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  1. Article ; Online: Current Approaches in Molecular Enzymology

    Eszter Szabo / Attila Ambrus

    Life, Vol 12, Iss 336, p

    2022  Volume 336

    Abstract: Enzymes are the main executioners of living organisms [.] ...

    Abstract Enzymes are the main executioners of living organisms [.]
    Keywords n/a ; Science ; Q
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Hydrogen-Deuterium Exchange Mass Spectrometry

    Oliver Ozohanics / Attila Ambrus

    Life, Vol 10, Iss 286, p

    A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes

    2020  Volume 286

    Abstract: Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other ... ...

    Abstract Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.
    Keywords hydrogen/deuterium exchange ; mass spectrometry ; HDX-MS ; protein dynamics ; protein conformation ; protein complexes ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Probing the E1o-E2o and E1a-E2o Interactions in Binary Subcomplexes of the Human 2-Oxoglutarate Dehydrogenase and 2-Oxoadipate Dehydrogenase Complexes by Chemical Cross-Linking Mass Spectrometry and Molecular Dynamics Simulation

    Oliver Ozohanics / Xu Zhang / Natalia S. Nemeria / Attila Ambrus / Frank Jordan

    International Journal of Molecular Sciences, Vol 24, Iss 4555, p

    2023  Volume 4555

    Abstract: The human 2-oxoglutarate dehydrogenase complex (hOGDHc) is a key enzyme in the tricarboxylic acid cycle and is one of the main regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. Evidence was obtained for formation of ... ...

    Abstract The human 2-oxoglutarate dehydrogenase complex (hOGDHc) is a key enzyme in the tricarboxylic acid cycle and is one of the main regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. Evidence was obtained for formation of a hybrid complex between the hOGDHc and its homologue the 2-oxoadipate dehydrogenase complex (hOADHc) in the L-lysine metabolic pathway, suggesting a crosstalk between the two distinct pathways. Findings raised fundamental questions about the assembly of hE1a (2-oxoadipate-dependent E1 component) and hE1o (2-oxoglutarate-dependent E1) to the common hE2o core component. Here we report chemical cross-linking mass spectrometry (CL-MS) and molecular dynamics (MD) simulation analyses to understand assembly in binary subcomplexes. The CL-MS studies revealed the most prominent loci for hE1o-hE2o and hE1a-hE2o interactions and suggested different binding modes. The MD simulation studies led to the following conclusions: (i) The N-terminal regions in E1s are shielded by, but do not interact directly with hE2o. (ii) The hE2o linker region exhibits the highest number of H-bonds with the N-terminus and α/β1 helix of hE1o, yet with the interdomain linker and α/β1 helix of hE1a. (iii) The C-termini are involved in dynamic interactions in complexes, suggesting the presence of at least two conformations in solution.
    Keywords 2-oxoglutarate dehydrogenase ; 2-oxoadipate dehydrogenase ; dihydrolipoyl succinyltransferase ; protein–protein interactions ; chemical cross-linking mass spectrometry ; molecular dynamics simulations ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Structural and Biochemical Investigation of Selected Pathogenic Mutants of the Human Dihydrolipoamide Dehydrogenase

    Eszter Szabo / Eva Nemes-Nikodem / Krisztina Rubina Vass / Zsofia Zambo / Eszter Zrupko / Beata Torocsik / Oliver Ozohanics / Balint Nagy / Attila Ambrus

    International Journal of Molecular Sciences, Vol 24, Iss 10826, p

    2023  Volume 10826

    Abstract: Clinically relevant disease-causing variants of the human dihydrolipoamide dehydrogenase (hLADH, hE3), a common component of the mitochondrial α-keto acid dehydrogenase complexes, were characterized using a multipronged approach to unravel the molecular ... ...

    Abstract Clinically relevant disease-causing variants of the human dihydrolipoamide dehydrogenase (hLADH, hE3), a common component of the mitochondrial α-keto acid dehydrogenase complexes, were characterized using a multipronged approach to unravel the molecular pathomechanisms that underlie hLADH deficiency. The G101del and M326V substitutions both reduced the protein stability and triggered the disassembly of the functional/obligate hLADH homodimer and significant FAD losses, which altogether eventually manifested in a virtually undetectable catalytic activity in both cases. The I12T-hLADH variant proved also to be quite unstable, but managed to retain the dimeric enzyme form; the LADH activity, both in the forward and reverse catalytic directions and the affinity for the prosthetic group FAD were both significantly compromised. None of the above three variants lent themselves to an in-depth structural analysis via X-ray crystallography due to inherent protein instability. Crystal structures at 2.89 and 2.44 Å resolutions were determined for the I318T- and I358T-hLADH variants, respectively; structure analysis revealed minor conformational perturbations, which correlated well with the residual LADH activities, in both cases. For the dimer interface variants G426E-, I445M-, and R447G-hLADH, enzyme activities and FAD loss were determined and compared against the previously published structural data.
    Keywords lipoamide dehydrogenase ; disease-causing mutation ; X-ray crystallography ; reactive oxygen species ; alpha-keto acid dehydrogenase complexes ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 572
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Functional Versatility of the Human 2-Oxoadipate Dehydrogenase in the L-Lysine Degradation Pathway toward Its Non-Cognate Substrate 2-Oxopimelic Acid

    Natalia S. Nemeria / Balint Nagy / Roberto Sanchez / Xu Zhang / João Leandro / Attila Ambrus / Sander M. Houten / Frank Jordan

    International Journal of Molecular Sciences, Vol 23, Iss 8213, p

    2022  Volume 8213

    Abstract: The human 2-oxoadipate dehydrogenase complex (OADHc) in L-lysine catabolism is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA and NADH (+H + ). Genetic findings have linked the DHTKD1 encoding 2-oxoadipate dehydrogenase ( ... ...

    Abstract The human 2-oxoadipate dehydrogenase complex (OADHc) in L-lysine catabolism is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA and NADH (+H + ). Genetic findings have linked the DHTKD1 encoding 2-oxoadipate dehydrogenase (E1a), the first component of the OADHc, to pathogenesis of AMOXAD, eosinophilic esophagitis (EoE), and several neurodegenerative diseases. A multipronged approach, including circular dichroism spectroscopy, Fourier Transform Mass Spectrometry, and computational approaches, was applied to provide novel insight into the mechanism and functional versatility of the OADHc. The results demonstrate that E1a oxidizes a non-cognate substrate 2-oxopimelate (OP) as well as OA through the decarboxylation step, but the OADHc was 100-times less effective in reactions producing adipoyl-CoA and NADH from the dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3). The results revealed that the E2o is capable of producing succinyl-CoA, glutaryl-CoA, and adipoyl-CoA. The important conclusions are the identification of: (i) the functional promiscuity of E1a and (ii) the ability of the E2o to form acyl-CoA products derived from homologous 2-oxo acids with five, six, and even seven carbon atoms. The findings add to our understanding of both the OADHc function in the L-lysine degradative pathway and of the molecular mechanisms leading to the pathogenesis associated with DHTKD1 variants.
    Keywords 2-oxoadipate dehydrogenase ; L-lysine degradation pathway ; 2-oxopimelate substrate ; 2-oxoadipate dehydrogenase complex ; E1a promiscuity ; H 2 O 2 production ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: GENERAL ASPECTS OF REGIONAL FERTILITY DIFFERENCES ON THE HAJDÚ-BIHAR – BIHOR EUROREGION BEFORE AND AFTER THE SYSTEM CHANGES

    Attila AMBRUS / Norbert BÁNTÓ

    Analele Universităţii din Oradea: Seria Geografie, Vol 23, Iss 1, Pp 12-

    2013  Volume 18

    Abstract: The temporal and spatial evolution of fertility is an essential feature in the demographic trends. The following analysis shows the territorial and fertility differences in Hajdú-Bihar-Bihor Euro region, compared to the national average and the values of ...

    Abstract The temporal and spatial evolution of fertility is an essential feature in the demographic trends. The following analysis shows the territorial and fertility differences in Hajdú-Bihar-Bihor Euro region, compared to the national average and the values of the European Union. It is also topic of the present analysis to look at the differences of fertility level in the Euro region and whether growth or decline can be detected in the recent decades. We review the certain changes that appeared in the demographic characteristics of women giving birth and their impact on childbearing behavior. The main focus is on regional differences that occurred after the changes of the political system. For the temporal characterization of the trends we have chosen the year 1980 before the changes, the year 1990 that represents a transition, the turn of the millennium, 2000, and the recently completed year 2010.
    Keywords fertility ; total fertility rate ; change of regime ; Bihor-Hajdú-Bihar Euro region ; demographic characteristics of women giving birth ; Environmental sciences ; GE1-350 ; Geography (General) ; G1-922
    Subject code 300
    Language English
    Publishing date 2013-06-01T00:00:00Z
    Publisher Editura Universitatii din Oradea
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: STUDY REGARDING THE POSSIBILITY TO DEVELOP TOURISM AND CROSS-BORDER COOPERATION THROUGH A BUSINESS INCUBATOR AT VADUL CRIªULUI (BIHOR COUNTY)

    Attila Ambrus / Norbert Bántó

    Annals of the University of Oradea : Economic Science, Vol 1, Iss 1, Pp 222-

    2012  Volume 228

    Abstract: In this article I have presented the results of a research realized at the end of the year 2011, within the framework of the cross-border project entitled n#8222;Business incubator for cross-border tourist developmentn#8221;. This incubator will be ... ...

    Abstract In this article I have presented the results of a research realized at the end of the year 2011, within the framework of the cross-border project entitled n#8222;Business incubator for cross-border tourist developmentn#8221;. This incubator will be constructed in Vadu Criºului Community, Bihor County, while the realized study intended to demonstrate the fact that such initiative on one hand will attract investors, respectively companies with activities linked directly or indirectly to tourism n#8211; because the area offers them all the necessary conditions for business development-, while on the other hand this initiative can encourage and support cross-border tourist co-operation, especially with the balneary spa resort in Hajdúszoboszló, Hungary. For this reason a questionnaire was realized, which was applied not just in the micro-region of Vadu Criºului but in Hajdúszoboszló as well, especially distributed among the economical agents that have tourism linked to their activity. The study showed not just the resources and the modalities of existing advertising but also the possibilities of cross-border co-operation as a chance to develop tourism from the two regions. In this way, the study shows the fact that in the case of the macro-region of Vadu Criºului, the extension of the tourism services must be based on the natural characteristics of the region and on highly emphasized own initiatives, rather than the initiatives and the support or the administrative authorities. In the case of the Hajdúszoboszló resort, a tendency outlines among those who consider the tourism development in the resort essential, tourism services must be diversified, and more emphasis must be put on the implication of local authorities, a chance seen in cooperation with the tourist area without similar characteristics (namely, direct non-competitor), but from the cross-border region (the opening towards the Romanian side is relevant, persuaded on the first place with the wish of learning the Romanian language), however, information and gaining creditability that Vadu Criºului and the surrounding area has a tourist potential needs real improvements. Hajdúszoboszló tends towards advertising the existing tourist potential and infrastructure, pulsing through ensuring the diversity of the programs. In comparison, the Vadu Criºului area, even if the first signs of diversification are observed towards the potential of the region, actually still needs extension, but lacks that particular force of grouping around one element or a set of elements that can assume the role of a promoter. As a solution for grouping the micro-region, followed by the extension of services, the central point must be occupied by an intermediate structure formed among local administrative bodies and entities who encourage own initiatives, including NGOn#8217;s, so one of the many solutions that can be viable would be the existence of an advertising center in the Vadu Criºului Defile, a function that will be fulfilled by the business incubator.
    Keywords business incubator ; questionnaire ; tourism development ; cross-border co-operation ; Economic theory. Demography ; HB1-3840 ; Social Sciences ; H ; DOAJ:Economics ; DOAJ:Business and Economics
    Subject code 910
    Publishing date 2012-07-01T00:00:00Z
    Publisher University of Oradea
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Computational analyses of the effect of novel amino acid clusters of human transglutaminase 2 on its structure and function

    Thangaraju, Kiruphagaran / Róbert Király / János András Mótyán / Viktor Attila Ambrus / Mónika Fuxreiter / László Fésüs

    Amino acids. 2017 Mar., v. 49, no. 3

    2017  

    Abstract: Transglutaminase 2 (TGM2) is a unique protein of a nine member family with several enzymatic and non-enzymatic activities and interacting partners. Its physiological and pathological roles, however, are not fully understood. Comparative genomic and ... ...

    Abstract Transglutaminase 2 (TGM2) is a unique protein of a nine member family with several enzymatic and non-enzymatic activities and interacting partners. Its physiological and pathological roles, however, are not fully understood. Comparative genomic and computational analysis reported here have revealed phylogenetic changes of TGM2 resulting in novel amino acid clusters in humans and other primates, which may impact secondary structure and increase protein stability. These clusters are located in intrinsically disordered regions and via short linear motifs influence interactions with TGM2 partners directly, or through post-translation modification (phosphorylation and N-glycosylation sites). Our data shed new light on the structural background and evolution of TGM2 multi-functionality and points to so far unrevealed biological roles of the enzyme.
    Keywords Primates ; amino acids ; glycosylation ; humans ; phosphorylation ; phylogeny ; protein-glutamine gamma-glutamyltransferase ; translation (genetics)
    Language English
    Dates of publication 2017-03
    Size p. 605-614.
    Publishing place Springer Vienna
    Document type Article
    ZDB-ID 1121341-3
    ISSN 1438-2199 ; 0939-4451
    ISSN (online) 1438-2199
    ISSN 0939-4451
    DOI 10.1007/s00726-016-2330-0
    Database NAL-Catalogue (AGRICOLA)

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