da Silva lab
Group Highlights
Enzymes catalyse virtually all chemical reactions in living organisms, making their rates compatible with life. These proteins have evolved to utilize a range of strategies to achieve incredible rate enhancements in comparison with the corresponding non-catalysed reactions. The study of enzymatic mechanisms is fundamental to elucidate how enzymes work in physical and chemical terms, and how their activity is regulated.
In the da Silva Lab, we apply techniques of molecular biology, biochemistry, structural biology and physical organic chemistry to unravel the mechanisms of enzymatic reactions catalysed by multi-protein allosteric complexes, tRNA methyltranferases, and nucleotide hydrolases. Particular attention is given to transition-state structure, inhibitor design, and fast protein dynamics.
We are part of the Biomedical Sciences Research Complex and the School of Biology at the University of St Andrews. Our lab is located in the BMS Annexe Building on North Haugh.
Our lab website: https://dasilva.wp.st-andrews.ac.uk/
Research
Research in our group concerns the enzymology of histidine biosynthesis and tRNA methylation. We employ a breadth of strategies and techniques (e.g. gene cloning and expression, site-directed mutagenesis, protein purification, steady-state and pre-steady-state kinetics, isothermal titration calorimetry, differential scanning fluorimetry, mass spectrometry, NMR, isotopic labelling of substrates and enzymes, kinetic and binding isotope effects, density-functional theory calculations, protein crystallography, inhibitor design and synthesis) to elucidate the mechanisms of enzymatic reactions. We harness that information to design specific enzyme inhibitors of promising novel targets for antibiotic and anticancer development.
ATP phosphoribosyltransferase and phosphoribosyl-ATP pyrophosphohydrolase/phosphoribosyl-AMP cyclohydrolase
The biosynthesis of histidine involves some unusual enzymatic reactions. Efforts are focused on the first, second and third steps of the pathway, the hetero-octameric and allosteric ATP phosphoribosyltransferase (ATPPRT) and the bifunctional phosphoribosyl-ATP pyrophosphohydrolase/phosphoribosyl-AMP cyclohydrolase (HisIE). The long-term goal is to understand the principles that underpin enzyme catalysis and allostery in these systems to enable inhibitor design towards novel antibiotics against Acinetobacter baumannii.
m1A22-tRNA methyltransferase
The enzyme m1A22-tRNA methyltransferase (TrmK) is essential for Staphylococcus aureus survival but absent in humans. We are elucidating the mechanism and substrate specificity of this enzyme, and developing covanlent inhibitors of TrmK towards novel antibiotics against MRSA. We are also investigating human tRNA methyltransferases involved in resistance to current cancer treatments.
Group Members
Dr Rafael G da Silva – Principal Investigator
I’m a native of Porto Alegre, a city in the south of Brazil. I received a BSc degree in Biology (2002) from Universidade Federal do Rio Grande do Sul, and MSc (2005) and PhD (2008) degrees in Biochemistry from the same university, under the supervision of Dr Luiz Basso. After post-doctoral training (2008-2012) with Dr Vern Schramm at the Albert Einstein College of Medicine in New York, I worked at Pfizer in Connecticut, first as Senior Scientist, then as Principal Scientist (2012-2014). In 2015, I moved to Scotland as a research group leader at the University of St Andrews.
Dr Suneeta Devi – Post-doctoral Fellow
I am from the historical city of Benaras, India. I was fascinated by the abilities of scientific research to alleviate human life throughout my school days, which led me to pursue my undergraduate degree in biology and master’s in biotechnology. My evolving scientific curiosities led me to pursue my PhD with Prof. S Gourinath in structural biology from Jawaharlal Nehru University, New Delhi, India. During my doctoral training, I investigated the structure-function relationship of sulfur metabolic enzymes using pathogenic bacteria as a model. Recently, I joined the da Silva lab at the University of St Andrews to investigate the underlying mechanism of the human DNPH1 enzyme and to develop biocatalytic routes to isotope-labelled nucleotides, funded by IBioIC.
Gemma Fisher – Biology (EASTBIO) PhD Student
I am from Glasgow and completed a BSc in Biochemistry at the University of St Andrews. I am now studying towards a PhD in Biology as part of the EASTBIO Doctoral Training Partnership. My research will elucidate the mechanism of P. arcticus ATP phosphoribosyltransferase with the aim to generate opportunities for protein engineering.
Ben Read – Biology (EASTBIO) PhD Student
Originally from the south-east of England, I came to the University of St Andrews where I completed my BSc in Biochemistry. I have continued at St Andrews to undertake a PhD in the da Silva lab as part of the EATBIO Doctoral Training Partnership. My project aims to elucidate the mechanism behind allosteric inhibition/activation of Acinetobacter baumannii ATP phosphoribosyltransferase, which has untapped antimicrobial potential.
Publications
Chapters
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
Articles
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
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
Contact
Join Us
We are always interested in recruiting enthusiastic and motivated students and post-docs to our group. Specific projects for Ph.D. students or post-docs are normally advertised here and on FindAPhD.
Prospective Ph.D. students and post-docs bringing their own fellowships, or who want to apply for a fellowship, and are interested in joining the lab, should email Dr da Silva ([email protected]) at any time to discuss available opportunities.
PhD Projects:
- Mechanisms of bacterial enzymes: towards novel antibiotics
Funding mechanisms for post-docs include:
Newton International Fellowships (http://www.newtonfellowships.org/)
Human Frontier Science Program Post-doctoral Fellowships (http://www.hfsp.org/funding/postdoctoral-fellowships)
Commonwealth Rutherford Fellowships (http://cscuk.dfid.gov.uk/apply/rutherford-fellowships/)
Marie Sklodowszka-Curie Individual Fellowships (https://ec.europa.eu/research/mariecurieactions/actions/get-funding/individual-fellowship-2018_en)
Related themes:
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