Publications

Representative publications

Griffith, M., Araújo, A.*, Travasso, R.*, Salvador, A.* (2023). 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]