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Instruments / Technical Area	Publication Details	Published
I24-Microfocus Macromolecular Crystallography	Revisiting SEPT7 and the slippage of β-strands in the septin family Gabriel Brognara , Humberto D'muniz Pereira , Jose Brandao-neto , Ana Paula Ulian Araujo , Richard Charles Garratt Journal Of Structural Biology DOI: 10.1016/j.jsb.2019.04.015 Diamond Proposal Number(s): [14496] Show Abstract ▼ Abstract: Septins are GTP-binding proteins that will often spontaneously assemble into filaments. In some species, particularly budding yeast, it is well known that these are capable of associating with membranes in order to fulfill their cellular role as a component of the cytoskeleton. Different from other human septins, SEPT7 appears to be unique in that it is an essential component of all hetero-oligomeric complexes described to date. As a step towards understanding the molecular basis of filament assembly, here we present two high-resolution structures of the SEPT7 GTPase domain complexed with GDP. One of these reveals a previously unreported coordination for the magnesium ion involving four water molecules and only a tenuous connection to the protein. The higher resolution structures provide unambiguous insight into the interactions at the G-interface where a structural motif based on an antiparallel β-bridge allows for the rationalization of why some septins show nucleotide-dependent β-strand slippage and others do not.	Apr 2019
I03-Macromolecular Crystallography	Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS Fernanda A. Sala , Gareth S. A. Wright , Svetlana V. Antonyuk , Richard C. Garratt , Samar Hasnain Plos Biology 17 DOI: 10.1371/journal.pbio.3000141 Open Access Show Abstract ▼ Abstract: Superoxide dismutase-1 (SOD1) maturation comprises a string of posttranslational modifications which transform the nascent peptide into a stable and active enzyme. The successive folding, metal ion binding, and disulphide acquisition steps in this pathway can be catalysed through a direct interaction with the copper chaperone for SOD1 (CCS). This process confers enzymatic activity and reduces access to noncanonical, aggregation-prone states. Here, we present the functional mechanisms of human copper chaperone for SOD1 (hCCS)–catalysed SOD1 activation based on crystal structures of reaction precursors, intermediates, and products. Molecular recognition of immature SOD1 by hCCS is driven by several interface interactions, which provide an extended surface upon which SOD1 folds. Induced-fit complexation is reliant on the structural plasticity of the immature SOD1 disulphide sub-loop, a characteristic which contributes to misfolding and aggregation in neurodegenerative disease. Complexation specifically stabilises the SOD1 disulphide sub-loop, priming it and the active site for copper transfer, while delaying disulphide formation and complex dissociation. Critically, a single destabilising amino acid substitution within the hCCS interface reduces hCCS homodimer affinity, creating a pool of hCCS available to interact with immature SOD1. hCCS substrate specificity, segregation between solvent and biological membranes, and interaction transience are direct results of this substitution. In this way, hCCS-catalysed SOD1 maturation is finessed to minimise copper wastage and reduce production of potentially toxic SOD1 species.	Feb 2019
I04-1-Macromolecular Crystallography (fixed wavelength)	Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases Víctor Castro-fernandez , Alejandra Herrera-morande , Ricardo Zamora , Felipe Merino , Felipe Gonzalez-ordenes , Felipe Padilla-salinas , Humberto Pereira , Jose Brandao-neto , Richard C. Garratt , Victoria Guixe Journal Of Biological Chemistry DOI: 10.1074/jbc.M117.790865 Show Abstract ▼ Abstract: One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales, Methanosarcinales, and Methanococcales, as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6P) as a substrate to a fructose-6P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales.	Jul 2017
I04-1-Macromolecular Crystallography (fixed wavelength)	Filaments and fingers: novel structural aspects of the single septin from Chlamydomonas reinhardtii Andressa P. A. Pinto , Humberto M. Pereira , Ana E. Zeraik , Heloisa Ciol , Frederico M. Ferreira , Jose Brandao-neto , Ricardo Demarco , Marcos V. A. S. Navarro , Cristina Risi , Vitold E. Galkin , Richard C. Garratt , Ana P. U. Araujo Journal Of Biological Chemistry DOI: 10.1074/jbc.M116.762229 Diamond Proposal Number(s): [5073] Show Abstract ▼ Abstract: Septins are filament−forming GTP−binding proteins involved in many essential cellular events related to cytoskeletal dynamics and maintenance. Septins can self−assemble into hetero−complexes, which polymerize into highly organized, cell membrane−interacting filaments. The number of septin genes varies among organisms, and although their structure and function have been thoroughly studied in opisthokonts (including animals and fungi), no structural studies have been reported for other organisms. This makes the single septin from Chlamydomonas (CrSEPT) a particularly attractive model for investigating whether functional homopolymeric septin filaments also exist. CrSEPT was detected at the base of the flagella in Chlamydomonas, suggesting that CrSEPT is involved in the formation of a membrane diffusion barrier. Using transmission electron microscopy, we observed that recombinant CrSEPT forms long filaments with dimensions comparable to those of the canonical structure described for opisthokonts. The GTP−binding domain of CrSEPT purified as a nucleotide−free monomer that hydrolyzes GTP and readily binds its analog GTPγS. We also found that on nucleotide binding, CrSEPT forms dimers that are stabilized by an interface involving the ligand (G−interface). Across this interface, one monomer supplied a catalytic arginine to the opposing subunit, greatly accelerating the rate of GTP hydrolysis. This is the first report of an arginine finger observed in a septin and suggests that CrSEPT may act as its own GTP−activating protein (GAP). The finger is conserved in all algal septin sequences, suggesting a possible correlation between the ability to form homo−polymeric filaments and the accelerated rate of hydrolysis which it provides.	May 2017
	Analysis of two Schistosoma mansoni Uridine Phosphorylases isoforms suggests the emergence of a protein with a non-canonical function Antônio Marinho Da Silva Neto , Juliana Roberta Torini De Souza , Larissa Romanelo , Alexandre Cassago , Vitor Hugo Balasco Serrão , Ricardo Demarco , José Brandão-neto , Richard Charles Garratt , Humberto D’ Muniz Pereira Biochimie 125, 12–22 DOI: 10.1016/j.biochi.2016.02.007 PMID: 26898674 Show Abstract ▼ Abstract: Reports of Schistosoma mansoni strains resistant to praziquantel, the only therapeutic strategy available for the treatment of schistosomiasis, have motivated the scientific community towards the search for new possible therapies. Biochemical characterization of the parasite's metabolism is an essential component for the rational development of new therapeutic alternatives. One of the so far uncharacterized enzymes is uridine phosphorylase (UP) (EC 2.4.2.3), for which the parasite genome presents two isoforms (SmUPa and SmUPb) that share 92% sequence identity. In this paper, we present crystal structures for SmUPa and SmUPb in their free states as well as bound to different ligands. This we have complemented by enzyme kinetic characterization and phylogenetic analyses. Both enzymes present an overall fold and active site structure similar to other known UPs. The kinetic analyses showed conclusively that SmUPa is a regular uridine phosphorylase but by contrast SmUPb presented no detectable activity. This is particularly noteworthy given the high level of sequence identity between the two isoforms and is probably the result of the significant differences observed for SmUPb in the vicinity of the active site itself, suggesting that it is not a UP at all. On the other hand, it was not possible to identify an alternative function for SmUPb, although our phylogenetic analyses and expression data suggest that SmUPb is still functional and plays a role in parasite metabolism. The unusual UPb isoform may open up new opportunities for understanding unique features of S. mansoni metabolism.	Jun 2016
I04-1-Macromolecular Crystallography (fixed wavelength)	The structure of the giant haemoglobin from Glossoscolex paulistus José Fernando Ruggiero Bachega , Fernando Vasconcelos Maluf , Babak Andi , Humberto D'muniz Pereira , Marcelo Falsarella Carazzollea , Allen M. Orville , Marcel Tabak , Jose Brandao-neto , Richard Charles Garratt , Eduardo Horjales Reboredo Acta Crystallographica Section D Biological Crystallography 71 (6), 1257 - 1271 DOI: 10.1107/S1399004715005453 PMID: 26057666 Show Abstract ▼ Abstract: The sequences of all seven polypeptide chains from the giant haemoglobin of the free-living earthworm Glossoscolex paulistus (HbGp) are reported together with the three-dimensional structure of the 3.6 MDa complex which they form. The refinement of the full particle, which has been solved at 3.2 Å resolution, the highest resolution reported to date for a hexagonal bilayer haemoglobin composed of 12 protomers, is reported. This has allowed a more detailed description of the contacts between subunits which are essential for particle stability. Interpretation of features in the electron-density maps suggests the presence of metal-binding sites (probably Zn2+ and Ca2+) and glycosylation sites, some of which have not been reported previously. The former appear to be important for the integrity of the particle. The crystal structure of the isolated d chain (d-HbGp) at 2.1 Å resolution shows different interchain contacts between d monomers compared with those observed in the full particle. Instead of forming trimers, as seen in the complex, the isolated d chains associate to form dimers across a crystallographic twofold axis. These observations eliminate the possibility that trimers form spontaneously in solution as intermediates during the formation of the dodecameric globin cap and contribute to understanding of the possible ways in which the particle self-assembles.	Jun 2015
I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	Crystal Structure of a Schistosoma mansoni Septin Reveals the Phenomenon of Strand Slippage in Septins Dependent on the Nature of the Bound Nucleotide A. E. Zeraik , H. M. Pereira , Y. V. Santos , J. Brandao-neto , M. Spoerner , M. S. Santos , L. A. Colnago , R. C. Garratt , A. P. U. Araujo , R. Demarco Journal Of Biological Chemistry 289 (11), 7799 - 7811 DOI: 10.1074/jbc.M113.525352 PMID: 24464615 Show Abstract ▼ Abstract: Background: Septins are filament-forming proteins involved in membrane-remodeling events. Results: Two crystal structures of a septin with the highest resolution to date reveal the phenomenon of -strand slippage. Conclusion: A novel mechanistic framework for the influence of the nature of the bound nucleotide and the presence of Mg2 in septins is proposed. Significance: Identification of strand slippage might contribute to elucidating the mechanism of septin association with membranes.	Jan 2014
I04-Macromolecular Crystallography	Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues Larissa Romanello , Jose Fernando Bachega , Alexandre Cassago , Jose Brandao-neto , Ricardo Demarco , Richard Charles Garratt , Humberto D'muniz Pereira Acta Crystallographica Section D Biological Crystallography 69, 126 - 136 DOI: 10.1107/S0907444912044800 PMID: 23275171 Show Abstract ▼ Abstract: In adult schistosomes, the enzyme adenosine kinase (AK) is responsible for the incorporation of some adenosine analogues, such as 2-fluoroadenosine and tubercidin, into the nucleotide pool, but not others. In the present study, the structures of four complexes of Schistosoma mansoni AK bound to adenosine and adenosine analogues are reported which shed light on this observation. Two differences in the adenosine-binding site in comparison with the human counterpart (I38Q and T36A) are responsible for their differential specificities towards adenosine analogues, in which the Schistosoma enzyme does not tolerate bulky substituents at the N7 base position. This aids in explaining experimental data which were reported in the literature more than two decades ago. Furthermore, there appears to be considerable plasticity within the substrate-binding sites that affects the side-chain conformation of Ile38 and causes a previously unobserved flexibility within the loop comprising residues 286-299. These results reveal that the latter can be sterically occluded in the absence of ATP. Overall, these results contribute to the body of knowledge concerning the enzymes of the purine salvage pathway in this important human parasite.	Jan 2013

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