Gergely N. Nagy

Gergely N. Nagy
University of Oxford | OX · Division of Structural Biology (STRUBI)

PhD

About

23
Publications
14,349
Reads
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204
Citations
Additional affiliations
September 2009 - December 2015
Hungarian Academy of Sciences
Position
  • young reserach fellow

Publications

Publications (23)
Article
Full-text available
The phospholipid biosynthesis of the malaria parasite, Plasmodium falciparum is a key process for its survival and its inhibition is a validated antimalarial therapeutic approach. The second and rate-limiting step of the de novo phosphatidylcholine biosynthesis is catalysed by CTP: phosphocholine cytidylyltransferase (PfCCT), which has a key regula...
Article
The enzyme catalyzed degradation of poly(3-hydroxybutyrate) (PHB) is a two-step process consisting of the adsorption of the enzyme on the surface of a PHB substrate and the cleavage of ester bonds. A deactivated enzyme was prepared by point mutagenesis to separate the two steps from each other. Measurements carried out with active and inactive enzy...
Article
Full-text available
The development of the malaria parasite, Plasmodium falciparum, in the human erythrocyte, relies on phospholipid metabolism to fulfil the massive need for membrane biogenesis. Phosphatidylcholine (PC) is the most abundant phospholipid in Plasmodium membranes. PC biosynthesis is mainly ensured by the de novo Kennedy pathway that is considered as an...
Article
Full-text available
The plasmodial CTP:phosphocholine cytidylyltransferase (PfCCT) is a promising antimalarial target, which can be inhibited to exploit the need for increased lipid biosynthesis during the erythrocytic life stage of Plasmodium falciparum. Notable structural and regulatory differences of plasmodial and mammalian CCTs offer the possibility to develop sp...
Article
Full-text available
Human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase), essential for DNA integrity, acts as a survival factor for tumor cells and is a target for cancer chemotherapy. Here we report that the Staphylococcal repressor protein StlSaPIBov1(Stl) forms strong complex with human dUTPase. Functional analysis reveals that this interaction results...
Article
Poly-[(R)-3-hydroxybutyrate] (PHB) films prepared by compression molding and solvent casting, respectively, were degraded with the intracellular depolymerase enzyme natively synthetized by the strain Bacillus megaterium. Quantitative analysis proved that practically only (R)-3-hydroxybutyric acid (3-HBA) forms in the enzyme catalyzed reaction, the...
Article
Repair of DNA damage relies on various pathways including the base excision repair (BER) which targets erroneous bases in the DNA. Here, Uracil-DNA glycosylases (UDGs) are responsible for recognition and removal of uracil base from the DNA. Here, we characterize the interaction of Staphylococcus aureus UDG (SAUDG) with a naturally occurring variant...
Article
A novel method was introduced for the quantitative determination of substances in aqueous solutions by using the evaporative light scattering (ELS) detector of a high performance liquid chromatograph (HPLC). The principle of the measurement is the different equilibrium vapor pressure of the solvent and the analyte resulting in decreasing evaporatio...
Article
Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all the above properties, all essential argini...
Article
Full-text available
dUTPase is essential for genome integrity. Interestingly, this enzyme from Drosophila virilis appears in an unusual form as three monomer repeats are fused together with short linker sequences, yielding a fused trimer-like dUTPase fold. Unlike homotrimeric dUTPases that are encoded by a single repeat dut gene copy, the three repeats of the D. viril...
Article
Full-text available
Control and elimination of malaria still represents a major public health challenge. Emerging parasite resistance to current therapies urges development of antimalarials with novel mechanism of action. Phospholipid biosynthesis of the Plasmodium parasite has been validated as promising candidate antimalarial target. The most prevalent de novo pathw...
Article
Cation–π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium...
Article
Cation–π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium...
Article
Full-text available
Nucleocytoplasmic trafficking of large macromolecules requires an active transport machinery. In many cases, this is initiated by binding of the nuclear localization signal (NLS) peptide of cargo proteins to importin- molecules. Fine orchestration of nucleocytoplasmic trafficking is of particularly high importance for proteins involved in maintenan...
Article
The occurrence of modified bases in DNA is attributed to some major factors: incorporation of altered nucleotide building blocks and chemical reactions or radiation effects on bases within the DNA structure. Several enzyme families are involved in preventing incorporation of non-canonical bases playing a “sanitizing” role. The catalytic mechanism o...
Article
Full-text available
A thermophilic strain producing an extracellular esterase/lipase was isolated from a hot spring in Tăşnad, Romania, and was identified phenotypically and by 16S rDNA sequencing as Anoxybacillus flavithermus (GenBank ID: JQ267733). The gene encoding the putative carboxyl esterase (GenBank ID: JX494348) was cloned by direct PCR amplification from gen...
Article
The enzyme CTP:phosphocholine cytidylyltransferase (CCT) is essential in lipid biosynthesis of Plasmodia (Haemosporida), presenting a promising antimalarial target. Here, we identified two independent gene duplication events of CCT within Apicomplexa and characterized a truncated construct of Plasmodium falciparum CCT that forms a dimer resembling...
Article
dUTP pyrophosphatases (dUTPases) are essential for genome integrity. Recent results allowed characterization of the role of conserved residues. Here we analyzed the Asp/Asn mutation within conserved Motif I of human and mycobacterial dUTPases, wherein the Asp residue was previously implicated in Mg(2+)-coordination. Our results on transient/steady-...

Questions

Questions (5)
Question
I would like to achieve heterologous overexpression of a mycobacterial enzyme in E coli that harbors a Fe-S cluster. Unfortunately, the expressed and purified His-tagged protein apparently lacked Fe judged by UV-VIs and also the inherent activity was also missing (not so much surprisingly, then). What would you recommend for promoting the expression of the holo enzyme? In fact, the FeCl3 supplement in the LB medium was also tested but was not successful.
Many thanks for the comments and suggestions!
Gergely
Question
Have you experienced/found a publication where positive heat of ligand binding was observed by ITC (ie. endothermic process)? Thanks in advance!
Question
I wish to perform a chemical crosslink experiment on a homodimer protein with low thermal stability. Due to thermal stability issues, the desired crosslink needs to be done <15°C, with preference for intra-oligomer crosslinking.
Thank you for helping me! Gergely
Question
Accidentally air was sucked in by the pumpwash protocol as the pump inlet was not immersed in solvent. Currently the pump is not capable of sucking up solvent whaterver hard it tries. Could you please give me an advice how to re-introduce solvent in the tube system? Thanks in advance!
Question
I tried to clean my Superdex 200 AKTA gel filtration column after an event of protein sample aggregation on the column during gel filtration. Unfortunately, the column seems to be literally blocked, even at the lowest possible 0.05 ml/min flow rate I cannot go further without reaching the pressure limit of 1.5 MPa. This final failure happened after about 8-9 ml of 0.5 M NaOH solution entered the column. I suppose it is not good to leave the column in these conditions (pH 10) overnight, therefore I would like to connect the column in reverse flow but I cannot find a procedure how to do this. Thank you for your kind help and supportive ideas- even a link to useful contents would be of great help.

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