Publications

Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release
Read, B., Mitchell, J. B. O. & da Silva, R. G., 6 Apr 2024, In: Communications Chemistry. 7, 13 p., 77.
Research output: Contribution to journal › Article › peer-review

Crystal structure, steady-state and pre-steady-state kinetics of Acinetobacter baumannii ATP phosphoribosyltransferase
Read, B., Cadzow, A., Alphey, M. S., Mitchell, J. B. O. & da Silva, R. G., 16 Jan 2024, In: Biochemistry. 63, 2, p. 230-240 11 p.
Research output: Contribution to journal › Article › peer-review

Human 2'-deoxynucleoside 5'-phosphate N-hydrolase 1: the catalytic roles of Tyr24 and Asp80
Carberry, A. E., Devi, S., Harrison, D. J. & da Silva, R. G., 2 Apr 2024, In: ChemBioChem. 25, 7, 10 p., e202400047.
Research output: Contribution to journal › Article › peer-review

Snapshots of the reaction coordinate of a thermophilic 2'-deoxyribonucleoside/ribonucleoside transferase
Tang, P., Harding, C. J., Dickson, A., da Silva, R. G., Harrison, D. J. & Melo Czekster, C., 1 Mar 2024, In: ACS Catalysis. 14, 5, p. 3090-3102 13 p.
Research output: Contribution to journal › Article › peer-review

Catalytic cycle of the bifunctional enzyme phosphoribosyl-ATP pyrophosphohydrolase/phosphoribosyl-AMP cyclohydrolase
Fisher, G., Pecaver, E., Read, B., Leese, S., Laing, E., Dickson, A., Melo Czekster, C. & da Silva, R. G., 2 Jun 2023, In: ACS Catalysis. 13, 11, p. 7669-7679 11 p.
Research output: Contribution to journal › Article › peer-review

Employing deuterium kinetic isotope effects to uncover the mechanism of (R)-3-hydroxybutyrate dehydrogenase
Machado, T. F. G. & da Silva, R. G., 5 Apr 2023, New experimental probes for enzyme specificity and mechanism. Richard, J. P. & Moran, G. (eds.). Amsterdam: Academic Press/Elsevier , p. 225-240 16 p. (Methods in enzymology; vol. 685).
Research output: Chapter in Book/Report/Conference proceeding › Chapter

Human 2'-deoxynucleoside 5'-phosphate N-hydrolase 1: mechanism of 2'-deoxyuridine 5'-monophosphate hydrolysis
Devi, S., Carberry, A. E., Zickuhr, G. M., Dickson, A., Harrison, D. J. & da Silva, R. G., 5 Sept 2023, In: Biochemistry. 62, 17, p. 2658-2668 11 p.
Research output: Contribution to journal › Article › peer-review

Allosteric inhibition of Acinetobacter baumannii ATP phosphoribosyltransferase by protein:dipeptide and protein:protein Interactions
Read, B. J., Fisher, G., Wissett, O. L. R., Machado, T. F. G., Nicholson, J., Mitchell, J. B. O. & da Silva, R. G., 14 Jan 2022, In: ACS Infectious Diseases. 8, 1, p. 197-209 13 p.
Research output: Contribution to journal › Article › peer-review

Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation
Fisher, G., Corbella, M., Alphey, M. S., Nicholson, J., Read, B., Kamerlin, S. C. L. & da Silva, R. G., 9 Dec 2022, In: Nature Communications. 13, 15 p., 7607.
Research output: Contribution to journal › Article › peer-review

Structure, dynamics, and molecular inhibition of the Staphylococcus aureus m1A22-tRNA methyltransferase TrmK
Sweeney, P., Galliford, A., Kumar, A., Raju, D., Krishna, N. B., Sutherland, E., Leo, C. J., Fisher, G., Lalitha, R., Muthuraj, L., Sigamani, G., Oehler, V., Synowsky, S. A., Shirran, S. L., Gloster, T., Melo Czekster, C., Kumar, P. & da Silva, R. G., May 2022, In: Journal of Biological Chemistry. 298, 6, 15 p., 102040.
Research output: Contribution to journal › Article › peer-review

Transition states for psychrophilic and mesophilic (R)-3-hydroxybutyrate dehydrogenase-catalyzed hydride transfer at sub-zero temperatures
Machado, T. F. G., Purg, M., Åqvist, J. & da Silva, R. G., 13 Jul 2021, In: Biochemistry. 60, 27, p. 2186–2194
Research output: Contribution to journal › Article › peer-review

Dissecting the mechanism of (R)-3-hydroxybutyrate dehydrogenase by kinetic isotope effects, protein crystallography, and computational chemistry
G. Machado, T. F., Purg, M., McMahon, S., Read, B., Oehler, V., Åqvist, J., Gloster, T. & da Silva, R. G., 18 Dec 2020, In: ACS Catalysis. 10, 24, p. 15019–15032
Research output: Contribution to journal › Article › peer-review

An exceptionally potent inhibitor of human CD73
Bowman, C. E., da Silva, R. G., Pham, A. & Young, S. W., 6 Aug 2019, In: Biochemistry. 58, 31, p. 3331-3334 4 p.
Research output: Contribution to journal › Article › peer-review

Mapping the structural path for allosteric inhibition of a short-form ATP phosphoribosyltransferase by histidine
Thomson, C. M., Alphey, M. S., Fisher, G. & da Silva, R. G., 16 Jul 2019, In: Biochemistry. 58, 28, p. 3078-3086
Research output: Contribution to journal › Article › peer-review

Allosteric activation shifts the rate-limiting step in a short-form ATP phosphoribosyltransferase
Fisher, G., Thomson, C. M., Stroek, R., Czekster, C. M., Hirschi, J. S. & da Silva, R. G., 24 Jul 2018, In: Biochemistry. 57, 29, p. 4357-4367
Research output: Contribution to journal › Article › peer-review

Catalytic and anticatalytic snapshots of a short-form ATP phosphoribosyltransferase
Alphey, M. S., Fisher, G., Ge, Y., Gould, E. R., Guerreiro Machado, T. F., Liu, H., Florence, G. J., Naismith, J. H. & da Silva, R. G., 1 Jun 2018, In: ACS Catalysis. 8, 6, p. 5601-5610 10 p.
Research output: Contribution to journal › Article › peer-review

Discovery of trifluoromethyl glycol carbamates as potent and selective covalent monoacylglycerol lipase (MAGL) inhibitors for treatment of neuroinflammation
McAllister, L., Butler, C., Mente, S., O'Neil, S. V., Fonseca, K., Piro, J., Cianfrogna, J., Foley, T., Gilbert, A., Harris, A., Helal, C. J., Johnson, D. S., Montgomery, J. I., Nason, D. M., Noell, S., Pandit, J., Rogers, B. N., Samad, T. A., Shaffer, C. L. & da Silva, R. G. & 3 others, Uccello, D. P., Webb, D. & Brodney, M. A., 12 Apr 2018, In: Journal of Medicinal Chemistry. 61, 7, p. 3008–3026
Research output: Contribution to journal › Article › peer-review

Linear Eyring plots conceal a change in rate-limiting step in an enzyme reaction
Machado, T. F. G., Gloster, T. & da Silva, R. G., 11 Dec 2018, In: Biochemistry. 57, 49, p. 6757-6761
Research output: Contribution to journal › Article › peer-review

Kinetics and structure of a cold-adapted hetero-octameric ATP phosphoribosyltransferase
Stroek, R., Ge, Y., Talbot, P. D., Glok, M. K., Bernas, K. E., Thomson, C. M., Gould, E. R., Alphey, M. S., Liu, H., Florence, G. J., Naismith, J. H. & da Silva, R. G., 7 Feb 2017, In: Biochemistry. 56, 5, p. 793-803 11 p.
Research output: Contribution to journal › Article › peer-review

A continuous and direct assay to monitor leucine-rich repeat kinase 2 activity
Silva, R. G., Geoghegan, K. F., Qiu, X. & Aulabaugh, A., 2014, In: Analytical Biochemistry. 450, 1, p. 63-69
Research output: Contribution to journal › Article › peer-review

Selective mitochondrial staining with small fluorescent probes: importance, design, synthesis, challenges and trends for new markers
Neto, B. A., Correa, J. R. & Silva, R. G., 2013, In: RSC Advances. 3, p. 5291-5301
Research output: Contribution to journal › Article › peer-review

The Biginelli reaction with an imidazolium-tagged recyclable iron catalyst: kinetics, mechanism, and antitumoral activity
Ramos, L. M., Guido, B. C., Nobrega, C. C., Correa, J. R., Silva, R. G., de Oliveira, H. C., Gomes, A. F., Gozzo, F. C. & Neto, B. A., 2013, In: Chemistry - A European Journal. 19, p. 4156-4168
Research output: Contribution to journal › Article › peer-review

Constrained bonding environment in the Michaelis complex of Trypanosoma cruzi uridine phosphorylase
Silva, R. G., Kipp, D. R. & Schramm, V. L., 2012, In: Biochemistry. 51, p. 6715-6717
Research output: Contribution to journal › Article › peer-review

Synthesis, properties and highly selective mitochondria staining with novel, stable and superior benzothiadiazole fluorescent probes
Neto, B. A., Carvalho, P. H., Santos, D. C., Gatto, C. C., Ramos, L. M., de Vasconcelos, N. M., Correa, J. R., Costa, M. B., de Oliveira, H. C. & Silva, R. G., 2012, In: RSC Advances. 2, p. 1524-1532
Research output: Contribution to journal › Article › peer-review

Arsenate and phosphate as nucleophiles at the transition states of human purine nucleoside phosphorylase
Silva, R. G., Hirschi, J. S., Ghanem, M., Murkin, A. S. & Schramm, V. L., 2011, In: Biochemistry. 50, p. 2701-2709
Research output: Contribution to journal › Article › peer-review

Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme
Silva, R. G., Murkin, A. S. & Schramm, V. L., 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, p. 18661-18665
Research output: Contribution to journal › Article › peer-review

Mass-dependent bond vibrational dynamics influence catalysis by HIV-1 protease
Kipp, D. R., Silva, R. G. & Schramm, V. L., 2011, In: Journal of the American Chemical Society. 133, p. 19358-19361
Research output: Contribution to journal › Article › peer-review

Transition-state analysis of Trypanosoma cruzi uridine phosphorylase-catalyzed arsenolysis of uridine
Silva, R. G., Vetticatt, M. J., Merino, E. F., Cassera, M. B. & Schramm, V. L., 2011, In: Journal of the American Chemical Society. 133, p. 9923-9931
Research output: Contribution to journal › Article › peer-review

Uridine phosphorylase from Trypanosoma cruzi: kinetic and chemical mechanisms
Silva, R. G. & Schramm, V. L., 2011, In: Biochemistry. 50, p. 9158-9166
Research output: Contribution to journal › Article › peer-review

Purine nucleoside phosphorylase activity and expression are upregulated in sites affected by periodontal disease
Batista Jr, E. L., Deves, C., Ayub, L., da Silva, R. G., Filho, L., Basso, L. A. & Santos, D. S., 2010, In: Journal of Periodontal Research. 45, p. 664–671
Research output: Contribution to journal › Article › peer-review

Mycobacterium tuberculosis beta-ketoacyl-ACP reductase: alpha-Secondary kinetic isotope effects and kinetic and equilibrium mechanisms of substrate binding
Silva, R. G., Rosado, L., Santos, D. S. & Basso, L. A., 2008, In: Archives of Biochemistry and Biophysics. 471, p. 1-10
Research output: Contribution to journal › Article › peer-review

Kinetic and chemical mechanisms of shikimate dehydrogenase from Mycobacterium tuberculosis
Fonseca, I. O., Silva, R. G., Fernandes, C., de Souza, O. N., Basso, L. A. & Santos, D. S., 2007, In: Archives of Biochemistry and Biophysics. 457, p. 123-133
Research output: Contribution to journal › Article › peer-review

Purine Nucleoside Phosphorylase: A Potential Target for the Development of Drugs to Treat T-Cell- and Apicomplexan Parasite-Mediated Diseases
Silva, R. G., Nunes, J. E. S., Canduri, F., Borges, J. C., Gava, L. M., Moreno, F. B., Basso, L. A. & Santos, D. S., 2007, In: Current Drug Targets. 8, p. 413-422
Research output: Contribution to journal › Article › peer-review

Beta-Ketoacyl-Acyl Carrier Protein (ACP) Reductase: Kinetic and Chemical Mechanisms
Silva, R. G., de Carvalho, L. P. S., Blanchard, J. S., Santos, D. S. & Basso, L. A., 2006, In: Biochemistry. 45, p. 13064-13073
Research output: Contribution to journal › Article › peer-review

Functional shikimate dehydrogenase from Mycobacterium tuberculosis H37Rv: Purification and characterization
Fonseca, I. O., Magalhaes, M. L. B., Oliveira, J. S., Silva, R. G., Mendes, M. A., Palma, M. S., Santos, D. S. & Basso, L. A., 2006, In: Protein Expression and Purification. 46, p. 429-437
Research output: Contribution to journal › Article › peer-review