MOLECULAR SIMULATION GROUP
Prof. Rodrigo L. Silveira | Institute of Chemistry - UFRJ
ARTICLES
28. Dias, A. H. S.; Skaf, M. S.; Silveira, R. L. Computational Insights into Glucose Tolerance and Stimulation in a Family 1 β-glucosidase. J. Chem. Inf. Model. 2025, 65, 7102-7112.
27. Rade, L. L.; Generoso, W. C.; Das, S.; Souza, A. S.; Silveira, R. L., et al. Dimer-assisted mechanism of (un)saturated fatty acid decarboxylation for alkene production. Proc. Natl. Acad. Sci. USA 2023, 120, e2221483120.
26. Trentin L. N.; Pereira C. S.; Silveira, R. L.; Hill, S.; Sorieul, M.; Skaf, M. S. Nanoscale wetting of crystalline cellulose. Biomacromolecules 2021, 22, 4251-4261.
25. Pereira, C. S.; Silveira, R. L.; Skaf, M. S. QM/MM simulations of enzymatic hydrolysis of cellulose: probing the viability of an endocyclic mechanism for an inverting cellulases. J. Chem. Inf. Model. 2021, 61, 1902-1912.
24. Silveira, R. L.; Knott, B. C.; Pereira, C. S.; Crowley, M. F.; Skar, M. S.; Beckham, G. T. Transition path sampling study of the feruloyl esterase mechanism. J. Phys. Chem. B 2021, 125, 2018-2030.
23. Mallison, S. J. B.; Machovina, M. M.; Silveira, R. L., Garcia-Borràs, M.; Gallup, N.; Johnson, C. W.; Allen, M. D.; Skaf, M. S.; Crowley, M. F.; Neidle, E. L.; Houk, K. N.; Beckham, G. T.; DuBois, J. L.; McGeehan, J. E. A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion. Nat. Commun., 2018, 9, 2487.
22. Austin, H. P.; Allen, M. D.; Donohoe, B. S.; Rorrer, N. A.; Kearns, F. L.; Silveira, R. L.; Pollard, B. C.; Dominick, G.; Duman, R.; Omari, K. E.; Mykhaylyk, V.; Wagner, A.; Michener, W. E.; Amore, A.; Skaf, M. S.; Crowley, M. F.; Thorne, A. W.; Johnson, C. W.; Woodcock, H. E.; McGeehan, J. E.; Beckham, G. T. Characterization and engineering of a plastic-degrading aromatic polyesterase. Proc. Natl. Acad. Sci. USA, 2018, 115, E4350-E4357.
21. Silveira, R. L., Skaf, M. S. Concerted motions and large scale fluctuations of the Trichoderma reesei Cel7A cellobiohydrolase. Phys. Chem. Chem. Phys. 2018, 20, 7498-7507.
20. Godoy, A.; Pereira, C. S.; Ramia, M.; Silveira, R. L., Camilo, C.; Kadowaki, M.; Lange, L.; Busk, P., Nascimento, A. S.; Skaf, M. S.; Polikarpov, I. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. Sci. Rep. 2018, 8, 3678.
19. Pereira, C. S.; Silveira, R. L.; Dupree, P.; Skaf, M. S. Effects of xylan side chain substitutions on xylan-cellulose interactions and implications for thermal pretreatment of cellulosic biomass. Biomacromolecules 2017, 18, 1311-1321.
18. Silveira, R. L.; Stoyanov, S. R.; Kovalenko, A.; Skaf, M. S. Cellulose aggregation under hydrothermal pretreatment conditions. Biomacromolecules 2016, 17, 2582-2590.
17. Silveira, R. L.; Skaf, M. S. Molecular dynamics of the Bacillus subtilis expansin EXLX1: interaction with substrates and structural basis of the lack of activity of mutants. Phys. Chem. Chem. Phys. 2016, 18, 3510-3521.
16. Liberato, M. V.*; Silveira, R. L.*; Prates, E. T.; Araujo, E. A.; Pellegrini, V.; Camilo, C.; Kadowaki, M.; Neto, M.; Popov, A.; Skaf, M. S.; Polikarpov, I. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci. Rep. 2016, 6, 23473.
15. Ricci, C. G.; Silveira, R. L.; Rivalta, I.; Batista, V. S.; Skaf, M. S. Allosteric pathways in the PPARγ-RXRα nuclear receptor complex. Sci. Rep. 2016, 6, 19940.
14. Busse-Wicher, M.; Li, A.; Silveira, R. L.; Pereira, C. S.; Tryfona, T.; Anders, N.; Gomes, T.; Skaf, M. S.; Dupree, P. Evolution of xylan substitution patterns in gymnosperms and angiosperms: implications for xylan interaction with cellulose. Plant Physiol. 2016, 171, 2418-2431.
13. Gale, E.; Wirawan, R. H.; Silveira, R. L.; Pereira, C. S.; Johns, M. A.; Skaf, M. S.; Scott, J. L. Directed discovery of greener cosolvents: new cosolvents for use in ionic liquid based organic electrolyte solutions for cellulose dissolution. ACS Sustainable Chem. Eng. 2016, 4, 6200-6207.
12. Carvalho, L. A.; Silveira, R. L.; Pereira, C. S.; Skaf, M. S.; Medeiros, C. B. Provenance-based multimodal retrieval: fostering reuse and reproducibility across scientific disciplines. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2016, v. 9672, p. 183-186. (Capítulo de livro)
11. Silveira, R. L.; Stoyanov, S. R.; Gusarov, S.; Skaf, M. S.; Kovalenko, A. Supramolecular interactions in secondary plant cell walls: effect of lignin chemical composition revealed with the molecular theory of solvation. J. Phys. Chem. Lett. 2015, 6, 206-211.
10. Silveira, R. L.; Skaf, M. S. Molecular dynamics simulations of family 7 cellobiohydrolase mutants aimed at reducing product inhibition. J. Phys. Chem. B 2015, 119, 9295-9303.
9. Silveira, R. L.; Stoyanov, S. R.; Gusarov, S.; Skaf, M. S.; Kovalenko, A. Plant biomass recalcitrance: effect of hemicellulose composition on nanoscale forces that control the cell wall strength. J. Am. Chem. Soc. 2013, 135, 19048-19051.
8. Textor, L. C.; Colussi, F.; Silveira, R. L.; Serpa, V.; Squina, F. M.; Pereira, N., Jr.; Skaf, M. S.; Polikarpov, I. Cellobiohydrolase I from Trichoderma harzianum: deciphering structural features of cellobiohydrolase catalytic activity. FEBS J. 2013, 280, 56-69.
7. Prates, E. T.; Stankovic, I.; Silveira, R. L.; Liberato, M. V.; Silva, F. H.; Pereira, N., Jr.; Polikarpov, I.; Skaf, M. S. X-ray structure and molecular dynamics simulations of endoglucanase 3 from Trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module.Plos One 2013, 8, e59069.
6. Silveira, R. L.; Mart ́ınez, J.; Skaf, M. S.; Martınez, L. Enzyme microheterogeneous hydration and stabilization in supercritical carbon dioxide. J. Phys. Chem. B 2012, 116, 5671-5678.
5. Liberato, M. V.; Nascimento, A. S.; Ayers, S.; Lin, J. Z.; Cvoro, A.; Silveira, R. L.; Martınez, L.; Souza, P. C. T.; Saidemberg, D.; Deng, T.; Amato, A. A.; Togashi, M.; Hsueh, W. A.; Baxter, J. D.;
Phillips, K.; Palma, M. S.; Neves, F. A. R.; Skaf, M. S.; Polikarpov, I. Medium chain fatty acids are selective peroxisome activated receptor (PPAR) activators and Pan-PPAR partial agonists. Plos One 2012, 7, e36297.
4. Puhl, A. C.; Bernardes, A.; Silveira, R. L.; Yuan, J.; Campos, J. L. O.; Saidemberg, D.; Palma, M. S.; Cvoro, A.; Ayers, S. D.; Webb, P.; Reinach, P. S.; Skaf, M. S.; Polikarpov, I. Mode of PPARγ activation by luteolin. Mol. Pharm. 2012, 81, 788-799.
3. Amato, A. A.; Rajagopalan, S.; Carvalho, B. M.; Ayers, S. D.; Figueira, A. C. M.; Mottin, M.; Silveira, R. L.; Souza, P. C. T.; Mourao, R. H. V.; Saad, M. J. A.; Carruthers, C. W.; Togashi, M.; Simeoni, L. A.; Abdalla, D. S. P.; Skaf, M. S.; Polikarpov, I.; Lima, M. C. A.; Galdino, S. L.; Brennan, R. G.; Baxter, J. D.; Pitta, I. R.; Webb, P.; Phillips, K. J.; Neves, F. A. R. GQ-16, a novel peroxisome proliferator-activated receptor (PPARγ) ligand, promotes insulin sensitization without weight gain. J. Biol. Chem. 2012, 287, 28169-28179.
2. Bleicher, L.; Prates, E. T.; Gomes, T. C. F.; Silveira, R. L.; Nascimento, A. S.; Rojas, A. L.; Golubev, A.; Martínez, L.; Skaf, M. S.; Polikarpov, I. Molecular basis of the thermostability and thermophilicity of laminarinases: x-ray structure of the hyperthermostable laminarinase from Rhodothermus marinus and molecular dynamics simulations. J. Phys. Chem. B 2011, 115, 7940-7949.
1. Hansson, A.; Souza, P. C. T.; Silveira, R. L.; Martínez, L.; Skaf, M. S. Charmm force field parametrization of rosiglitazone. Int. J. Quantum Chem. 2011, 111, 1346-1354.