Hereby you may find some highlights making you eager to read this very interesting article.
A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies.
A) Secondary structure content determination of UDE and its fragments using VUVCD and SELCON3 program. Vacuum-ultraviolet circular dichroism (Δε) spectra of the UDE protein and some of its truncated fragments measured over the wavelength region of λ=170-255 nm. spectrum of UDE is shown in red. B) Final estimate for the secondary structure of UDE obtained as an average of the structure of full-length UDE protein and in its nine truncated fragments were determined from the CD spectra and the amino acid sequence using a neural network algorithm. The α-helical segments and β-strands are displayed in blue and red, respectively, while both turns and disordered parts appear in yellow.
Article of Judit Szabó et al. published in Scientific Reports
Hereby you may find some highlights making you eager to read this very interesting article.
Abstract Members of the dUTPase superfamily play an important role in the maintenance of the pyrimidine nucleotide balance and of genome integrity. dCTP deaminases and the bifunctional dCTP deaminase-dUTPases are cooperatively regulated by dTTP. However, the manifestation of allosteric behavior within the same trimeric protein architecture of dUTPases, the third member of the superfamily, has been a question of debate for decades. Therefore, we designed hybrid dUTPase trimers to access conformational states potentially mimicking the ones observed in the cooperative relatives. We studied how the interruption of different steps of the enzyme cycle affects the active site cross talk. We found that subunits work independently in dUTPase. The experimental results combined with a comparative structural analysis of dUTPase superfamily enzymes revealed that subtile structural differences within the allosteric loop and the central channel in these enzymes give rise to their dramatically different cooperative behavior. We demonstrate that the lack of allosteric regulation in dUTPase is related to the functional adaptation to more efficient dUTP hydrolysis which is advantageous in uracil-DNA prevention.
Asymmetric hybrid enzymes exhibit non-cooperative kinetics in the different reaction steps.
(a) Schematic representation of the created hybrids (covalent heterotrimers). Blue, red and yellow spheres represent dUTPase protomers containing the D102N, A98F and T148STOP mutations, respectively. Note, that all protomers contain the F158W mutation as well, except for the T148STOP mutant. Grey areas indicate enzymatic inactivity. (b) Steady-state kinetics of human dUTPase constructs: WWW (solid square), WWN (solid triangles), WNN (open triangles), WWF (solid stars), WWS (solid circle). Smooth lines through the data are hyperbolic fits yielding Vmax= 7.9 ± 0.5 s−1 for WWW, Vmax = 4.4 ± 0.2 s−1 for WWF, Vmax = 3.8 ± 0.2 s−1 for WWN, Vmax = 1.8 ± 0.1 s−1 for WNN, Vmax = 2.9 ± 0.3 s−1 for WWS. KM values are listed in Table 1. (c) Comparison of the catalytic constants (striped bar) and apparent catalytic constants (grey bar) for determined by single turnover (transient kinetics) and steady-state experiments, respectively. See also Table 1 for the data. (d) Fluorescence intensity titrations upon dUTP binding to the various dUTPase constructs measured by stopped-flow (the symbol code is identical to that in panel (b). Smooth lines through data are hyperbolic fits yielding Kd values summarized in Table 1.
Five members of the laboratory were awarded by Richter Gedeon Short Term Research Grant
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András Benedek, Kinga Nyíri, Veronika Papp-Kádár, Hajnalka Pálinkás and Judit Eszter Szabó
The Awardees thank to Richter Gedeon Ltd. for supporting their attendance at international conferences and courses.
Beáta G. Vértessy, Chair of Board of the US-Hungarian Fulbright Foundation, signed agreement with Prof László Lovász, President of the Hungarian Academy of Sciences for joint support
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The Hungarian Academy of Sciences, represented by its President, Professor László Lovász, and the Hungarian-American Fulbright Commission, represented by Board Chair Professor Beáta Vértessy and Károly Jókay, Executive Director, signed a multi-year agreement on March 23, 2016, in the the ornate concert hall in the Academy’s main building. Fulbright Board members Tamás Magyarics, Tibor Frank and Eric Watnik (representing the US Embassy) also took part in the ceremony.
The agreement will support Hungarian scholars who are employees of the Academy’s research network, on various “Momentum” (Lendület) teams, or are active in Academy-funded projects at Hungary’s universities. During the upcoming academic year 2016-17, two Hungarian researchers will be in the US on jointly-funded Fulbrights: one geophysicist and one astrophysicist. US scholars will also be eligible for the joint grants, and in 2016-17, one US sociologist will arrive in Budapest.
The Academy and Fulbright expect that up to 4 additional scholars per year will be able to conduct research in the US and in Hungary based on the terms of the agreement just signed.
For US scholars interested in applying for the 2017-18 Academic Year, see the CIES catalog of awards at: catalog.cies.org
For further information contact the Fulbright Commission in Budapest at: This email address is being protected from spambots. You need JavaScript enabled to view it.
New paper published in Structural Chemistry
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Our paper entitled "Exploring the role of the phage-specific insert of
bacteriophage Φ11 dUTPase" has been published in Structural Chemistry.
dUTPases are essential for maintaining genome integrity. Recently, in the
case of a dUTPase from a Staphylococcal phage, another different
physiological function was also suggested. Namely, it was shown that
dUTPase from the Staphylococcus aureus bacteriophage Ф11 is capable of
binding to the Staphylococcal Stl repressor protein. This binding
interferes with the function of Stl. In the present study, we investigated
the putative role of a phage dUTPase-specific peptide segment in the
interaction of dUTPase with Stl and in impeding Stl–DNA complex formation.
We show that dUTPase from Mycobacterium tuberculosis that lacks the
phage-specific insert is also capable of disrupting the complexation
between Stl and DNA. Hence, the insert segment is not essential for
perturbation of the Stl function. However, we also demonstrate that in case
of the phage dUTPase, the insert-lacking construct is deficient in
perturbation of Stl activity. These findings clearly indicate that the
phage-specific insert has a well-defined role only in the context of the
phage dUTPase.
Structural Chemistry, 30 August 2015, doi: 10.1007/s11224-015-0652-2
DESY synchrotron visit for SAXS data collection
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From 28-30 June three members of our group (Ibolya Leveles, Kinga Nyíri and
Gergely Nagy) visited the DESY synchrotron in Hamburg for measuring small
angle X-ray scattering (SAXS) of proteins from various projects. During the
24-hour long shift they performed several batch-mode and SEC-SAXS
experiments, hopefully the results will reveal yet unknow structural
properties of the proteins of our interest. We wish to thank dr. Haydyn
Mertens at DESY P12 beamline for his kind help in the SAXS data collection.
A BME három oktatója részesült Mestertanár Aranyérem kitüntetésben.
Az Országos Tudományos Diákköri Tanács (OTDT) kétévente ismeri el aranyéremmel a kiemelkedő oktatói és hallgatói teljesítményeket. Idén 46 oktató, kutató részesült Mestertanár Aranyérem kitüntetésben a hallgatói tudományos tevékenység szervezéséért, elősegítéséért, hosszú idő óta számos diák eredményes felkészítésében közreműködő, a színvonalas tanár-diák együttműködésben megvalósuló műhelymunkáért és a tudományos iskolateremtésért. Őket egyrészt az intézményük, másrészt az OTDT szakmai bizottságai jelölték az elismerésre.
/A Budapesti Műszaki és Gazdaságtudományi Egyetem Mestertanár Aranyérmesei:/
*Pokol Gergő*, a BME TTK Nukleáris Technikai Intézet docense (Fizika, Földtudományok és Matematika Szekció)
*Tapolcai János*, a BME VIK Távközlési és Médiainformatikai Tanszék docense (Informatika Tudományi Szekció)
*Vértessy Beáta*, a BME VBK Alkalmazott Biotechnológia és Élelmiszertudományi Tanszék egyetemi tanára (Kémiai és Vegyipari Szekció)
A testület június végén döntött a pályázatokról, a kitüntetéseket pedig 2015 őszén, a XXXII. Országos Tudományos Diákköri Konferencia záró és értékelő ünnepségén adják át a Magyar Tudományos Akadémián.
Practical X-ray course, Oulu, 18-22, May
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Between 18-22 May, Gergely N. Nagy has attended the Practical X-ray course on methods in protein crystallography: data collection, data processing, and phasing at Oulu, Finland. Throughout the outstanding and intense lectures he gained considerable knowledge of the theoretical basis of these crystallographic processes. He also got familiar with the X-ray data collection possibilities at key European synchrotrons. In addition he acquired hands-on experience with various relevant softwares e.g. XDS, iMosflm, CCP4 package.
K&H Marathon
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Our group has again considered an athletic challenge with success - six of us ran a marathon relay in recordhigh temperatures on June 14, 2015 in the Városliget. Our "Futprinting" team (Beáta
Vértessy, András Benedek, Kinga Nagy, Tímea Nagy, Zsófia Bata and Dávid Szabó) each ran 7 km thus completing together the 42 km race in the beautiful, although rather hot weather.
Great Success of lab members at Scientific Students' Associations Conference
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Paula Dobrotka, Fanni Hajdú, Bianka Kőhegyi, Gergely Tihanyi and Lilla Vida made high level presentations at the Biocemistry Section of the Scientific Students' Associations Conference at the Budapest University of Technology and Economics yesterday.
The jury honoured them with two prize of merit awards and three 1st prizes, from which two also included a special prize funded by pharmaceutical companies.
Congratulation for their great to all of them and their great supervisors!
Lívia Marton at Proteins and Nanoparticles at Membranes Workshop
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Lívia Marton is participating at the Proteins and Nanoparticles at Membranes Workshop at Jülich, Germany (19-22 October 2014).
She is presenting a poster about her PhD project on the “Localization study of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in mammalian cell lines”.
dUTPases are essential for maintaining genome integrity. Recently, in the
case of a dUTPase from a Staphylococcal phage, another different
physiological function was also suggested. Namely, it was shown that
dUTPase from the Staphylococcus aureus bacteriophage Ф11 is capable of
binding to the Staphylococcal Stl repressor protein. This binding
interferes with the function of Stl. In the present study, we investigated
the putative role of a phage dUTPase-specific peptide segment in the
interaction of dUTPase with Stl and in impeding Stl–DNA complex formation.
We show that dUTPase from Mycobacterium tuberculosis that lacks the
phage-specific insert is also capable of disrupting the complexation
between Stl and DNA. Hence, the insert segment is not essential for
perturbation of the Stl function. However, we also demonstrate that in case
of the phage dUTPase, the insert-lacking construct is deficient in
perturbation of Stl activity. These findings clearly indicate that the
phage-specific insert has a well-defined role only in the context of the
phage dUTPase.
Structural Chemistry, 30 August 2015, doi: 10.1007/s11224-015-0652-2
