physics 21, 1682-1688. DOI: 10.1039/c8cp06064a (2018 PCCP HOT Article) [Full text]

Filipe, H. A. L., Javanainen, M., Salvador, A., Galvão, A. M., Vattulainen, I., Loura, L. M. S., Moreno, M. J. (2018). "Quantitative assessment of methods used to obtain rate constants from molecular dynamics simulations – translocation of cholesterol across lipid bilayers". Journal of Chemical Theory and Computation 14:3840–3848. DOI: 10.1021/acs.jctc.8b00150.

Selvaggio, G., Coelho, P.M.B.M., Salvador, A. (2018) "Mapping the phenotypic repertoire of the cytoplasmic 2-Cys peroxiredoxin - thioredoxin system. 1. Understanding commonalities and differences among cell types". Redox Biology  15:297-315. DOI:10.1016/j.redox.2017.12.008 [Full text]

Filipe, H.A.L. Cardoso, R.M.S., Loura, L.M.S., Moreno, M.J. (2017) "Interaction of amphiphilic molecules with lipid bilayers: kinetics of insertion, desorption and translocation", In: Chattopadhyay, A. (Ed.) Membrane Organization and Dynamics  Springer, pp.49-89. DOI:10.1007/978-3-319-66601-3_4.

Travasso, R.D.M., Sampaio dos Aidos, F., Bayani, A., Abranches, P., Salvador, A. (2017) "Localized Redox Relays as a Privileged Mode of Cytoplasmic Hydrogen Peroxide Signaling". Redox Biology 12:233–245. DOI:10.1016/j.redox.2017.01.003. [PDF]

Rubens, J.R., Selvaggio, G., Lu, T.K. (2016) "Synthetic mixed-signal computation in living cells". Nature Communications. 7:11658. DOI:10.1038/ncomms11658. [Full text]

Amaro, M., Filipe, H.A.L., Prates Ramalho, J.P., Hof, M., Loura, L.M.S. (2016) "Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location". Physical Chemistry Chemical Physics 18:7042–7054. DOI:10.1039/C5CP05238F [PDF]

Filipe, H., Bowman, D., Palmeira, T., Cardoso, R., Loura, L., Moreno, M.J. (2015) "Interaction of NBD-labelled fatty amines with liquid-ordered membranes: a combined molecular dynamics simulation and fluorescence spectroscopy study". Physical Chemistry Chemical Physics 17:27534-27537. DOI: 10.1039/C5CP04191K. [PDF]

Filipe, H., Santos, L., Prates-Ramalho, J., Moreno, M.J., Loura, L. (2015) "Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: A molecular dynamics study". Physical Chemistry Chemical Physics 17:20066-20079. DOI: 10.1039/C5CP01596K (cover article) [PDF]. 

Miranda-Santos, I., Gramacho, S., Pineiro, M., Martinez-Gomez, K., Fritz, M., Hollemeyer, K., Salvador, A., Heinzle, E. (2015). "Mass isotopomer analysis of nucleosides isolated from RNA and DNA using GC-MS" Analytical Chemistry 87:617-623.

Filipe, H., Salvador, A., Silvestre, J., Vaz, W., Moreno, M.J. (2014). "Beyond Overton’s rule - Quantitative Modeling of Passive Permeation Through Tight Cell Monolayers" Molecular Pharmaceutics 11:3696-706.

Benfeitas, R., Selvaggio, G., Antunes, F., Coelho, P. M. B. M., Salvador, A. (2014). "Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II." Free Radical Biology & Medicine 74, 35-49. [PDF]

Estronca, L. M. B. B., Filipe, H. A. L., Salvador, A., Moreno, M. J., Vaz, W. L. C. (2014). "Homeostasis of Free Cholesterol in the Blood - a Preliminary Evaluation and Modeling of Its Passive Transport." Journal of Lipid Research, 55, 1033-1043. [Abstract][PDF]

Dehmer, M., Emmert-Streib, F., Graber, A., Salvador, A. (Ed.s) (2011). “Applied Statistics for Network Biology”, Weinheim: Wiley. [Buy]

Coelho, P. M. B. M., Salvador, A., Savageau, M. A. (2010). “Relating Mutant Genotype to Phenotype via Quantitative Behavior of the NADPH Redox Cycle in Human Erythrocytes” PLoS ONE 5:e13031 [Full text] [PDF]

Savageau, M.A., Coelho, P.M.B.M., Fasani, R.A., Tolla, D.A., Salvador, A. (2009). “Phenotypes and tolerances in the design space of biochemical systems.” Proceedings of the National Academy of Sciences of the USA 106, 6435-6440 [Abstract] [PDF] [PNAS]

Coelho, P. M. B. M., Salvador, A., Savageau, M. A. (2009). "Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles." PLoS Computational Biology 5, e1000319. [Abstract] [PDF] [PLoS Comput. Biol.]

Salvador, A. (2008). “Book review: Uri Alon (2008). ‘An introduction to systems biology: design principles of biological circuits’ London: Chapman & Hall/CRC”, Mathematical Biosciences 215, 193-195. [Math. Biosci.]

Alves, R., Antunes, F., Salvador, A. (2006). “Tools for kinetic modeling of biochemical systems”, Nature Biotechnology 24, 667-672. [Abstract] [PDF] [Nature Biotechnology]

Gardner, R., Moradas-Ferreira, P., Salvador, A. (2006). “Why does superoxide dismutase overexpression often increase hydrogen peroxide concentrations? An alternative explanation”, Journal of Theoretical Biology 242, 798-800. [PDF]

Salvador, A., Savageau, M. A. (2006) "Evolution of enzymes in a series is driven by dissimilar functional demands”.Proceedings of the National Academy of Sciences of the USA 103, 2226-2231. [Abstract] [PDF] [PNAS]