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1.

001-es BibID:BIBFORM076746
Első szerző:Bozóki Beáta (molekuláris biológus)
Cím:Use of Recombinant Fusion Proteins in a Fluorescent Protease Assay Platform and Their In-gel Renaturation / Bozóki Beáta, Mótyán János András, Miczi Márió, Gazda Lívia Diána, Tőzsér József
Dátum:2019
ISSN:1940-087X
Megjegyzések:Proteases are intensively studied enzymes due to their essential roles in several biological pathways of living organisms and in pathogenesis; therefore, they are important drug targets. We have developed a magnetic-agarose-bead-based assay platform for the investigation of proteolytic activity, which is based on the use of recombinant fusion protein substrates. In order to demonstrate the use of this assay system, a protocol is presented on the example of human immunodeficiency virus type 1 (HIV-1) protease. The introduced assay platform can be utilized efficiently in the biochemical characterization of proteases, including enzyme activity measurements in mutagenesis, kinetic, inhibition, or specificity studies, and it may be suitable for high-throughput substrate screening or may be adapted to other proteolytic enzymes. In this assay system, the applied substrates contain N-terminal hexahistidine (His6) and maltose-binding protein (MBP) tags, cleavage sites for tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein. The substrates can be efficiently produced in Escherichia coli cells and easily purified using nickel (Ni)-chelate-coated beads. During the assay, the proteolytic cleavage of bead-attached substrates leads to the release of fluorescent cleavage fragments, which can be measured by fluorimetry. Additionally, cleavage reactions can be analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A protocol for the in-gel renaturation of assay components is also described, as partial renaturation of fluorescent proteins enables their detection based on molecular weight and fluorescence.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
recombinant fusion protein substrate
protease assay
Ni-NTA magnetic agarose beads
fluorescent protein
in-gel renaturation
human immunodeficiency virus type 1 protease
Megjelenés:Journal of Visualized Experiments. - 143 (2019), p. 1-15. -
További szerzők:Mótyán János András (1981-) (biokémikus, molekuláris biológus) Miczi Márió Gazda Lívia Diána (1989-) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:GINOP-2.3.2-15-2016-00044
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2.

001-es BibID:BIBFORM072540
Első szerző:Bozóki Beáta (molekuláris biológus)
Cím:A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening / Beáta Bozóki, Lívia Gazda, Ferenc Tóth, Márió Miczi, János András Mótyán, József Tőzsér
Dátum:2018
ISSN:0003-2697
Megjegyzések:In connection with the intensive investigation of proteases, several methods have been developed for analysis of the substrate specificity. Due to the great number of proteases and the expected target molecules to be analyzed, time- and cost-efficient high-throughput screening (HTS) methods are preferred. Here we describe the development and application of a separation-based HTS-compatible fluorescent protease assay, which is based on the use of recombinant fusion proteins as substrates of proteases. The protein substrates used in this assay consists of N-terminal (hexahistidine and maltose binding protein) fusion tags, cleavage sequences of the tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein (mApple or mTurquoise2). The assay is based on the fluorimetric detection of the fluorescent proteins, which are released from the magnetic bead-attached substrates by the proteolytic cleavage. The protease assay has been applied for activity measurements of TEV and HIV-1 proteases to test the suitability of the system for enzyme kinetic measurements, inhibition studies, and determination of pH optimum. We also found that denatured fluorescent proteins can be renatured after SDS-PAGE of denaturing conditions, but showed differences in their renaturation abilities. After in-gel renaturation both substrates and cleavage products can be identified by in-gel UV detection.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:Analytical Biochemistry. - 540-541 (2018), p. 52-63. -
További szerzők:Gazda Lívia Diána (1989-) Tóth Ferenc (1980-) (molekuláris biológus) Miczi Márió Mótyán János András (1981-) (biokémikus, molekuláris biológus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:GINOP-2.3.2-15-2016-00044
GINOP
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3.

001-es BibID:BIBFORM089444
035-os BibID:(cikkazonosító)190 (WOS)000595728400003 (Scopus)85096570971
Első szerző:Mahdi, Mohamed (orvos, tudományos segédmunkatárs)
Cím:Analysis of the efficacy of HIV protease inhibitors against SARS-CoV-2·s main protease / Mahdi Mohamed, Mótyán János András, Szojka Zsófia Ilona, Golda Mária, Miczi Márió, Tőzsér József
Dátum:2020
ISSN:1743-422X
Megjegyzések:Background: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of infections worldwide. While the search for an effective antiviral is still ongoing, experimental therapies based on repurposing of available antivirals is being attempted, of which HIV protease inhibitors (PIs) have gained considerable interest. Inhibition profiling of the PIs directly against the viral protease has never been attempted in vitro, and while few studies reported an efficacy of lopinavir and ritonavir in SARS-CoV-2 context, the mechanism of action of the drugs remains to be validated. Methods We carried out an in-depth analysis of the efficacy of HIV PIs against the main protease of SARS-CoV-2 (Mpro) in cell culture and in vitro enzymatic assays, using a methodology that enabled us to focus solely on any potential inhibitory effects of the inhibitors against the viral protease. For cell culture experiments a dark-to-bright GFP reporter substrate system was designed. Results Lopinavir, ritonavir, darunavir, saquinavir, and atazanavir were able to inhibit the viral protease in cell culture, albeit in concentrations much higher than their achievable plasma levels, given their current drug formulations. While inhibition by lopinavir was attributed to its cytotoxicity, ritonavir was the most effective of the panel, with IC50 of 13.7 ?M. None of the inhibitors showed significant inhibition of SARS-CoV-2 Mpro in our in vitro enzymatic assays up to 100 ?M concentration. Conclusion Targeting of SARS-CoV-2 Mpro by some of the HIV PIs might be of limited clinical potential, given the high concentration of the drugs required to achieve significant inhibition. Therefore, given their weak inhibition of the viral protease, any potential beneficial effect of the PIs in COVID-19 context might perhaps be attributed to acting on other molecular target(s), rather than SARS-CoV-2 Mpro.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
SARS-CoV-2
Inhibition profling
In vitro assay
HIV protease inhibitors
Protease
Megjelenés:Virology Journal. - 17 : 1 (2020), p. 1-8. -
További szerzők:Mótyán János András (1981-) (biokémikus, molekuláris biológus) Szojka Zsófia (1991-) (molekuláris biológus) Golda Mária (1986-) (molekuláris biológus) Miczi Márió Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:NKFIH-1150?6/2019
Egyéb
NKFI 125238
Egyéb
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Intézményi repozitóriumban (DEA) tárolt változat
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4.

001-es BibID:BIBFORM095389
Első szerző:Miczi Márió
Cím:Development of a Bio-Layer Interferometry-Based Protease Assay Using HIV-1 Protease as a Model / Márió Miczi, Ádám Diós, Beáta Bozóki, József Tőzsér, János András Mótyán
Dátum:2021
ISSN:1999-4915 1999-4915
Megjegyzések:first_page settings Open AccessArticle Development of a Bio-Layer Interferometry-Based Protease Assay Using HIV-1 Protease as a Model by Márió Miczi 1,2, Ádám Diós 2,3, Beáta Bozóki 1, József Tőzsér 1 [OrcID] and János András Mótyán 1,* [OrcID] 1 Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary 2 Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary 3 Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary * Author to whom correspondence should be addressed. Academic Editor: Alan Rein Viruses 2021, 13(6), 1183; https://doi.org/10.3390/v13061183 (registering DOI) Received: 30 April 2021 / Revised: 9 June 2021 / Accepted: 19 June 2021 / Published: 21 June 2021 (This article belongs to the Special Issue In Memory of Stephen Oroszlan) Download PDF Browse Figures Citation Export Abstract Proteolytic enzymes have great significance in medicine and the pharmaceutical industry and are applied in multiple fields of life sciences. Therefore, cost-efficient, reliable and sensitive real-time monitoring methods are highly desirable to measure protease activity. In this paper, we describe the development of a new experimental approach for investigation of proteolytic enzymes. The method was designed by the combination of recombinant fusion protein substrates and bio-layer interferometry (BLI). The protease (PR) of human immunodeficiency virus type 1 (HIV-1) was applied as model enzyme to set up and test the method. The principle of the assay is that the recombinant protein substrates immobilized to the surface of biosensor are specifically cleaved by the PR, and the substrate processing can be followed by measuring change in the layer thickness by optical measurement. We successfully used this method to detect the HIV-1 PR activity in real time, and the initial rate of the signal decrease was found to be proportional to the enzyme activity. Substrates representing wild-type and modified cleavage sites were designed to study HIV-1 PR's specificity, and the BLI-based measurements showed differential cleavage efficiency of the substrates, which was proven by enzyme kinetic measurements. We applied this BLI-based assay to experimentally confirm the existence of extended binding sites at the surface of HIV-1 PR. We found the measurements may be performed using lysates of cells expressing the fusion protein, without primary purification of the substrate. The designed BLI-based protease assay is high-throughput-compatible and enables real-time and small-volume measurements, thus providing a new and versatile approach to study proteolytic enzymes.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
protease assay
protease
HIV-1
BLItz
human immunodeficiency virus
bio-layer interferometry
recombinant fluorescent protein substrate
specificity
substrate specificity
recombinant protein
Megjelenés:Viruses-Basel. - 13 : 6 (2021), p. 1-20. -
További szerzők:Diós Ádám (1994-) (molekuláris biológus) Bozóki Beáta (1986-) (molekuláris biológus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész) Mótyán János András (1981-) (biokémikus, molekuláris biológus)
Pályázati támogatás:TKP2020-IKA-04
Egyéb
EFOP-3.6.3-VEKOP-16-2017-00009
EFOP
GINOP-2.3.2-15-2016-00044
GINOP
GINOP-2.3.2-15-2016-00015
GINOP
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Intézményi repozitóriumban (DEA) tárolt változat
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5.

001-es BibID:BIBFORM089970
035-os BibID:(cikkazonosító)9523 (wos)000602881500001 (scopus)85098234996
Első szerző:Miczi Márió
Cím:Identification of Host Cellular Protein Substrates of SARS-COV-2 Main Protease / Márió Miczi, Mária Golda, Balázs Kunkli, Tibor Nagy, József Tőzsér, János András Mótyán
Dátum:2020
ISSN:1661-6596 1422-0067
Megjegyzések:The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease-19 (COVID-19) being associated with severe pneumonia. Like with other viruses, the interaction of SARS-CoV-2 with host cell proteins is necessary for successful replication, and cleavage of cellular targets by the viral protease also may contribute to the pathogenesis, but knowledge about the human proteins that are processed by the main protease (3CLpro) of SARS-CoV-2 is still limited. We tested the prediction potentials of two different in silico methods for the identification of SARS-CoV-2 3CLpro cleavage sites in human proteins. Short stretches of homologous host-pathogen protein sequences (SSHHPS) that are present in SARS-CoV-2 polyprotein and human proteins were identified using BLAST analysis, and the NetCorona 1.0 webserver was used to successfully predict cleavage sites, although this method was primarily developed for SARS-CoV. Human C-terminal-binding protein 1 (CTBP1) was found to be cleaved in vitro by SARS-CoV-2 3CLpro, the existence of the cleavage site was proved experimentally by using a His6-MBP-mEYFP recombinant substrate containing the predicted target sequence. Our results highlight both potentials and limitations of the tested algorithms. The identification of candidate host substrates of 3CLpro may help better develop an understanding of the molecular mechanisms behind the replication and pathogenesis of SARS-CoV-2.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
host protein cleavage
cleavage site prediction
cleavage site identification
SSHHPS
NetCorona
COVID-19
SARS
SARS-CoV-2
protease
3CL protease
coronavirus
main protease
Megjelenés:International Journal Of Molecular Sciences. - 21 : 24 (2020), p. 1-19. -
További szerzők:Golda Mária (1986-) (molekuláris biológus) Kunkli Balázs Nagy Tibor (1988-) (vegyész) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész) Mótyán János András (1981-) (biokémikus, molekuláris biológus)
Pályázati támogatás:GINOP-2.3.3-15-2016-00021
GINOP
NKFIH-1150-6/2019
Egyéb
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Intézményi repozitóriumban (DEA) tárolt változat
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6.

001-es BibID:BIBFORM108752
035-os BibID:(cikkazonosító)3236 (Scopus)85148962397 (WoS)000938549700001
Első szerző:Miltner Noémi (molekuláris biológus)
Cím:Identification of SARS-CoV-2 Main Protease (Mpro) Cleavage Sites Using Two-Dimensional Electrophoresis and In Silico Cleavage Site Prediction / Noémi Miltner, Gergő Kalló, Éva Csősz, Márió Miczi, Tibor Nagy, Mohamed Mahdi, János András Mótyán, József Tőzsér
Dátum:2023
ISSN:1422-0067
Megjegyzések:The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a crucial role in its life cycle. The Mpro-mediated limited proteolysis of the viral polyproteins is necessary for the replication of the virus, and cleavage of the host proteins of the infected cells may also contribute to viral pathogenesis, such as evading the immune responses or triggering cell toxicity. Therefore, the identification of host substrates of the viral protease is of special interest. To identify cleavage sites in cellular substrates of SARS-CoV-2 Mpro, we determined changes in the HEK293T cellular proteome upon expression of the Mpro using two-dimensional gel electrophoresis. The candidate cellular substrates of Mpro were identified by mass spectrometry, and then potential cleavage sites were predicted in silico using NetCorona 1.0 and 3CLP web servers. The existence of the predicted cleavage sites was investigated by in vitro cleavage reactions using recombinant protein substrates containing the candidate target sequences, followed by the determination of cleavage positions using mass spectrometry. Unknown and previously described SARS-CoV-2 Mpro cleavage sites and cellular substrates were also identified. Identification of target sequences is important to understand the specificity of the enzyme, as well as aiding the improvement and development of computational methods for cleavage site prediction.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
coronavirus
SARS-CoV-2
main protease
Mpro
COVID-19
two-dimensional gel electrophoresis
cleavage site identification
cleavage site prediction
protease
host protein cleavage
specificity
Megjelenés:International Journal Of Molecular Sciences. - 24 : 4 (2023), p. 1-19. -
További szerzők:Kalló Gergő (1989-) (molekuláris biológus) Csősz Éva (1977-) (biokémikus, molekuláris biológus) Miczi Márió Nagy Tibor (1988-) (vegyész) Mahdi, Mohamed (1979-) (orvos, tudományos segédmunkatárs) Mótyán János András (1981-) (biokémikus, molekuláris biológus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:GINOP-2.3.3-15-2016-00020
GINOP
GINOP-2.3.3-15-2016-00021
GINOP
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Intézményi repozitóriumban (DEA) tárolt változat
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7.

001-es BibID:BIBFORM094951
Első szerző:Mótyán János András (biokémikus, molekuláris biológus)
Cím:Specificity of the HIV-1 Protease on Substrates Representing the Cleavage Site in the Proximal Zinc-Finger of HIV-1 Nucleocapsid Protein / Mótyán János András, Miczi Márió, Stephen Oroszlan, Tőzsér József
Dátum:2021
ISSN:1999-4915 1999-4915
Megjegyzések:o explore the sequence context-dependent nature of the human immunodeficiency virus type 1 (HIV-1) protease's specificity and to provide a rationale for viral mutagenesis to study the potential role of the nucleocapsid (NC) processing in HIV-1 replication, synthetic oligopeptide substrates representing the wild-type and modified versions of the proximal cleavage site of HIV-1 NC were assayed as substrates of the HIV-1 protease (PR). The S1· substrate binding site of HIV-1 PR was studied by an in vitro assay using KIVKCF?NCGK decapeptides having amino acid substitutions of N17 residue of the cleavage site of the first zinc-finger domain, and in silico calculations were also performed to investigate amino acid preferences of S1· site. Second site substitutions have also been designed to produce "revertant" substrates and convert a non-hydrolysable sequence (having glycine in place of N17) to a substrate. The specificity constants obtained for peptides containing non-charged P1· substitutions correlated well with the residue volume, while the correlation with the calculated interaction energies showed the importance of hydrophobicity: interaction energies with polar residues were related to substantially lower specificity constants. Cleavable "revertants" showed one residue shift of cleavage position due to an alternative productive binding mode, and surprisingly, a double cleavage of a substrate was also observed. The results revealed the importance of alternative binding possibilities of substrates into the HIV-1 PR. The introduction of the "revertant" mutations into infectious virus clones may provide further insights into the potential role of NC processing in the early phase of the viral life-cycle.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
substrate specificity
retroviruses
nucleocapsid protein
nucleocapsid
viral proteins
specificity
viral proteases
human immunodeficiency virus
protease
HIV-1
Megjelenés:Viruses-Basel. - 13 : 6 (2021), p. 1-14. -
További szerzők:Miczi Márió Oroszlan, Stephen Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:TKP2020-IKA-04
Egyéb
EFOP-3.6.3-VEKOP-16-2017-00009
EFOP
GINOP-2.3.2-15-2016-00044
GINOP
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Intézményi repozitóriumban (DEA) tárolt változat
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8.

001-es BibID:BIBFORM083676
035-os BibID:(cikkazonosító)1352 (scopus)85079688785 (wos)000522524400179
Első szerző:Mótyán János András (biokémikus, molekuláris biológus)
Cím:Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases / János András Mótyán, Márió Miczi, József Tőzsér
Dátum:2020
ISSN:1661-6596 1422-0067
Megjegyzések:The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
retrovirus
retrovirus-like
protease
retroviral protease
dimerization
comparative analysis
contact map
DNA damage-inducible protein
Ddi1
Ddi2
HIV protease
Megjelenés:International Journal of Molecular Sciences. - 21 : 4 (2020), p. 1-24. -
További szerzők:Miczi Márió Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:GINOP-2.3.2-15-2016-00044
GINOP
NKFIH-1150-6/2019
Egyéb
EFOP-3.6.3-VEKOP-16-2017-00009
EFOP
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Intézményi repozitóriumban (DEA) tárolt változat
DOI
Borító:

9.

001-es BibID:BIBFORM072696
Első szerző:Mótyán János András (biokémikus, molekuláris biológus)
Cím:Data supporting Ni-NTA magnetic bead-based fluorescent protease assay using recombinant fusion protein substrates / Mótyán János András, Miczi Márió, Bozóki Beáta, Tőzsér József
Dátum:2018
ISSN:2352-3409
Megjegyzések:Data provided here are related to the research article entitled as ♭A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening'. Here we describe data related to the investigation of the properties of the His6-MBP-VSQNY?PIVQ-mApple recombinant protein substrate and its interactions with Ni-NTA magnetic beads, including the dependence of substrate attachment on incubation time and concentration. Data on the folding efficiency and conformational stability of the recombinant substrate assessed by tryptic digestion are also presented. We describe here the changes of fluorescent properties and binding abilities upon treatments commonly used for stopping enzymatic reactions: trichloroacetic acid (TCA) or heat treatment.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
recombinant fusion protein substrate
protease assay
fluorescent protein
Megjelenés:Data in Brief. - 18 (2018), p. 203-208. -
További szerzők:Miczi Márió Bozóki Beáta (1986-) (molekuláris biológus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:GINOP-2.3.2-15-2016-00044
GINOP
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Intézményi repozitóriumban (DEA) tárolt változat
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10.

001-es BibID:BIBFORM087577
035-os BibID:(cikkazonosító)5907 (scopus)85089663597 (wos)000565075500001
Első szerző:Szojka Zsófia (molekuláris biológus)
Cím:Y44A Mutation in the Acidic Domain of HIV-2 Tat Impairs Viral Reverse Transcription and LTR-Transactivation / Szojka Zsófia, Mótyán János András, Miczi Márió, Mahdi Mohamed, Tőzsér József
Dátum:2020
ISSN:1661-6596 1422-0067
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
human immunodeficiency virus
HIV-2
Tat
stability analysis
reverse transcriptase activity
transactivator protein
mutation design
Megjelenés:International Journal Of Molecular Sciences. - 21 : 16 (2020), p. 1-17. -
További szerzők:Mótyán János András (1981-) (biokémikus, molekuláris biológus) Miczi Márió Mahdi, Mohamed (1979-) (orvos, tudományos segédmunkatárs) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
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Intézményi repozitóriumban (DEA) tárolt változat
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