44 papers, preprints and other outputs, each with a one-paragraph summary of the main finding.
2025
Aragão D, Savko M, Oram D, Smith K, Shepard W, Flaig R
Struct Dyn (ACA 2025 meeting abstract) (2025) · Other
Meeting abstract on the automated sample-centring pipeline prototyped on I04: the murko machine-learning model from SOLEIL for finding the loop and crystal, Ophyd and Bluesky to drive the beamline, and Kubernetes and Docker so it can be deployed at other facilities.
My part: I led the project and its UKRI/BBSRC funding, and presented it at the ACA meeting in Chicago.
Flaig R, Romano P, Aragão D
J Phys Conf Ser (2025) · Methods / instrumentation · cited once
How dose-aware data collection on I04 helps users choose exposure settings that balance signal against radiation damage, which matters especially on a beamline where the beam size is changed routinely, down to microfocus.
Flaig R, Romano P, Aragão D
Struct Dyn (2025) · Other
Meeting abstract describing I04’s variable-focus optics (from 8 × 5 μm microfocus up to 110 × 100 μm), the 2022 source upgrade that raised flux across 6–18 keV, and the dose-aware and unattended data collection modes now offered to users.
2022
Munasinghe TS, Edwards MR, Tsimbalyuk S, Vogel OA, Smith KM, …, Aragão D, …, Forwood JK
Nat Commun (2022) · PubMed · cited 29 times
MERS-CoV ORF4b binds importin α through an unusual mechanism that lacks the usual lysine at the P2 site, and overlaps the binding site of NF-κB p50, a structural explanation for how the virus blocks innate immunity.
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Teakel S, Marama M, Aragão D, Tsimbalyuk S, Mackie ERR, Soares da Costa TP, Forwood JK, Cahill MA
FEBS Lett (2022) · PubMed · cited 2 times
An archaeal cytochrome b5M domain shows the same unusual haem orientation as an earlier cytb5M structure, supporting the idea that the mammalian MAPR protein family inherited it from a prokaryotic ancestor.
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2021
Cross EM, Adams FG, Waters JK, Aragão D, Eijkelkamp BA, Forwood JK
Sci Rep (2021) · PubMed · cited 25 times
Comparing annotated FabG homologs in Acinetobacter baumannii identified a low-molecular-weight 3-oxoacyl-ACP reductase as the most likely true FabG in its fatty acid synthesis pathway, a potential antibiotic target.
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Tamarit D, Teakel S, Marama M, Aragão D, Gerdes SY, Forwood JK, Ettema TJG, Cahill MA
bioRxiv (preprint) (2021) · Other · cited 7 times
The MAPR protein family, which includes the human progesterone-receptor-associated protein PGRMC1, turns out to be related to a newly recognised class of bacterial cytochrome b5 proteins. The first structure of this class (6NZX) shares the MAPR-like fold and haem orientation, supporting a bacterial origin for the family.
6NZX
Jagga B, Edwards M, Pagin M, Wagstaff KM, Aragão D, …, Forwood JK
Nat Commun (2021) · PubMed · cited 40 times
The two distant nuclear localisation signals of SOX2 form one continuous interface spanning nine of the ten ARM repeats of importin α3. This explains SOX2’s preference for importin α3 and its importance for neural stem cells and fly development.
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2019
Maghool S, Cooray NDG, Stroud DA, Aragão D, Ryan MT, Maher MJ
Life Sci Alliance (2019) · PubMed · cited 25 times
Structures of the human complex IV assembly factor Coa6 and its disease-causing W59C mutant show a disulfide-tethered helical bundle with a likely copper site, and explain the mutant’s loss of function by disulfide-linked oligomerisation.
Cross EM, Aragão D, Smith KM, Shaw KI, Nanson JD, Raidal SR, Forwood JK
Biochem Biophys Res Commun (2019) · PubMed · cited 8 times
A putative FabG enzyme from multidrug-resistant Acinetobacter baumannii has a FabG-like fold (2.0 Å) but is inactive against the FabG substrate, so it is not the fatty-acid-synthesis enzyme it was annotated as.
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Petri J, Nakatani Y, Montgomery MG, Ferguson SA, Aragão D, …, Cook GM
Open Biol (2019) · PubMed · cited 6 times
The F1-ATPase from the anaerobic pathogen Fusobacterium nucleatum is partly inhibited in ATP hydrolysis, and its structure suggests that, as in mitochondria, the activity is regulated by the ADP concentration.
6Q45
Sikanyika M, Aragão D, McDevitt CA, Maher MJ
Acta Crystallogr F Struct Biol Commun (2019) · PubMed · cited 14 times
Structure and kinetics of glutathione reductase from Streptococcus pneumoniae (2.56 Å). Its dimer interface allowed these enzymes to be grouped into three classes, and it has an unusually high Km for oxidised glutathione.
2018
Aragão D, Aishima J, Cherukuvada H, Clarken R, Clift M, …, Caradoc-Davies TT
J Synchrotron Radiat (2018) · Methods / instrumentation · PubMed · cited 554 times
MX2, the high-flux undulator microfocus beamline at the Australian Synchrotron: its design, robotic sample handling, current status, future plans and recent science.
My part: I wrote the paper and was involved in most of the upgrades it describes.
Smith KM, Tsimbalyuk S, Edwards MR, Cross EM, Batra J, …, Aragão D, …, Forwood JK
Nat Commun (2018) · PubMed · cited 75 times
Hendra and Nipah virus W proteins bind importin α3 through a larger interface and with over 50-fold higher affinity than importin α1. Chimeric importins show that the difference lies in the positioning of armadillo repeats 7 and 8.
My part: data collection, and co-supervising the PhD students on data collection, structure determination, refinement and analysis.
In the news: Charles Sturt University.
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Petri J, Shimaki Y, Jiao W, Bridges HR, Russell ER, …, Aragão D, …, Nakatani Y
Biochim Biophys Acta Bioenerg (2018) · PubMed · cited 48 times
NDH-2 bound to the quinolone inhibitor HQNO shows how inhibitors sit in the quinone-binding tunnel, a basis for designing drugs against pathogens such as Mycobacterium tuberculosis and Plasmodium falciparum.
6BDO
2017
Nakatani Y, Jiao W, Aragão D, Shimaki Y, Petri J, Parker EJ, Cook GM
Acta Crystallogr F Struct Biol Commun (2017) · PubMed · cited 15 times
A new crystallisation platform gave a 2.15 Å structure of bacterial type II NADH:quinone oxidoreductase (NDH-2), a drug target, which was then used to model how quinone substrates bind.
My part: help getting past the crystallisation problems, then data collection and processing, structure solution, refinement and analysis.
5WED
Swarbrick CM, Bythrow GV, Aragão D, Germain GA, Quadri LE, Forwood JK
Biochemistry (2017) · PubMed · cited 7 times
Mycobacteria carry an inactive class of TesB thioesterase. The Mycobacterium avium enzyme has an alanine where the catalytic aspartate should be, and restoring the aspartate restores activity, a change conserved across mycobacteria but not seen in other organisms.
My part: data collection and processing, structure solution, refinement and the structural comparison of the enzymes.
Khandokar YB, Srivastava P, Cowieson N, Sarker S, Aragão D, …, Forwood JK
J Biol Chem (2017) · PubMed · cited 13 times
A TE6 thioesterase from Neisseria meningitidis forms a hexamer with six bound GDP molecules, revealing a nucleotide-based way of regulating this enzyme family.
My part: data collection and processing, structure solution, refinement and analysis.
Blaza JN, Bridges HR, Aragão D, Dunn EA, Heikal A, Cook GM, Nakatani Y, Hirst J
Sci Rep (2017) · PubMed · cited 80 times
Kinetics, mutagenesis and structures show that NDH-2 handles its two substrates independently at separate sites, so the reaction can follow either a ping-pong or a ternary mechanism. This reconciles conflicting earlier data on this antimicrobial target.
My part: data collection from tens of crystals with a microfocus beam to pick the best wedges for merging, then processing, structure solution, refinement and the discussion of the mechanism.
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2016
Khandokar YB, Srivastava P, Sarker S, Swarbrick CMD, Aragão D, Cowieson N, Forwood JK
J Biol Chem (2016) · PubMed · cited 8 times
The PaaI thioesterase from Streptococcus pneumoniae is a tetramer of double hotdog domains that can hydrolyse both phenylacetyl-CoA and medium-chain fatty acyl-CoAs, and binds CoA through an induced-fit mechanism.
My part: data collection and processing, structure solution, refinement, and helping propose the mechanism.
Chaston JJ, Smits C, Aragão D, Wong AS, Ahsan B, …, Stewart AG
Structure (2016) · PubMed · cited 33 times
Sulfolobales archaea combine three chaperonin subunits into different complexes for cold, normal and heat-stress conditions. Crystallography and electron microscopy show their geometry, including a new subunit arrangement.
My part: input on the experimental design, data collection and processing, structure solution, refinement and analysis.
Sarker S, Terrón MC, Khandokar Y, Aragão D, Hardy JM, …, Forwood JK
Nat Commun (2016) · PubMed · cited 79 times
Structures of the capsid protein of beak and feather disease virus, one of the simplest animal viruses, show how single-stranded DNA regulates its assembly and how the assemblies switch the exposure of its DNA-binding, nuclear-targeting arm.
My part: data collection with a microfocus beam and fine slicing to cope with the very large unit cells, processing, structure solution and refinement, and ideas for the DNA-loading experiments.
In the news: Cosmos (with my image of the capsid), ANSTO, Charles Sturt University, Australian Geographic and SBS News.
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2015
Cowieson NP, Aragão D, Clift M, Ericsson DJ, Gee C, …, Caradoc-Davies T
J Synchrotron Radiat (2015) · Methods / instrumentation · PubMed · cited 469 times
The design, endstation and science highlights of MX1, the bending-magnet crystallography beamline at the Australian Synchrotron that serves both chemical and macromolecular crystallographers.
My part: I co-wrote the paper with Nathan Cowieson and took part in most of the upgrades it describes.
Li D, Stansfeld PJ, Sansom MSP, Keogh A, Vogeley L, …, Aragão D, …, Caffrey M
Nat Commun (2015) · PubMed · cited 43 times
Diacylglycerol kinase captured with both its lipid substrate and an ATP analogue, with the phosphate positioned for transfer. This led to a proposed catalytic mechanism and evidence that the active site arose by convergent evolution.
My part: I suggested using a non-hydrolysable ATP analogue to trap the enzyme partway through its reaction, and metals to help the ligand bind; I worked on the analysis and refinement of several of the structures and on the manuscript.
In the news: Phys.org and Trinity College Dublin.
4UXW
2013
Li D, Lyons JA, Pye VE, Vogeley L, Aragão D, …, Caffrey M
Nature (2013) · PubMed · cited 95 times
Crystal structures of three functional forms of diacylglycerol kinase, a 121-residue membrane enzyme studied for half a century, show a trimer with shared active sites and contradict the domain swapping proposed by an earlier NMR model.
My part: lead crystallographer, from data collection and processing to solving the structure by experimental phasing, refinement and the analysis of the mechanism.
In the news: GM/CA at the Advanced Photon Source.
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2012
Li D, Boland C, Aragão D, Walsh K, Caffrey M
J Vis Exp (2012) · Methods / instrumentation · PubMed · cited 44 times
A video protocol for harvesting and cryo-cooling the small, fragile crystals that grow in sticky lipidic mesophases, one of the practical bottlenecks of the in meso method for membrane proteins.
Lyons JA, Aragão D, Slattery O, Pisliakov AV, Soulimane T, Caffrey M
Nature (2012) · PubMed · cited 126 times
The 2.36 Å structure of the Thermus thermophilus caa3 oxidase, which carries its own cytochrome c domain, shows how the electron-transfer complex between cytochrome c and the oxidase is built, and revealed a new membrane subunit and a bound native lipid.
In the news: Phys.org and Silicon Republic.
2YEV
2011
Stepanov S, Hilgart M, Yoder DW, Makarov O, Becker M, …, Aragão D, …, Fischetti RF
J Appl Crystallogr (2011) · Methods / instrumentation · PubMed · cited 17 times
New X-ray fluorescence tools on the GM/CA beamlines at the Advanced Photon Source: fast on-the-fly energy scans, fluorescence rastering to find small or invisible crystals, and automatic signal optimisation to reduce radiation damage.
Höfer N, Aragão D, Lyons JA, Caffrey M
Cryst Growth Des (2011) · PubMed · cited 33 times
Tests how the choice of host lipid in the lipidic mesophase affects the crystallisation and structure of the pore-forming antibiotic gramicidin, and whether the membrane environment can favour one of its conformations.
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Pye VE, Aragão D, Lyons JA, Caffrey M
Cryst Growth Des (2011) · Other · cited 3 times
An overview of the 13th International Conference on the Crystallization of Biological Macromolecules (ICCBM13), introducing the special issue that collected work presented at the meeting.
Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragão D, …, Kobilka BK
Nature (2011) · PubMed · cited 784 times
An agonist designed to bind covalently to the β2 adrenergic receptor made it possible to crystallise an agonist-bound receptor in the lipidic cubic phase, giving a view of how agonists bind and start to activate this G-protein-coupled receptor.
In the news: FCT NOVA and ITQB NOVA (2012). Brian Kobilka’s Nobel lecture.
3PDS
Höfer N, Aragão D, Caffrey M
Biophys J (meeting abstract) (2011) · Other · cited 2 times
Meeting abstract on using the lipidic cubic phase as a mimic of the cell membrane, from the in meso crystallisation work on transmembrane peptides.
2008
Frazão C, Aragão D, Coelho R, Leal SS, Gomes CM, Teixeira M, Carrondo MA
FEBS Lett (2008) · PubMed · cited 11 times
A 2.0 Å structure of the native ferredoxin from the archaeon Acidianus ambivalens, with its zinc site and both iron-sulfur clusters ([3Fe-4S] and [4Fe-4S]) intact, unlike the earlier, artificially converted structure from a related species.
My part: I grew the crystals at ITQB around 2000, long before the paper.
2VKR
Aragão D, Mitchell EP, Frazão CF, Carrondo MA, Lindley PF
Acta Crystallogr D Biol Crystallogr (2008) · PubMed · cited 30 times
The hybrid cluster protein from D. vulgaris, purified and crystallised without oxygen and solved by MAD at the iron edge (1.35 Å). Its similarity to carbon monoxide dehydrogenases helps explain the hybrid cluster and predicts a dimeric structure for class 3 proteins.
This paper was on the cover of the June 2008 issue of Acta Crystallographica D.
1W9M
2007
PhD thesis
Structure to function studies in hybrid cluster proteins and glucose-1-phosphate uridylyltransferases
PhD thesis in Biochemistry, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, with the ESRF, Grenoble. Supervisors: Carlos Frazão (ITQB) and Edward Mitchell (ESRF). Final exam 9 October 2007. ISBN 978-989-20-0807-3. Funded by FCT scholarship SFRH/BD/6480/2001
Crystal structures of two very different protein families. The hybrid cluster proteins from Desulfovibrio carry an unusual iron–sulfur–oxygen cluster, and the structures help explain how it is built and what it might do. Glucose-1-phosphate uridylyltransferase (UgpG) from Sphingomonas elodea makes a sugar building block for gellan gum. The work was split between ITQB NOVA in Oeiras and the ESRF in Grenoble. (ITQB list of PhD theses, archived copy)
Thesis (PDF, 7 MB)
Aragão D, Fialho AM, Marques AR, Mitchell EP, Sá-Correia I, Frazão C
J Bacteriol (2007) · PubMed · cited 33 times
The structure of S. elodea UgpG, a key enzyme in making the food thickener gellan gum, reveals a quaternary structure not seen before in its enzyme family, even though each subunit closely resembles the related thymidylyltransferases.
2UX8
2003
Aragão D, Macedo S, Mitchell EP, Romão CV, Liu MY, …, Lindley P
J Biol Inorg Chem (2003) · PubMed · cited 47 times
High-resolution structures of the hybrid cluster protein from two Desulfovibrio species, solved after reduction (1.25 and 1.55 Å). The protein fold is unchanged, but the iron and sulfur atoms of the unusual hybrid cluster move, giving clues to how these proteins work.
A figure from this paper was chosen for the 2003 cover of the Journal of Biological Inorganic Chemistry.
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Aragão D, Frazão C, Sieker L, Sheldrick GM, LeGall J, Carrondo MA
Acta Crystallogr D Biol Crystallogr (2003) · PubMed · cited 25 times
The dimeric cytochrome c3 from Desulfovibrio gigas, refined to 1.2 Å. Comparing it with every known cytochrome c3 domain revealed regions conserved despite very different sequences, and a buried water molecule that probably carries electrons between two of the haems.
1GYO
Macedo S, Aragão D, Mitchell EP, Lindley P
Acta Crystallogr D Biol Crystallogr (2003) · PubMed · cited 13 times
Knowing the fully oxidised and fully reduced forms made it possible to resolve a 1.25 Å structure of the hybrid cluster protein containing molecules in both states, clarifying how the cluster’s iron and persulfide atoms move on reduction.
1UPX
1999
Fonseca A, Gouveia C, Fernandes JP, Câmara AS, Pinheiro A, Aragão D, Silva JP, Sousa MI
In: Câmara AS, Raper J (eds), Spatial Multimedia and Virtual Reality, pp. 71–88. Taylor & Francis, London (1999; reissued by CRC Press, 2021) (1999) · Other
A book chapter on the multimedia CD-ROM that GASA, the environmental systems group at FCT NOVA, made for Expo 98 in Lisbon, letting people explore environmental information about Portugal. My part, as an undergraduate, was entering much of the data behind it.
