Dr Ana Cordeiro Gomes Da Silva

Postdoctoral Research Associate
School of Life and Envinromental Sciences

G08 - Biochemistry and Microbiology Building
The University of Sydney

Telephone + 61 2 9351 3907
Fax +61 2 9351 5858

Biographical details

Dr Ana Silva is a Structural Biologist in the laboratory of Professor Joel Mackay with a special interest in genome regulation. Ana joined the laboratory in 2012 as an X-ray protein crystallography expert, but since then she has also become experienced in Nuclear Magnetic Resonance (NMR) and Electron Microscopy (EM) methods.

Before moving to Sydney, Ana completed her MSc degree in Chemistry at the Faculdade de Ciências da Universidade de Lisboa, Portugal (2003) and her PhD degree at the University of York, U.K. (2009). During her PhD studies in the laboratory of Professor Fred Antson, Ana was interested in the structure and function of uncharacterised RNA-binding proteins from the archaeon Methanothermobacter thermautotrophicus. After that Ana moved to the University of Manchester to work on a structural-based drug design project focused on the Mycobacterial tuberculosis MptpB phosphatase.

Research interests

At the moment, Ana works on the Nucleosome Remodelling and Deacetylase (NuRD) complex, a transcription regulator that is essential for normal embryonic development with associations to cancer progression and cell differentiation. Her main focus is the structural studies of the intact complex, as well as sub-complexes and individual subunits, by using a combination of X-ray Crystallography, Electron Microscopy and Mass Spectrometry.

Ana is also interested in the chromatin remodeller CHD4 protein, which is important for effective DNA-damage response and maintenance of genome integrity. Ana has published work on the N-terminal region of CHD4, where she determined the structure of an HMG-like domain that binds poly-ADP-ribose. This work also showed that this region is important for full nucleosome remodelling activity and for localizing CHD4 to sites of DNA-damage.

Teaching and supervision

Ana helps co-supervise undergraduate and PhD students, as well as visiting international researchers in the Mackay laboratory.

Ana has also demonstrated in the 1st year undergraduate labs.

Associations

Ana is associated with the Sydney Protein Group (SPG) since 2012; and was on the organising committee of the SPG East Coast Protein Meeting (ECPM) 2013.

Awards and honours

PhD studentship awarded by the Fundação para a Ciência e Tecnologia, Portugal, 2004-2008.

Sydney Protein Group ComBio ECR prize (shortlisted), 2012.

Themes

Biochemistry and metabolism

Selected publications

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Journals

  • Stokes, P., Robertson, N., Silva, A., Estephan, T., Trewhella, J., Guss, J., Matthews, J. (2019). Mutation in a flexible linker modulates binding affinity for modular complexes. Proteins: Structure, Function, and Bioinformatics, In Press. [More Information]
  • Sani, H., Hamzeh-Mivehroud, M., Silva, A., Walshe, J., Mohammadi, S., Rahbar-Shahrouziasl, M., Abbasi, M., Jamshidi, O., Low, J., Dastmalchi, S., Mackay, J. (2018). Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana. BioImpacts, 8(3), 167-176. [More Information]
  • Wai, D., Szyszka, T., Campbell, A., Kwong, C., Wilkinson-White, L., Silva, A., Low, J., Kwan, A., Gamsjaeger, R., Chalmers, J., Mackay, J., et al (2018). The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. Journal of Biological Chemistry, 293(19), 7160-7175. [More Information]
  • Li, C., Lev, S., Desmarini, D., Kaufman-Francis, K., Saiardi, A., Silva, A., Mackay, J., Thompson, P., Sorrell, T., Djordjevic, J. (2017). IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote clearance of Cryptococcus neoformans infection in a mouse model. Virulence, 8(8), 1833-1848. [More Information]
  • Torrado Del Rey, M., Low, J., Silva, A., Schmidberger, J., Sana, M., Sharifi Tabar, M., Isilak, M., Winning, C., Kwong, C., Bedward, M., Mackay, J., et al (2017). Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex. FEBS Journal, 284(24), 4216-4232. [More Information]
  • Mohanty, B., Silva, A., Mackay, J., Ryan, D. (2016). 1H, 13C and 15N resonance assignments of a C-terminal domain of human CHD1. Biomolecular NMR Assignments, 10(1), 31-34. [More Information]
  • Low, J., Webb, S., Silva, A., Saathoff, H., Ryan, D., Torrado Del Rey, M., Brofelth, M., Parker, B., Shepherd, N., Mackay, J. (2016). CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex. Journal of Biological Chemistry, 291(30), 15853-15866. [More Information]
  • Ittner, A., Chua, S., Bertz, J., Volkerling, A., van der Hoven, J., Gladbach, A., Przybyla, M., Bi, M., van Hummel, A., Stevens, C., Suh, L., Sutherland, G., Kril, J., Silva, A., Mackay, J., et al (2016). Site-specific phosphorylation of tau inhibits amyloid-b toxicity in Alzheimer's mice. Science, 354(6314), 904-908. [More Information]
  • Mohanty, B., Helder, S., Silva, A., Mackay, J., Ryan, D. (2016). The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain. Journal of Molecular Biology, 428(21), 4298-4314. [More Information]
  • Schmidberger, J., Sharifi Tabar, M., Torrado Del Rey, M., Silva, A., Landsberg, M., Brillault, L., Alqarni, S., Zeng, Y., Parker, B., Low, J., Mackay, J. (2016). The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7. Protein Science, 25, 1472-1482. [More Information]
  • Silva, A., Ryan, D., Galanty, Y., Low, J., Vandevenne, M., Jackson, S., Mackay, J. (2016). The N-terminal Region of Chromodomain Helicase DNA-binding Protein 4 (CHD4) Is Essential for Activity and Contains a High Mobility Group (HMG) Box-like-domain That Can Bind Poly(ADP-ribose). Journal of Biological Chemistry, 291(2), 924-938. [More Information]
  • Saathoff, H., Brofelth, M., Trinh, A., Parker, B., Ryan, D., Low, J., Webb, S., Silva, A., Mackay, J., Shepherd, N. (2015). A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells. Bioorganic and Medicinal Chemistry, 23(5), 960-965. [More Information]
  • Silva, A., Kwan, A., Mackay, J. (2014). 1H, 13C and 15N resonance assignments of an N-terminal domain of CHD4. Biomolecular NMR Assignments, 8(1), 137-139. [More Information]
  • Alqarni, S., Murthy, A., Zhanh, W., Przewloka, M., Silva, A., Watson, A., Lejon, S., Pei, X., Smits, A., Kloet, S., Shepherd, N., Stokes, P., Mackay, J., et al (2014). Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 sub-complex. Journal of Biological Chemistry, 289(32), 21844-21855. [More Information]
  • Thom, C., Traxler, E., Khandros, E., Nickas, J., Zhou, O., Lazarus, J., Silva, A., Prabhu, D., Yao, Y., Aribeana, C., Mackay, J., et al (2014). Trim58 Degrades Dynein and Regulates Terminal Erythropoiesis. Developmental Cell, 30(6), 688-700. [More Information]
  • Cui, H., Carrero-Lerida, J., Silva, A., Whittingham, J., Brannigan, J., Ruiz-Perez, L., Read, K., Gonzalez-Pacanowska, D., Gilbert, I. (2012). Synthesis and Evaluation of a-Thymidine Analogues as Novel Antimalarials. Journal of Medicinal Chemistry, 55(24), 10948-10957. [More Information]
  • Silva, A., Chechik, M., Byrne, R., Waterman, D., Ng, C., Dodson, E., Koonin, E., Antson, A., Smits, C. (2011). Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. Structure, 19(5), 622-632. [More Information]
  • Silva, A., Tabernero, L. (2010). New strategies in fighting TB: Targeting Mycobacterium tuberculosis- secreted phosphatases MptpA & MptpB. Future Medicinal Chemistry, 2(8), 1325-1337. [More Information]
  • Whittingham, J., Carrero-Lerida, J., Brannigan, J., Ruiz-Perez, L., Silva, A., Fogg, M., Wilkinson, A., Gilbert, I., Wilson, K., Gonzales-Pacanowska, D. (2010). Structural basis for the efficient phosphorylation of AZT-MP (3'-azido-3'-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase. Biochemical Journal, 428(3), 499-509. [More Information]
  • Silva, A., Byrne, R., Chechik, M., Smits, C., Waterman, D., Antson, A. (2008). Expression, purification, crystallization and preliminary X-ray studies of the TAN1 orthologue from Methanothermobacter thermautotrophicus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, F64(11), 1183-1086. [More Information]

2019

  • Stokes, P., Robertson, N., Silva, A., Estephan, T., Trewhella, J., Guss, J., Matthews, J. (2019). Mutation in a flexible linker modulates binding affinity for modular complexes. Proteins: Structure, Function, and Bioinformatics, In Press. [More Information]

2018

  • Sani, H., Hamzeh-Mivehroud, M., Silva, A., Walshe, J., Mohammadi, S., Rahbar-Shahrouziasl, M., Abbasi, M., Jamshidi, O., Low, J., Dastmalchi, S., Mackay, J. (2018). Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana. BioImpacts, 8(3), 167-176. [More Information]
  • Wai, D., Szyszka, T., Campbell, A., Kwong, C., Wilkinson-White, L., Silva, A., Low, J., Kwan, A., Gamsjaeger, R., Chalmers, J., Mackay, J., et al (2018). The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. Journal of Biological Chemistry, 293(19), 7160-7175. [More Information]

2017

  • Li, C., Lev, S., Desmarini, D., Kaufman-Francis, K., Saiardi, A., Silva, A., Mackay, J., Thompson, P., Sorrell, T., Djordjevic, J. (2017). IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote clearance of Cryptococcus neoformans infection in a mouse model. Virulence, 8(8), 1833-1848. [More Information]
  • Torrado Del Rey, M., Low, J., Silva, A., Schmidberger, J., Sana, M., Sharifi Tabar, M., Isilak, M., Winning, C., Kwong, C., Bedward, M., Mackay, J., et al (2017). Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex. FEBS Journal, 284(24), 4216-4232. [More Information]

2016

  • Mohanty, B., Silva, A., Mackay, J., Ryan, D. (2016). 1H, 13C and 15N resonance assignments of a C-terminal domain of human CHD1. Biomolecular NMR Assignments, 10(1), 31-34. [More Information]
  • Low, J., Webb, S., Silva, A., Saathoff, H., Ryan, D., Torrado Del Rey, M., Brofelth, M., Parker, B., Shepherd, N., Mackay, J. (2016). CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex. Journal of Biological Chemistry, 291(30), 15853-15866. [More Information]
  • Ittner, A., Chua, S., Bertz, J., Volkerling, A., van der Hoven, J., Gladbach, A., Przybyla, M., Bi, M., van Hummel, A., Stevens, C., Suh, L., Sutherland, G., Kril, J., Silva, A., Mackay, J., et al (2016). Site-specific phosphorylation of tau inhibits amyloid-b toxicity in Alzheimer's mice. Science, 354(6314), 904-908. [More Information]
  • Mohanty, B., Helder, S., Silva, A., Mackay, J., Ryan, D. (2016). The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain. Journal of Molecular Biology, 428(21), 4298-4314. [More Information]
  • Schmidberger, J., Sharifi Tabar, M., Torrado Del Rey, M., Silva, A., Landsberg, M., Brillault, L., Alqarni, S., Zeng, Y., Parker, B., Low, J., Mackay, J. (2016). The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7. Protein Science, 25, 1472-1482. [More Information]
  • Silva, A., Ryan, D., Galanty, Y., Low, J., Vandevenne, M., Jackson, S., Mackay, J. (2016). The N-terminal Region of Chromodomain Helicase DNA-binding Protein 4 (CHD4) Is Essential for Activity and Contains a High Mobility Group (HMG) Box-like-domain That Can Bind Poly(ADP-ribose). Journal of Biological Chemistry, 291(2), 924-938. [More Information]

2015

  • Saathoff, H., Brofelth, M., Trinh, A., Parker, B., Ryan, D., Low, J., Webb, S., Silva, A., Mackay, J., Shepherd, N. (2015). A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells. Bioorganic and Medicinal Chemistry, 23(5), 960-965. [More Information]

2014

  • Silva, A., Kwan, A., Mackay, J. (2014). 1H, 13C and 15N resonance assignments of an N-terminal domain of CHD4. Biomolecular NMR Assignments, 8(1), 137-139. [More Information]
  • Alqarni, S., Murthy, A., Zhanh, W., Przewloka, M., Silva, A., Watson, A., Lejon, S., Pei, X., Smits, A., Kloet, S., Shepherd, N., Stokes, P., Mackay, J., et al (2014). Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 sub-complex. Journal of Biological Chemistry, 289(32), 21844-21855. [More Information]
  • Thom, C., Traxler, E., Khandros, E., Nickas, J., Zhou, O., Lazarus, J., Silva, A., Prabhu, D., Yao, Y., Aribeana, C., Mackay, J., et al (2014). Trim58 Degrades Dynein and Regulates Terminal Erythropoiesis. Developmental Cell, 30(6), 688-700. [More Information]

2012

  • Cui, H., Carrero-Lerida, J., Silva, A., Whittingham, J., Brannigan, J., Ruiz-Perez, L., Read, K., Gonzalez-Pacanowska, D., Gilbert, I. (2012). Synthesis and Evaluation of a-Thymidine Analogues as Novel Antimalarials. Journal of Medicinal Chemistry, 55(24), 10948-10957. [More Information]

2011

  • Silva, A., Chechik, M., Byrne, R., Waterman, D., Ng, C., Dodson, E., Koonin, E., Antson, A., Smits, C. (2011). Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. Structure, 19(5), 622-632. [More Information]

2010

  • Silva, A., Tabernero, L. (2010). New strategies in fighting TB: Targeting Mycobacterium tuberculosis- secreted phosphatases MptpA & MptpB. Future Medicinal Chemistry, 2(8), 1325-1337. [More Information]
  • Whittingham, J., Carrero-Lerida, J., Brannigan, J., Ruiz-Perez, L., Silva, A., Fogg, M., Wilkinson, A., Gilbert, I., Wilson, K., Gonzales-Pacanowska, D. (2010). Structural basis for the efficient phosphorylation of AZT-MP (3'-azido-3'-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase. Biochemical Journal, 428(3), 499-509. [More Information]

2008

  • Silva, A., Byrne, R., Chechik, M., Smits, C., Waterman, D., Antson, A. (2008). Expression, purification, crystallization and preliminary X-ray studies of the TAN1 orthologue from Methanothermobacter thermautotrophicus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, F64(11), 1183-1086. [More Information]

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