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Litso I, Plaitakis A, Fadouloglou VE, Providaki M, Kokkinidis M, Zaganas I. Structural Evolution of Primate Glutamate Dehydrogenase 2 as Revealed by In Silico Predictions and Experimentally Determined Structures. Biomolecules 2023; 14:22. [PMID: 38254622 PMCID: PMC10812971 DOI: 10.3390/biom14010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
Glutamate dehydrogenase (GDH) interconverts glutamate to a-ketoglutarate and ammonia, interconnecting amino acid and carbohydrate metabolism. In humans, two functional GDH genes, GLUD1 and GLUD2, encode for hGDH1 and hGDH2, respectively. GLUD2 evolved from retrotransposition of the GLUD1 gene in the common ancestor of modern apes. These two isoenzymes are involved in the pathophysiology of human metabolic, neoplastic, and neurodegenerative disorders. The 3D structures of hGDH1 and hGDH2 have been experimentally determined; however, no information is available about the path of GDH2 structure changes during primate evolution. Here, we compare the structures predicted by the AlphaFold Colab method for the GDH2 enzyme of modern apes and their extinct primate ancestors. Also, we analyze the individual effect of amino acid substitutions emerging during primate evolution. Our most important finding is that the predicted structure of GDH2 in the common ancestor of apes was the steppingstone for the structural evolution of primate GDH2s. Two changes with a strong functional impact occurring at the first evolutionary step, Arg443Ser and Gly456Ala, had a destabilizing and stabilizing effect, respectively, making this step the most important one. Subsequently, GDH2 underwent additional modifications that fine-tuned its enzymatic properties to adapt to the functional needs of modern-day primate tissues.
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Affiliation(s)
- Ionela Litso
- Neurology/Neurogenetics Laboratory, School of Medicine, University of Crete, Voutes, 71003 Heraklion, Greece; (I.L.); (A.P.)
| | - Andreas Plaitakis
- Neurology/Neurogenetics Laboratory, School of Medicine, University of Crete, Voutes, 71003 Heraklion, Greece; (I.L.); (A.P.)
| | - Vasiliki E. Fadouloglou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, 70013 Heraklion, Greece; (M.P.); (M.K.)
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, 70013 Heraklion, Greece; (M.P.); (M.K.)
- Department of Biology, University of Crete, Vasilika Vouton, 71409 Heraklion, Greece
| | - Ioannis Zaganas
- Neurology/Neurogenetics Laboratory, School of Medicine, University of Crete, Voutes, 71003 Heraklion, Greece; (I.L.); (A.P.)
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Kotsaridis K, Michalopoulou VA, Tsakiri D, Kotsifaki D, Kefala A, Kountourakis N, Celie PHN, Kokkinidis M, Sarris PF. The functional and structural characterization of Xanthomonas campestris pv. campestris core effector XopP revealed a new kinase activity. Plant J 2023; 116:100-111. [PMID: 37344990 DOI: 10.1111/tpj.16362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Exo70B1 is a protein subunit of the exocyst complex with a crucial role in a variety of cell mechanisms, including immune responses against pathogens. The calcium-dependent kinase 5 (CPK5) of Arabidopsis thaliana (hereafter Arabidopsis), phosphorylates AtExo70B1 upon functional disruption. We previously reported that, the Xanthomonas campestris pv. campestris effector XopP compromises AtExo70B1, while bypassing the host's hypersensitive response, in a way that is still unclear. Herein we designed an experimental approach, which includes biophysical, biochemical, and molecular assays and is based on structural and functional predictions, utilizing AplhaFold and DALI online servers, respectively, in order to characterize the in vivo XccXopP function. The interaction between AtExo70B1 and XccXopP was found very stable in high temperatures, while AtExo70B1 appeared to be phosphorylated at XccXopP-expressing transgenic Arabidopsis. XccXopP revealed similarities with known mammalian kinases and phosphorylated AtExo70B1 at Ser107, Ser111, Ser248, Thr309, and Thr364. Moreover, XccXopP protected AtExo70B1 from AtCPK5 phosphorylation. Together these findings show that XccXopP is an effector, which not only functions as a novel serine/threonine kinase upon its host target AtExo70B1 but also protects the latter from the innate AtCPK5 phosphorylation, in order to bypass the host's immune responses. Data are available via ProteomeXchange with the identifier PXD041405.
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Affiliation(s)
- Konstantinos Kotsaridis
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Vassiliki A Michalopoulou
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Dimitra Tsakiri
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
| | - Dina Kotsifaki
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
| | - Aikaterini Kefala
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Patrick H N Celie
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Kokkinidis
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Panagiotis F Sarris
- Department of Biology, University of Crete, Heraklion, 714 09, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Biosciences, University of Exeter, Exeter, UK
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Arnittali M, Rissanou AN, Kefala A, Kokkinidis M, Harmandaris V. Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations. J Biomol Struct Dyn 2023:1-15. [PMID: 37671833 DOI: 10.1080/07391102.2023.2252903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
This study aims to the investigation of the advantages of designing new proteins presume upon a 'bias' sequence of amino acids, based on the reversed sequence of parent proteins, such as the retro ones. The structural simplicity of wtRop offers a very attractive model system to study these aspects. The current work is based on all-atom Molecular Dynamics (MD) simulations and corresponding experimental evidence on two different types of reversed wtRop protein, one with a fully reversed sequence of amino acids (rRop) and another with a partially reversed sequence (prRop), where only the five residues of the loop region (30ASP-34GLN) were not reversed. The exploration of the structure of the two retro proteins is performed highlighting the similarities and the differences with their parent protein, by employing various measures. Two models have been studied for both reversed proteins, a dimeric and a monomeric with the former one found to be more stable than the latter. Preferable equilibrium structures that the protein molecule can attain are explored, indicating the equilibration pathway. Simulation findings indicate a disruption of the α-helical structure and the appearance of additional secondary structures for both retro proteins. Reduced structural stability compared to their parent protein (wtRop) is also found. A corruption of the hydrophobic core is observed in the dimeric models. Furthermore, the simulations findings are consistent with the experimental characterization of prRop by circular dichroism spectroscopy (CD) which highlights an unstable, highly α-helical protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maria Arnittali
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia, Cyprus
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion, Crete, Greece
| | - Anastassia N Rissanou
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, Athens, Greece
| | - Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia, Cyprus
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion, Crete, Greece
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4
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Makraki E, Miliara S, Pagkalos M, Kokkinidis M, Mylonas E, Fadouloglou VE. Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA. Front Mol Biosci 2023; 10:1219668. [PMID: 37555016 PMCID: PMC10406553 DOI: 10.3389/fmolb.2023.1219668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
The non-coding 6S RNA is a master regulator of the cell cycle in bacteria which binds to the RNA polymerase-σ70 holoenzyme during the stationary phase to inhibit transcription from the primary σ factor. Inhibition is reversed upon outgrowth from the stationary phase by synthesis of small product RNA transcripts (pRNAs). 6S and its complex with a pRNA were structurally characterized using Small Angle X-ray Scattering. The 3D models of 6S and 6S:pRNA complex presented here, demonstrate that the fairly linear and extended structure of 6S undergoes a major conformational change upon binding to pRNA. In particular, 6S:pRNA complex formation is associated with a compaction of the overall 6S size and an expansion of its central domain. Our structural models are consistent with the hypothesis that the resultant particle has a shape and size incompatible with binding to RNA polymerase-σ70. Overall, by use of an optimized in vivo methodological approach, especially useful for structural studies, our study considerably improves our understanding of the structural basis of 6S regulation by offering a mechanistic glimpse of the 6S transcriptional control.
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Affiliation(s)
- Eleni Makraki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Sophia Miliara
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Michalis Pagkalos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Vasiliki E. Fadouloglou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Komotini, Greece
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5
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Kouyianou K, Mitsikas DA, Kotsifaki D, Providaki M, Bouriotis V, Kokkinidis M. Purification, Crystallization, and Preliminary X-Ray Analysis of the BseCI DNA Methyltransferase from Geobacillus stearothermophilus in Complex with Its Cognate DNA in Two Distinct Methylation States. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522070070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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6
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Arnittali M, Rissanou AN, Amprazi M, Kokkinidis M, Harmandaris V. Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments. Int J Mol Sci 2021; 22:ijms22115931. [PMID: 34073028 PMCID: PMC8199364 DOI: 10.3390/ijms22115931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023] Open
Abstract
In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.
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Affiliation(s)
- Maria Arnittali
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | - Anastassia N. Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Correspondence: ; Tel.: +30-2810-393746
| | - Maria Amprazi
- Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece; (M.A.); (M.K.)
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece; (M.A.); (M.K.)
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
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7
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Gazi AD, Kokkinidis M, Fadouloglou VE. α-Helices in the Type III Secretion Effectors: A Prevalent Feature with Versatile Roles. Int J Mol Sci 2021; 22:ijms22115412. [PMID: 34063760 PMCID: PMC8196651 DOI: 10.3390/ijms22115412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Type III Secretion Systems (T3SSs) are multicomponent nanomachines located at the cell envelope of Gram-negative bacteria. Their main function is to transport bacterial proteins either extracellularly or directly into the eukaryotic host cell cytoplasm. Type III Secretion effectors (T3SEs), latest to be secreted T3S substrates, are destined to act at the eukaryotic host cell cytoplasm and occasionally at the nucleus, hijacking cellular processes through mimicking eukaryotic proteins. A broad range of functions is attributed to T3SEs, ranging from the manipulation of the host cell's metabolism for the benefit of the bacterium to bypassing the host's defense mechanisms. To perform this broad range of manipulations, T3SEs have evolved numerous novel folds that are compatible with some basic requirements: they should be able to easily unfold, pass through the narrow T3SS channel, and refold to an active form when on the other side. In this review, the various folds of T3SEs are presented with the emphasis placed on the functional and structural importance of α-helices and helical domains.
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Affiliation(s)
- Anastasia D. Gazi
- Unit of Technology & Service Ultrastructural Bio-Imaging (UTechS UBI), Institut Pasteur, 75015 Paris, France
- Correspondence: (A.D.G.); (V.E.F.)
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion, 70013 Crete, Greece;
- Department of Biology, Voutes University Campus, University of Crete, Heraklion, 70013 Crete, Greece
| | - Vasiliki E. Fadouloglou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Correspondence: (A.D.G.); (V.E.F.)
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8
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Kefala A, Amprazi M, Mylonas E, Kotsifaki D, Providaki M, Pozidis C, Fotiadou M, Kokkinidis M. Probing Protein Folding with Sequence-Reversed α-Helical Bundles. Int J Mol Sci 2021; 22:ijms22041955. [PMID: 33669383 PMCID: PMC7920257 DOI: 10.3390/ijms22041955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.
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Affiliation(s)
- Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Maria Amprazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Charalambos Pozidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Melina Fotiadou
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
- Correspondence: ; Tel.: +30-2810-394350
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9
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Dimovasili C, Fadouloglou VE, Kefala A, Providaki M, Kotsifaki D, Kanavouras K, Sarrou I, Plaitakis A, Zaganas I, Kokkinidis M. Crystal structure of glutamate dehydrogenase 2, a positively selected novel human enzyme involved in brain biology and cancer pathophysiology. J Neurochem 2021; 157:802-815. [PMID: 33421122 DOI: 10.1111/jnc.15296] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/04/2020] [Accepted: 01/06/2021] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Mammalian glutamate dehydrogenase (hGDH1 in human cells) interconverts glutamate to α-ketoglutarate and ammonia while reducing NAD(P) to NAD(P)H. During primate evolution, humans and great apes have acquired hGDH2, an isoenzyme that underwent rapid evolutionary adaptation concomitantly with brain expansion, thereby acquiring unique catalytic and regulatory properties that permitted its function under conditions inhibitory to its ancestor hGDH1. Although the 3D-structures of GDHs, including hGDH1, have been determined, attempts to determine the hGDH2 structure were until recently unsuccessful. Comparison of the hGDH1/hGDH2 structures would enable a detailed understanding of their evolutionary differences. This work aimed at the determination of the hGDH2 crystal structure and the analysis of its functional implications. Recombinant hGDH2 was produced in the Spodoptera frugiperda ovarian cell line Sf21, using the Baculovirus expression system. Purification was achieved via a two-step chromatography procedure. hGDH2 was crystallized, X-ray diffraction data were collected using synchrotron radiation and the structure was determined by molecular replacement. The hGDH2 structure is reported at a resolution of 2.9 Å. The enzyme adopts a novel semi-closed conformation, which is an intermediate between known open and closed GDH1 conformations, differing from both. The structure enabled us to dissect previously reported biochemical findings and to structurally interpret the effects of evolutionary amino acid substitutions, including Arg470His, on ADP affinity. In conclusion, our data provide insights into the structural basis of hGDH2 properties, the functional evolution of hGDH isoenzymes, and open new prospects for drug design, especially for cancer therapeutics.
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Affiliation(s)
- Christina Dimovasili
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece.,Departments of Psychiatry and Neuroscience, Center for Molecular Biology and Genetics of Neurodegeneration, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vasiliki E Fadouloglou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantinos Kanavouras
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece.,Department of Neurology, "G. Gennimatas" General Hospital, Athens, Greece
| | - Iosifina Sarrou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Center for Free-Electron Laser Science/DESY, Hamburg, Germany
| | - Andreas Plaitakis
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Zaganas
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Heraklion, Crete, Greece
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10
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Khalid RR, Maryam A, Sezerman OU, Mylonas E, Siddiqi AR, Kokkinidis M. Probing the Structural Dynamics of the Catalytic Domain of Human Soluble Guanylate Cyclase. Sci Rep 2020; 10:9488. [PMID: 32528025 PMCID: PMC7289801 DOI: 10.1038/s41598-020-66310-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/04/2020] [Indexed: 01/25/2023] Open
Abstract
In the nitric oxide (NO) signaling pathway, human soluble guanylate cyclase (hsGC) synthesizes cyclic guanosine monophosphate (cGMP); responsible for the regulation of cGMP-specific protein kinases (PKGs) and phosphodiesterases (PDEs). The crystal structure of the inactive hsGC cyclase dimer is known, but there is still a lack of information regarding the substrate-specific internal motions that are essential for the catalytic mechanism of the hsGC. In the current study, the hsGC cyclase heterodimer complexed with guanosine triphosphate (GTP) and cGMP was subjected to molecular dynamics simulations, to investigate the conformational dynamics that have functional implications on the catalytic activity of hsGC. Results revealed that in the GTP-bound complex of the hsGC heterodimer, helix 1 of subunit α (α:h1) moves slightly inwards and comes close to helix 4 of subunit β (β:h4). This conformational change brings loop 2 of subunit β (β:L2) closer to helix 2 of subunit α (α:h2). Likewise, loop 2 of subunit α (α:L2) comes closer to helix 2 of subunit β (β:h2). These structural events stabilize and lock GTP within the closed pocket for cyclization. In the cGMP-bound complex, α:L2 detaches from β:h2 and establishes interactions with β:L2, which results in the loss of global structure compactness. Furthermore, with the release of pyrophosphate, the interaction between α:h1 and β:L2 weakens, abolishing the tight packing of the binding pocket. This study discusses the conformational changes induced by the binding of GTP and cGMP to the hsGC catalytic domain, valuable in designing new therapeutic strategies for the treatment of cardiovascular diseases.
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Affiliation(s)
- Rana Rehan Khalid
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.,Department of Biology, University of Crete, 70013, Heraklion, Greece.,Department of Biostatistics and Medical Informatics, Acibadem M. A. A. University, Istanbul, 34752, Turkey
| | - Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.,Department of Pharmaceutical Chemistry, Biruni Universitesi, Istanbul, 34010, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, Acibadem M. A. A. University, Istanbul, 34752, Turkey
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013, Heraklion, Greece
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.
| | - Michael Kokkinidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece. .,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013, Heraklion, Greece.
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11
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Khalid RR, Siddiqi AR, Mylonas E, Maryam A, Kokkinidis M. Dynamic Characterization of the Human Heme Nitric Oxide/Oxygen (HNOX) Domain under the Influence of Diatomic Gaseous Ligands. Int J Mol Sci 2019; 20:ijms20030698. [PMID: 30736292 PMCID: PMC6387030 DOI: 10.3390/ijms20030698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/29/2019] [Accepted: 02/03/2019] [Indexed: 01/25/2023] Open
Abstract
Soluble guanylate cyclase (sGC) regulates numerous physiological processes. The β subunit Heme Nitric Oxide/Oxygen (HNOX) domain makes this protein sensitive to small gaseous ligands. The structural basis of the activation mechanism of sGC under the influence of ligands (NO, O2, CO) is poorly understood. We examine the effect of different ligands on the human sGC HNOX domain. HNOX systems with gaseous ligands were generated and explored using Molecular Dynamics (MD). The distance between heme Fe2+ and histidine in the NO-ligated HNOX (NO-HNOX) system is larger compared to the O2, CO systems. NO-HNOX rapidly adopts the conformation of the five-group metal coordination system. Loops α, β, γ and helix-f exhibit increased mobility and different hydrogen bond networks in NO-HNOX compared to the other systems. The removal of His from the Fe coordination sphere in NO-HNOX is assisted by interaction of the imidazole ring with the surrounding residues which in turn leads to the release of signaling helix-f and activation of the sGC enzyme. Insights into the conformational dynamics of a human sGC HNOX domain, especially for regions which are functionally critical for signal transduction, are valuable in the understanding of cardiovascular diseases.
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Affiliation(s)
- Rana Rehan Khalid
- Department of Biosciences, COMSATS University, Islamabad 45550, Pakistan.
- Department of Biology, University of Crete, 70013 Heraklion, Greece.
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University, Islamabad 45550, Pakistan.
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013 Heraklion, Greece.
| | - Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad 45550, Pakistan.
| | - Michael Kokkinidis
- Department of Biology, University of Crete, 70013 Heraklion, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013 Heraklion, Greece.
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12
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Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. J Am Chem Soc 2017; 139:5330-5337. [DOI: 10.1021/jacs.6b12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Arnaouteli
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Anastasia Tomatsidou
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Giorgos Efstathiou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Miliara
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Marianna Griniezaki
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Aleka Tsalafouta
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Spiros A. Pergantis
- Department
of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Ivo G. Boneca
- Biology
and Genetics of the Bacterial Cell Wall Unit, Institut Pasteur, 75015 Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Nicholas M. Glykos
- Department
of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
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13
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Kefala A, Kotsifaki D, Providaki M, Amprazi M, Kokkinidis M. Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle. Acta Crystallogr F Struct Biol Commun 2017; 73:51-53. [PMID: 28045394 DOI: 10.1107/s2053230x16020173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/19/2016] [Indexed: 11/10/2022]
Abstract
Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four-α-helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and preliminary crystallographic characterization of revRM6 are reported. The protein was overexpressed in Escherichia coli, purified to homogeneity and crystallized. The crystals belonged to space group P41212, with unit-cell parameters a = b = 44.98, c = 159.74 Å, and diffracted to a resolution of 3.45 Å.
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Affiliation(s)
- Aikaterini Kefala
- Department of Biology, University of Crete, Voutes University Campus, PO Box 2208, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| | - Maria Amprazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Nikolaou Plastira Street 100, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, Voutes University Campus, PO Box 2208, 70013 Heraklion, Crete, Greece
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14
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Fadouloglou VE, Stavrakoudis A, Bouriotis V, Kokkinidis M, Glykos NM. Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity. J Chem Theory Comput 2015; 5:3299-311. [PMID: 26602510 DOI: 10.1021/ct9002338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BcZBP is an LmbE-like, homohexameric, zinc-dependent deacetylase from the opportunistic pathogen Bacillus cereus with three, thus far uncharacterized, homologues in B. anthracis. Although its specific substrate is still unknown, the enzyme has been shown to preferentially deacetylate N-acetylglucosamine and diacetylchitobiose via an active site based on a zinc-binding motif of the type HXDDXnH. In the crystal structure, the active site is located at a deep and partially blocked cleft formed at the interface between monomers related by the molecular 3-fold axis, although the major, in structural terms, building block of the enzyme is not the trimer, but the intertwined dimer. Here, we report results from a 50 ns molecular dynamics simulation of BcZBP in explicit solvent with full electrostatics and show that (i) the view of the intertwined dimer as the major structural and functional building block of this class of hexameric enzymes is possibly an oversimplification of the rather complex dynamics observed in the simulation, (ii) the most mobile (with respect to their atomic fluctuations) parts of the structure coincide with three surface loops surrounding the active site, and (iii) these mobile loops define the active site's accessibility, and may be implicated in the determination of the enzyme's specificity.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Athanassios Stavrakoudis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
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15
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Mastorodemos V, Kanavouras K, Sundaram S, Providaki M, Petraki Z, Kokkinidis M, Zaganas I, Logothetis DE, Plaitakis A. Side-chain interactions in the regulatory domain of human glutamate dehydrogenase determine basal activity and regulation. J Neurochem 2015; 133:73-82. [DOI: 10.1111/jnc.13019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/16/2014] [Accepted: 12/15/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Vasileios Mastorodemos
- Faculty of Medicine; Department of Neurology; School of Health Sciences; University of Crete; Heraklion Crete Greece
| | - Konstantinos Kanavouras
- Faculty of Medicine; Department of Neurology; School of Health Sciences; University of Crete; Heraklion Crete Greece
| | - Shobana Sundaram
- Department of Physiology and Biophysics; Virginia Commonwealth University; School of Medicine; Richmond Virginia USA
| | - Maria Providaki
- Department of Biology; University of Crete; Heraklion Crete Greece
| | - Zoe Petraki
- Faculty of Medicine; Department of Neurology; School of Health Sciences; University of Crete; Heraklion Crete Greece
| | | | - Ioannis Zaganas
- Faculty of Medicine; Department of Neurology; School of Health Sciences; University of Crete; Heraklion Crete Greece
| | - Diomedes E. Logothetis
- Department of Physiology and Biophysics; Virginia Commonwealth University; School of Medicine; Richmond Virginia USA
| | - Andreas Plaitakis
- Faculty of Medicine; Department of Neurology; School of Health Sciences; University of Crete; Heraklion Crete Greece
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16
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Gazi AD, Charova S, Aivaliotis M, Panopoulos NJ, Kokkinidis M. HrpG and HrpV proteins from the Type III secretion system of Erwinia amylovora form a stable heterodimer. FEMS Microbiol Lett 2014; 362:1-8. [PMID: 25790492 DOI: 10.1093/femsle/fnu011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Bacterial type III secretion systems (T3SSs) are specialized multicomponent nanomachines that mediate the transport of proteins either to extracellular locations or directly into eukaryotic host cell cytoplasm. Erwinia amylovora, the main agent of rosaceous plants fireblight disease, employs an Hrp/Hrc1 T3SS to accomplish its pathogenesis. The regulatory network that controls the activation of this T3SS is largely unknown in E. amylovora. However, in Pseudomonas syringae pathovars, the HrpG/HrpV complex has been shown to directly regulate the activity of transcription factor HrpS and consequently the upregulation of the Hrp/Hrc1 T3SS related genes. In this work, we report the successful recombinant production and purification of a stable E. amylovora HrpG/HrpV complex, using pPROpET, a bicistronic expression vector. Furthermore, we present the first solution structure of this complex based on small-angle X-ray scattering data.
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Affiliation(s)
- Anastasia D Gazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece Biology Department, University of Crete, Vasilika Vouton, 71409 Heraklio, Crete, Greece
| | - Spyridoula Charova
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece
| | - Nicholas J Panopoulos
- Professor Emeritus, Biology Department, University of Crete, Vasilika Vouton, 71409 Heraklio, Crete, Greece Professor Emeritus, Department of Environmental Sciences, Policy, and Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720-3114, USA
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece Biology Department, University of Crete, Vasilika Vouton, 71409 Heraklio, Crete, Greece
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17
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Barrier E, Braz Fernandes FM, Bujan M, Feiters MC, Froideval A, Ghijsen J, Hase T, Hough MA, Jergel M, Jimenez I, Kajander T, Kikas A, Kokkinidis M, Kover L, Larsen HB, Lawson DM, Lawniczak-Jablonska K, Mariani C, Mikulik P, Monnier J, Morera S, McGuinness C, Müller-Buschbaum P, Meedom Nielson M, Pietsch U, Tromp M, Simon M, Stangl J, Zanotti G. The benefit of the European User Community from transnational access to national radiation facilities. J Synchrotron Radiat 2014; 21:638-639. [PMID: 24763656 DOI: 10.1107/s1600577514007619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 06/03/2023]
Abstract
Transnational access (TNA) to national radiation sources is presently provided via programmes of the European Commission by BIOSTRUCT-X and CALIPSO with a major benefit for scientists from European countries. Entirely based on scientific merit, TNA allows all European scientists to realise synchrotron radiation experiments for addressing the Societal Challenges promoted in HORIZON2020. In addition, by TNA all European users directly take part in the development of the research infrastructure of facilities. The mutual interconnection of users and facilities is a strong prerequisite for future development of the research infrastructure of photon science. Taking into account the present programme structure of HORIZON2020, the European Synchrotron User Organization (ESUO) sees considerable dangers for the continuation of this successful collaboration in the future.
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Affiliation(s)
- Elise Barrier
- CNRS, Unité de Catalyse et de Chimie du Solide, Université Lille 1, 59655 Villeneuve d'Ascq Cedex, France
| | - Francisco Manuel Braz Fernandes
- CENIMAT/I3N, Departamento de Ciências dos Materiais, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Maya Bujan
- Rudjer Boskovic Institute, Bijenicka Cesta 54, Zagreb 10000, Croatia
| | - Martin C Feiters
- Faculty of Science, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | | | - Jacques Ghijsen
- Department of Physics (PMR-LISE), University Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Thomas Hase
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Matej Jergel
- Department of Multilayers and Nanostructures, Institute of Physics of the Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava 845 11, Slovak Republic
| | - Ignacio Jimenez
- Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Ines de la Cruz 3, Madrid 28049, Spain
| | - Tommi Kajander
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Arvo Kikas
- Institute of Physics, University of Tartu, Riia 142, Tartu 51014, Estonia
| | - Michael Kokkinidis
- Department of Biology and IMBB/FORTH, University of Crete, PO Box 2208, Heraklion 71409, Greece
| | - Laszlo Kover
- Electron Spectroscopy and Materials Science Section, Institute for Nuclear Research, Hungarian Academy of Sciences, Bem tér 18/a, Debrecen 4026, Hungary
| | - Helge B Larsen
- Department of Materials Science, University of Stavanger, Ullandhaug, Stavanger 4036, Norway
| | - David Mark Lawson
- Biological Chemistry, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | | | - Carlo Mariani
- Dipartimento di Fisica, Università di Roma `La Sapienza', Roma 00185, Italy
| | - Petr Mikulik
- Department of Condensed Matter Physics, Masaryk University, Kotlarska 2, Brno 61137, Czech Republic
| | - Judith Monnier
- Institut de Chimie et des Matériaux Paris, ICMPE-CMTR, CNRS UMR 7182, 2-8 rue H. Dunant, 94320 Thiais, France
| | - Solange Morera
- CNRS, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 91190 Gif-sur-Yvette, France
| | - Cormac McGuinness
- School of Physics, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Peter Müller-Buschbaum
- Physik-Department, Lehrstuhl für Funktionelle Materialien, Technische Universität München, James-Franck-Strasse 1, Garching 85748, Germany
| | | | - Ullrich Pietsch
- Festkörperphysik, Universität Siegen, Walter Flex Strasse 2, Postfach 601553, Siegen 57068, Germany
| | - Moniek Tromp
- Catalyst Characterisation, Department of Chemistry, Catalysis Research Center, Technische Universität München, Lichtenbergstrasse 4, Garching 85748, Germany
| | - Marc Simon
- CNRS, Unité de Catalyse et de Chimie du Solide, Université Lille 1, 59655 Villeneuve d'Ascq Cedex, France
| | - Julian Stangl
- CENIMAT/I3N, Departamento de Ciências dos Materiais, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Giuseppe Zanotti
- Rudjer Boskovic Institute, Bijenicka Cesta 54, Zagreb 10000, Croatia
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18
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Fadouloglou V, Aleka T, Bouriotis V, Glykos N, Kokkinidis M. Crystal structures of two polysaccharide deacetylases from Bacillus cereus. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313097213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Fadouloglou VE, Kapanidou M, Agiomirgianaki A, Arnaouteli S, Bouriotis V, Glykos NM, Kokkinidis M. Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus. Acta Crystallogr D Biol Crystallogr 2013; 69:276-83. [PMID: 23385463 DOI: 10.1107/s0907444912045829] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/06/2012] [Indexed: 11/10/2022]
Abstract
The structure of BC0361, a polysaccharide deacetylase from Bacillus cereus, has been determined using an unconventional molecular-replacement procedure. Tens of putative models of the C-terminal domain of the protein were constructed using a multitude of homology-modelling algorithms, and these were tested for the presence of signal in molecular-replacement calculations. Of these, only the model calculated by the SAM-T08 server gave a consistent and convincing solution, but the resulting model was too inaccurate to allow phase determination to proceed to completion. The application of slow-cooling torsion-angle simulated annealing (started from a very high temperature) drastically improved this initial model to the point of allowing phasing through cycles of model building and refinement to be initiated. The structure of the protein is presented with emphasis on the presence of a C(α)-modified proline at its active site, which was modelled as an α-hydroxy-L-proline.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
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20
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Gazi AD, Sarris PF, Fadouloglou VE, Charova SN, Mathioudakis N, Panopoulos NJ, Kokkinidis M. Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains. BMC Microbiol 2012; 12:188. [PMID: 22937899 PMCID: PMC3574062 DOI: 10.1186/1471-2180-12-188] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/21/2012] [Indexed: 11/30/2022] Open
Abstract
Background The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. Some Pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterized Hrc1 T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. The aim of this study is to perform an in silico analysis of T3SS-2, and to compare it with other known T3SSs. Results Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of the P. syringae pv. phaseolicola strain is grouped with a second T3SS found in the pNGR234b plasmid of Rhizobium sp. These additional T3SS gene clusters define a subgroup within the Rhizobium T3SS family. Although, T3SS-2 is not distributed as widely as the Hrc1 T3SS in P. syringae strains, it was found to be constitutively expressed in P. syringae pv phaseolicola through RT-PCR experiments. Conclusions The relatedness of the P. syringae T3SS-2 to a second T3SS from the pNGR234b plasmid of Rhizobium sp., member of subgroup II of the rhizobial T3SS family, indicates common ancestry and/or possible horizontal transfer events between these species. Functional analysis and genome sequencing of more rhizobia and P. syringae pathovars may shed light into why these bacteria maintain a second T3SS gene cluster in their genome.
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Affiliation(s)
- Anastasia D Gazi
- Department of Biology, University of Crete, Vasilika Vouton, P,O, Box 2208, Heraklion, Crete GR 71409, Greece
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Kefala K, Kotsifaki D, Providaki M, Kapetaniou EG, Rahme L, Kokkinidis M. Purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal fragment of the MvfR protein from Pseudomonas aeruginosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:695-7. [PMID: 22684073 DOI: 10.1107/s1744309112016661] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 04/17/2012] [Indexed: 11/10/2022]
Abstract
The LysR-type transcriptional regulator MvfR plays a critical role in Pseudomonas aeruginosa pathogenicity via the transcriptional regulation of multiple quorum-sensing-regulated virulence factors. The protein also controls pathogenic type VI secretion loci. MvfRC87, a 242-residue C-terminal segment of MvfR, was produced in Escherichia coli, purified and crystallized. X-ray diffraction data were collected using synchrotron radiation and crystallographic parameters were determined.
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Affiliation(s)
- Katerina Kefala
- Department of Biology, University of Crete, PO Box 2208, GR-71003 Heraklion, Crete, Greece
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N. S, D. A, Kotzabasaki M, F. P, E. V, J. N, Kokkinidis M. Protein Flexibility and Coiled-Coil Propensity: New Insights Into Type III and Other Bacterial Secretion Systems. Biochemistry 2012. [DOI: 10.5772/32582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
It has been proposed that certain type II restriction enzymes (REs), such as EcoRV, track the helical pitch of DNA as they diffuse along DNA, a so-called rotation-coupled sliding. As of yet, there is no direct experimental observation of this phenomenon, but mounting indirect evidence gained from single-molecule imaging of RE-DNA complexes support the hypothesis. We address this issue by conjugating fluorescent labels of varying size (organic dyes, proteins and quantum dots) to EcoRV, and by fusing it to the engineered Rop protein scRM6. Single-molecule imaging of these modified EcoRVs sliding along DNA provides us with their linear diffusion constant (D(1)), revealing a significant size dependency. To account for the dependence of D(1) on the size of the EcoRV label, we have developed four theoretical models describing different types of motion along DNA and find that our experimental results are best described by rotation-coupled sliding of the protein. The similarity of EcoRV to other type II REs and DNA binding proteins suggests that this type of motion could be widely preserved in other biological contexts.
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Affiliation(s)
- Jasmina Dikić
- Laboratoire Kastler Brossel, ENS, UPMC-Paris6, CNRS UMR 8552, 24 rue Lhomond, 75005 Paris, France.
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Kokkinidis M, Glykos N, Fadouloglou V. Protein Flexibility and Enzymatic Catalysis. Structural and Mechanistic Enzymology - Bringing Together Experiments and Computing 2012; 87:181-218. [DOI: 10.1016/b978-0-12-398312-1.00007-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sarris PF, Skandalis N, Kokkinidis M, Panopoulos NJ. In silico analysis reveals multiple putative type VI secretion systems and effector proteins in Pseudomonas syringae pathovars. Mol Plant Pathol 2010; 11:795-804. [PMID: 21091602 PMCID: PMC6640432 DOI: 10.1111/j.1364-3703.2010.00644.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Type VI secretion systems (T6SS) of Gram-negative bacteria form injectisomes that have the potential to translocate effector proteins into eukaryotic host cells. In silico analysis of the genomes in six Pseudomonas syringae pathovars revealed that P. syringae pv. tomato DC3000, pv. tabaci ATCC 11528, pv. tomato T1 and pv. oryzae 1-6 each carry two putative T6SS gene clusters (HSI-I and HSI-II; HSI: Hcp secretion island), whereas pv. phaseolicola 1448A and pv. syringae B728 each carry one. The pv. tomato DC3000 HSI-I and pv. tomato T1 HSI-II possess a highly similar organization and nucleotide sequence, whereas the pv. tomato DC3000, pv. oryzae 1-6 and pv. tabaci 11528 HSI-II are more divergent. Putative effector orthologues vary in number among the strains examined. The Clp-ATPases and IcmF orthologues form distinct phylogenetic groups: the proteins from pv. tomato DC3000, pv. tomato T1, pv. oryzae and pv. tabaci 11528 from HSI-II group together with most orthologues from other fluorescent pseudomonads, whereas those from pv. phaseolicola, pv. syringae, pv. tabaci, pv. tomato T1 and pv. oryzae from HSI-I group closer to the Ralstonia solanacearum and Xanthomonas orthologues. Our analysis suggests multiple independent acquisitions and possible gene attrition/loss of putative T6SS genes by members of P. syringae.
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Affiliation(s)
- Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece.
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Tampakaki AP, Skandalis N, Gazi AD, Bastaki MN, Sarris PF, Charova SN, Kokkinidis M, Panopoulos NJ. Playing the "Harp": evolution of our understanding of hrp/hrc genes. Annu Rev Phytopathol 2010; 48:347-370. [PMID: 20455697 DOI: 10.1146/annurev-phyto-073009-114407] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
With the advent of recombinant DNA techniques, the field of molecular plant pathology witnessed dramatic shifts in the 1970s and 1980s. The new and conventional methodologies of bacterial molecular genetics put bacteria center stage. The discovery in the mid-1980s of the hrp/hrc gene cluster and the subsequent demonstration that it encodes a type III secretion system (T3SS) common to Gram negative bacterial phytopathogens, animal pathogens, and plant symbionts was a landmark in molecular plant pathology. Today, T3SS has earned a central role in our understanding of many fundamental aspects of bacterium-plant interactions and has contributed the important concept of interkingdom transfer of effector proteins determining race-cultivar specificity in plant-bacterium pathosystems. Recent developments in genomics, proteomics, and structural biology enable detailed and comprehensive insights into the functional architecture, evolutionary origin, and distribution of T3SS among bacterial pathogens and support current research efforts to discover novel antivirulence drugs.
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Geel TM, Meiss G, van der Gun BT, Kroesen BJ, de Leij LF, Zaremba M, Silanskas A, Kokkinidis M, Pingoud A, Ruiters MH, McLaughlin PM, Rots MG. Endonucleases induced TRAIL-insensitive apoptosis in ovarian carcinoma cells. Exp Cell Res 2009; 315:2487-95. [PMID: 19540229 DOI: 10.1016/j.yexcr.2009.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 06/08/2009] [Accepted: 06/08/2009] [Indexed: 11/16/2022]
Abstract
TRAIL induced apoptosis of tumor cells is currently entering phase II clinical settings, despite the fact that not all tumor types are sensitive to TRAIL. TRAIL resistance in ovarian carcinomas can be caused by a blockade upstream of the caspase 3 signaling cascade. We explored the ability of restriction endonucleases to directly digest DNA in vivo, thereby circumventing the caspase cascade. For this purpose, we delivered enzymatically active endonucleases via the cationic amphiphilic lipid SAINT-18((R)):DOPE to both TRAIL-sensitive and insensitive ovarian carcinoma cells (OVCAR and SKOV-3, respectively). Functional nuclear localization after delivery of various endonucleases (BfiI, PvuII and NucA) was indicated by confocal microscopy and genomic cleavage analysis. For PvuII, analysis of mitochondrial damage demonstrated extensive apoptosis both in SKOV-3 and OVCAR. This study clearly demonstrates that cellular delivery of restriction endonucleases holds promise to serve as a novel therapeutic tool for the treatment of resistant ovarian carcinomas.
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Affiliation(s)
- Tessa M Geel
- Department of Pathology and Medical Biology, Groningen University Institute for Drug Exploration, University Medical Center Groningen, Hanzeplein 1, Groningen, The Netherlands
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Fadouloglou VE, Bastaki MN, Ashcroft AE, Phillips SE, Panopoulos NJ, Glykos NM, Kokkinidis M. On the quaternary association of the type III secretion system HrcQB-C protein: Experimental evidence differentiates among the various oligomerization models. J Struct Biol 2009; 166:214-25. [DOI: 10.1016/j.jsb.2009.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gazi AD, Charova SN, Panopoulos NJ, Kokkinidis M. Coiled-coils in type III secretion systems: structural flexibility, disorder and biological implications. Cell Microbiol 2009; 11:719-29. [PMID: 19215225 DOI: 10.1111/j.1462-5822.2009.01297.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent structural studies and analyses of microbial genomes have consolidated the understanding of the structural and functional versatility of coiled-coil domains in proteins from bacterial type III secretion systems (T3SS). Such domains consist of two or more α-helices forming a bundle structure. The occurrence of coiled-coils in T3SS is considerably higher than the average predicted occurrence in prokaryotic proteomes. T3SS proteins comprising coiled-coil domains are frequently characterized by an increased structural flexibility, which may vary from localized structural disorder to the establishment of molten globule-like state. The propensity for coiled-coil formation and structural disorder are frequently essential requirements for various T3SS functions, including the establishment of protein-protein interaction networks and the polymerization of extracellular components of T3SS appendages. Possible correlations between the frequently observed N-terminal structural disorder of effectors and the T3SS secretion signal are discussed. The results for T3SS are also compared with other Gram-negative secretory systems.
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Affiliation(s)
- Anastasia D Gazi
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology and Department of Biology, University of Crete, Vasilika Vouton, Heraklion, Crete, Greece
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Gazi AD, Bastaki M, Charova SN, Gkougkoulia EA, Kapellios EA, Panopoulos NJ, Kokkinidis M. Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems. J Biol Chem 2008; 283:34062-8. [PMID: 18836182 PMCID: PMC2662227 DOI: 10.1074/jbc.m803408200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 09/11/2008] [Indexed: 11/06/2022] Open
Abstract
Gene clusters encoding various type III secretion system (T3SS) injectisomes, frequently code downstream of the conserved atpase gene for small hydrophilic proteins whose amino acid sequences display a propensity for intrinsic disorder and coiled-coil formation. These properties were confirmed experimentally for a member of this class, the HrpO protein from the T3SS of Pseudomonas syringae pv phaseolicola: HrpO exhibits high alpha-helical content with coiled-coil characteristics, strikingly low melting temperature, structural properties that are typical for disordered proteins, and a pronounced self-association propensity, most likely via coiled-coil interactions, resulting in heterogeneous populations of quaternary complexes. HrpO interacts in vivo with HrpE, a T3SS protein for which coiled-coil formation is also strongly predicted. Evidence from HrpO analogues from all T3SS families and the flagellum suggests that the extreme flexibility and propensity for coiled-coil interactions of this diverse class of small, intrinsically disordered proteins, whose structures may alter as they bind to their cognate folded protein targets, might be important elements in the establishment of protein-protein interaction networks required for T3SS function.
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Affiliation(s)
- Anastasia D Gazi
- Institute of Molecular Biology & Biotechnology, Foundation of Research & Technology, Vasilika Vouton, Heraklion, Crete, Greece
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Meramveliotaki C, Androulaki M, Eliopoulos E, Kokkinidis M. A new nicking enzyme is developed from a mutant of the modified type II restriction enzyme scPvuII. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308090211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Ambrazi M, Fellas G, Kapetaniou EG, Kotsifaki D, Providaki M, Kokkinidis M. Purification, crystallization and preliminary X-ray diffraction analysis of a variant of the ColE1 Rop protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:432-4. [PMID: 18453719 PMCID: PMC2376389 DOI: 10.1107/s1744309108011342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 04/21/2008] [Indexed: 11/10/2022]
Abstract
Rop is the paradigm of a canonical four-alpha-helical bundle. Its loop region has attracted considerable interest because a single alanine-to-proline substitution (A31P) in the loop is sufficient to change the topology of this small protein. In order to further analyse the loop region as a possible folding-control element, the double mutant D30P/A31G (RopPG) was produced, purified and crystallized. The crystals belonged to space group P2(1), with unit-cell parameters a = 26.7, b = 38.8, c = 56.6 A, beta = 100.9 degrees and two molecules in the asymmetric unit. A complete data set was collected at 100 K to a resolution of 1.4 A using synchrotron radiation.
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Affiliation(s)
- Maria Ambrazi
- Department of Biology, University of Crete, PO Box 2208, GR-71003 Heraklion, Crete, Greece
| | - George Fellas
- Department of Biology, University of Crete, PO Box 2208, GR-71003 Heraklion, Crete, Greece
| | - Evangelia G. Kapetaniou
- Institute of Molecular Biology and Biotechnology, PO Box 1527, GR-71110 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, PO Box 1527, GR-71110 Heraklion, Crete, Greece
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, PO Box 1527, GR-71110 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, PO Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, PO Box 1527, GR-71110 Heraklion, Crete, Greece
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Tsalafouta A, Psylinakis E, Kapetaniou EG, Kotsifaki D, Deli A, Roidis A, Bouriotis V, Kokkinidis M. Purification, crystallization and preliminary X-ray analysis of the peptidoglycan N-acetylglucosamine deacetylase BC1960 from Bacillus cereus in the presence of its substrate (GlcNAc)6. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:203-5. [PMID: 18323609 PMCID: PMC2374148 DOI: 10.1107/s1744309108002510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 01/23/2008] [Indexed: 11/10/2022]
Abstract
The peptidoglycan N-acetylglucosamine (GlcNAc) deacetylase BC1960 from Bacillus cereus (EC 3.5.1.33), an enzyme consisting of 275 amino acids, was crystallized in the presence of its substrate (GlcNAc)(6). The crystals belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 92.7, c = 242.9 A and four molecules in the asymmetric unit. A complete data set was collected at 100 K to a resolution of 2.38 A using synchrotron radiation.
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Affiliation(s)
- Aleka Tsalafouta
- Department of Biology, University of Crete, PO Box 2208, GR-71110, Heraklion, Crete, Greece
| | - Emmanuel Psylinakis
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Evangelia G. Kapetaniou
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Alexandra Deli
- Department of Biology, University of Crete, PO Box 2208, GR-71110, Heraklion, Crete, Greece
| | - Alexandros Roidis
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Vasilis Bouriotis
- Department of Biology, University of Crete, PO Box 2208, GR-71110, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, PO Box 2208, GR-71110, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
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Fadouloglou VE, Kokkinidis M, Glykos NM. Determination of protein oligomerization state: Two approaches based on glutaraldehyde crosslinking. Anal Biochem 2008; 373:404-6. [DOI: 10.1016/j.ab.2007.10.027] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 10/11/2007] [Accepted: 10/11/2007] [Indexed: 10/22/2022]
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Meramveliotaki C, Kotsifaki D, Androulaki M, Hountas A, Eliopoulos E, Kokkinidis M. Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:836-8. [PMID: 17909283 PMCID: PMC2339719 DOI: 10.1107/s1744309107040377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022]
Abstract
The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type homodimeric form into the enzymatically active single-chain variant scPvuII by tandemly joining the two subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is suitable for the development of programmed restriction endonucleases for highly specific DNA cleavage, was purified and crystallized. The crystals diffract to a resolution of 2.35 A and belong to space group P4(2), with unit-cell parameters a = b = 101.92, c = 100.28 A and two molecules per asymmetric unit. Phasing was successfully performed by molecular replacement.
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Affiliation(s)
- Chrysi Meramveliotaki
- Department of Science, Agricultural University of Athens, Athens, Greece
- Department of Biology, University of Crete, PO Box 2208, GR-71110 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110 Heraklion, Crete, Greece
- Department of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110 Heraklion, Crete, Greece
| | - Maria Androulaki
- Department of Science, Agricultural University of Athens, Athens, Greece
- Department of Biology, University of Crete, PO Box 2208, GR-71110 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110 Heraklion, Crete, Greece
- Department of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Athanasios Hountas
- Department of Science, Agricultural University of Athens, Athens, Greece
| | - Elias Eliopoulos
- Department of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, PO Box 2208, GR-71110 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110 Heraklion, Crete, Greece
- Correspondence e-mail:
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Abstract
Bacillus cereus is an opportunistic pathogenic bacterium closely related to Bacillus anthracis, the causative agent of anthrax in mammals. A significant portion of the B. cereus chromosomal genes are common to B. anthracis, including genes which in B. anthracis code for putative virulence and surface proteins. B. cereus thus provides a convenient model organism for studying proteins potentially associated with the pathogenicity of the highly infectious B. anthracis. The zinc-binding protein of B. cereus, BcZBP, is encoded from the bc1534 gene which has three homologues to B. anthracis. The protein exhibits deacetylase activity with the N-acetyl moiety of the N-acetylglucosamine and the diacetylchitobiose and triacetylchitotriose. However, neither the specific substrate of the BcZBP nor the biochemical pathway have been conclusively identified. Here, we present the crystal structure of BcZBP at 1.8 A resolution. The N-terminal part of the 234 amino acid protein adopts a Rossmann fold whereas the C-terminal part consists of two beta-strands and two alpha-helices. In the crystal, the protein forms a compact hexamer, in agreement with solution data. A zinc binding site and a potential active site have been identified in each monomer. These sites have extensive similarities to those found in two known zinc-dependent hydrolases with deacetylase activity, MshB and LpxC, despite a low degree of amino acid sequence identity. The functional implications and a possible catalytic mechanism are discussed.
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Kapetaniou EG, Kotsifaki D, Providaki M, Rina M, Bouriotis V, Kokkinidis M. Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:12-4. [PMID: 17183163 PMCID: PMC2330102 DOI: 10.1107/s1744309106051530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Accepted: 11/28/2006] [Indexed: 11/11/2022]
Abstract
The DNA methyltransferase M.BseCI from Bacillus stearothermophilus (EC 2.1.1.72), a 579-amino-acid enzyme, methylates the N6 atom of the 3' adenine in the sequence 5'-ATCGAT-3'. M.BseCI was crystallized in complex with its cognate DNA. The crystals were found to belong to the hexagonal space group P6, with unit-cell parameters a = b = 87.0, c = 156.1 A, beta = 120.0 degrees and one molecule in the asymmetric unit. Two complete data sets were collected at wavelengths of 1.1 and 2.0 A to 2.5 and 2.8 A resolution, respectively, using synchrotron radiation at 100 K.
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Affiliation(s)
- Evangelia G. Kapetaniou
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Maria Rina
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
- University of Crete, Department of Biology, PO Box 2208, GR-71110, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
- University of Crete, Department of Biology, PO Box 2208, GR-71110, Heraklion, Crete, Greece
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Glykos NM, Papanikolau Y, Vlassi M, Kotsifaki D, Cesareni G, Kokkinidis M. Loopless Rop: structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein. Biochemistry 2006; 45:10905-19. [PMID: 16953576 DOI: 10.1021/bi060833n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The repressor of primer (Rop) protein has become a steady source of surprises concerning the relationship between the sequences and the structures of several of its mutants and variants. Here we add another piece to the puzzle of Rop by showing that an engineered deletion mutant of the protein (corresponding to a deletion of residues 30-34 of the wild-type protein and designed to restore the heptad periodicity at the turn region) results in a complete reorganization of the bundle which is converted from a homodimer to a homotetramer. In contrast (and as previously shown), a two-residue insertion, which also restores the heptad periodicity, is essentially identical with wild-type Rop. The new deletion mutant structure is a canonical, left-handed, all-antiparallel bundle with a completely different hydrophobic core and distinct surface properties. The structure agrees and qualitatively explains the results from functional, thermodynamic, and kinetic studies which indicated that this deletion mutant is a biologically inactive hyperstable homotetramer. Additional insight into the stability and dynamics of the mutant structure has been obtained from extensive molecular dynamics simulations in explicit water and with full treatment of electrostatics.
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Affiliation(s)
- Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Dimitras 19, 68100 Alexandroupolis, Greece
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39
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Fadouloglou VE, Kotsifaki D, Gazi AD, Fellas G, Meramveliotaki C, Deli A, Psylinakis E, Bouriotis V, Kokkinidis M. Purification, crystallization and preliminary characterization of a putative LmbE-like deacetylase from Bacillus cereus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:261-4. [PMID: 16511317 PMCID: PMC2197166 DOI: 10.1107/s1744309106004660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 02/07/2006] [Indexed: 11/10/2022]
Abstract
The Bacillus cereus BC1534 protein, a putative deacetylase from the LmbE family, has been purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. Crystals of the 26 kDa protein grown from MPD and acetate buffer belong to space group R32, with unit-cell parameters a = b = 76.7, c = 410.5 A (in the hexagonal setting). A complete native data set was collected to a resolution of 2.5 A from a single cryoprotected crystal using synchrotron radiation. As BC1534 shows significant sequence homology with an LmbE-like protein of known structure from Thermus thermophilus, molecular replacement will be used for crystal structure determination.
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Affiliation(s)
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, PO Box 1527, Vasilika Vouton, GR-71110 Heraklion, Crete, Greece
| | - Anastasia D. Gazi
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
| | - Georgios Fellas
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
| | - Chrysi Meramveliotaki
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
| | - Alexandra Deli
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
| | - Emmanuel Psylinakis
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, PO Box 1527, Vasilika Vouton, GR-71110 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, PO Box 1527, Vasilika Vouton, GR-71110 Heraklion, Crete, Greece
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40
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Meramveliotaki C, Eliopoulos E, Kokkinidis M. Sructure determination of sc PvuII by crystallographic and SAXS methods. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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41
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Abstract
Type III secretion systems (TTSSs) are essential mediators of the interaction of many Gram-negative bacteria with human, animal or plant hosts. Extensive sequence and functional similarities exist between components of TTSS from bacteria as diverse as animal and plant pathogens. Recent crystal structure determinations of TTSS proteins reveal extensive structural homologies and novel structural motifs and provide a basis on which protein interaction networks start to be drawn within the TTSSs, that are consistent with and help rationalize genetic and biochemical data. Such studies, along with electron microscopy, also established common architectural design and function among the TTSSs of plant and mammalian pathogens, as well as between the TTSS injectisome and the flagellum. Recent comparative genomic analysis, bioinformatic genome mining and genome-wide functional screening have revealed an unsuspected number of newly discovered effectors, especially in plant pathogens and uncovered a wider distribution of TTSS in pathogenic, symbiotic and commensal bacteria. Functional proteomics and analysis further reveals common themes in TTSS effector functions across phylogenetic host and pathogen boundaries. Based on advances in TTSS biology, new diagnostics, crop protection and drug development applications, as well as new cell biology research tools are beginning to emerge.
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Affiliation(s)
- A P Tampakaki
- Institute of Molecular Biology and Biotechnology, PO Box 1527, GR-71110 Heraklion, Crete, Greece
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42
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Glykos NM, Kokkinidis M, Kokkindis M. Structural polymorphism of a marginally stable 4-alpha-helical bundle. Images of a trapped molten globule? Proteins 2004; 56:420-5. [PMID: 15229876 DOI: 10.1002/prot.20167] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Glykos NM, Kokkinidis M. Structural polymorphism of a marginally stable 4-α-helical bundle. images of a trapped molten globule? Proteins 2004. [DOI: 10.1002/prot.20271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Papanikolau Y, Kotsifaki D, Fadouloglou VE, Gazi AD, Glykos NM, Cesareni G, Kokkinidis M. Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants. Acta Crystallogr D Biol Crystallogr 2004; 60:1334-7. [PMID: 15213408 DOI: 10.1107/s0907444904008546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Accepted: 04/11/2004] [Indexed: 11/10/2022]
Abstract
Detailed knowledge of the influence of various parameters on macromolecular solubility is essential for crystallization. The concept of so-called 'ionic strength reducers' provides insight into the changes in solubility induced by organic solvents and hydrophilic polymers in aqueous electrolytic solutions. A simple and efficient procedure is presented which exploits the properties of ionic strength reducers in the purification and crystallization of proteins. Using two designed variants of the Rop protein as model systems, superior crystals have been obtained compared with conventional techniques. This procedure is particularly useful in cases where excessive nucleation leads to the growth of a large number of tiny crystals that are useless for crystallographic analysis.
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Affiliation(s)
- Yannis Papanikolau
- University of Crete, Department of Biology, PO Box 2208, GR-71409 Heraklion, Crete, Greece
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45
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Abstract
Classical molecular replacement methods and the newer six-dimensional searches treat molecular replacement as a succession of sub-problems of reduced dimensionality. Due to their `divide-and-conquer' approach, these methods necessarily ignore (at least during their early stages) the very knowledge that a target crystal structure may comprise, for example, more than one copy of a search model, or several models of different types. An algorithm for a stochastic multi-dimensional molecular replacement search has been described previously and shown to locate solutions successfully, even in cases as complex as a 23-dimensional 4-body search. The original description of the method only dealt with a special case of molecular replacement, namely with the problem of placingncopies of only one search model in the asymmetric unit of a target crystal structure. Here a natural generalization of this algorithm is presented to deal with the full molecular replacement problem, that is, with the problem of determining the orientations and positions of a total ofncopies ofmdifferent models (withn≥m) which are assumed to be present in the asymmetric unit of a target crystal structure. The generality of this approach is illustrated through its successful application to a 17-dimensional 3-model problem involving one DNA and two protein molecules.
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Fadouloglou VE, Tampakaki AP, Glykos NM, Bastaki MN, Hadden JM, Phillips SE, Panopoulos NJ, Kokkinidis M. Structure of HrcQB-C, a conserved component of the bacterial type III secretion systems. Proc Natl Acad Sci U S A 2003; 101:70-5. [PMID: 14694203 PMCID: PMC314140 DOI: 10.1073/pnas.0304579101] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. In addition, type III secretion systems are also required for biogenesis of the bacterial flagellum. The HrcQ(B) protein, a component of the secretion apparatus of Pseudomonas syringae with homologues in all type III systems, has a variable N-terminal and a conserved C-terminal domain (HrcQ(B)-C). Here, we report the crystal structure of HrcQ(B)-C and show that this domain retains the ability of the full-length protein to interact with other type III components. A 3D analysis of sequence conservation patterns reveals two clusters of residues potentially involved in protein-protein interactions. Based on the analogies between HrcQ(B) and its flagellum homologues, we propose that HrcQ(B)-C participates in the formation of a C-ring-like assembly.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Biology, University of Crete, PO Box 2208, GR-71409 Heraklion, Crete, Greece
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47
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Spyridaki A, Matzen C, Lanio T, Jeltsch A, Simoncsits A, Athanasiadis A, Scheuring-Vanamee E, Kokkinidis M, Pingoud A. Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII. J Mol Biol 2003; 331:395-406. [PMID: 12888347 DOI: 10.1016/s0022-2836(03)00692-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+). According to the structural data, divalent metal ion binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+) complex has two distinct metal ion binding sites, one in each monomer. One site is formed by the catalytic residues Asp58 and Glu68, and has extensive similarities to a catalytically important site found in all structurally examined restriction endonucleases. The other binding site is located in the other monomer, in the immediate vicinity of the hydroxyl group of Tyr94; it has no analogy to metal ion binding sites found so far in restriction endonucleases. To assign the number of metal ions involved and to better understand the role of Mg(2+) binding to Tyr94 for the function of PvuII, we have exchanged Tyr94 by Phe and characterized the metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F variant. Wild-type PvuII cleaves both strands of the DNA in a concerted reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA cleavage, occurs with a Hill coefficient of 4, meaning that at least two metal ions are bound to each subunit in a cooperative fashion upon formation of the active complex. Quenched-flow experiments show that DNA cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with enzyme or DNA than if preformed enzyme-DNA complexes are mixed with Mg(2+). These results show that Mg(2+) cannot easily enter the active center of the preformed enzyme-DNA complex, but that for fast cleavage the metal ions must already be bound to the apoenzyme and carried with the enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to wild-type PvuII, does not cleave DNA in a concerted manner and metal ion binding occurs with a Hill coefficient of 1. These results indicate that removal of the Mg(2+) binding site at Tyr94 completely disrupts the cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F cleaves DNA about ten times more slowly than wild-type PvuII, regardless of the order of mixing. From these results we conclude that wild-type PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+) required for catalysis are already bound at the enzyme, one of them at Tyr94. We suggest that this Mg(2+) is shifted to the active center during binding of a specific DNA substrate. These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter the catalytic center of restriction endonucleases.
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Affiliation(s)
- Aspasia Spyridaki
- Department of Biology, IMBB/FORTH, University of Crete, PO Box 1527, Heraklion, GR-71110, Crete, Greece
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48
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Abstract
The gene encoding chitinase ArChiB from the Antarctic Arthrobacter sp. TAD20 has been expressed in Escherichia coli and the recombinant enzyme purified to homogeneity. In an effort to engineer cold-adapted biocatalysts through rational redesign to operate at elevated temperatures, we performed several mutations aiming to increase the rigidity of the molecular edifice of the selected psychrophilic chitinase. The mutations were designed on the basis of a homology-based three-dimensional model of the enzyme, and included an attempt to introduce a salt bridge (mutant N198K) and replacements of selected Gly residues by either Pro (mutants G93P, G254P) or Gln (G406Q). Mutant N198K resulted in a more stable protein (DeltaTm = 0.6 degrees C). Mutant G93P exhibited a DeltaTm of 1.2 degrees C, while mutants G254P and G406Q exhibited decreased stability. We conclude that the effect of mutating Gly residues on enzyme stability is rather complex and can only be understood in the context of the structural environment. Kinetic and spectroscopic analysis of these enzyme variants revealed that the kinetic parameters kcat and Km have been significantly modified.
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Affiliation(s)
- K Mavromatis
- Enzyme Technology Division, Institute of Molecular Biology and Biotechnology, PO Box 1515, 71110 Heraklion, Crete, Greece
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49
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Glykos NM, Kokkinidis M. Structure determination of a small protein through a 23-dimensional molecular-replacement search. Acta Crystallogr D Biol Crystallogr 2003; 59:709-18. [PMID: 12657790 DOI: 10.1107/s0907444903002889] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2002] [Accepted: 02/03/2003] [Indexed: 11/10/2022]
Abstract
The crystal structure of a 4-alpha-helical bundle protein has been determined by the application of a 23-dimensional molecular-replacement search performed using a stochastic method. The search model for the calculation was a 26-residue-long polyalanine helix amounting to less than 13% of the total number of atoms in the asymmetric unit of the target crystal structure. The crystal structure determination procedure is presented in detail, with emphasis on the molecular-replacement calculations.
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50
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Roidis A, Kokkinidis M, Kotsifaki D. Crystallization and structural studies of type I chloramphenicol acetyltransferase. Acta Crystallogr A 2002. [DOI: 10.1107/s010876730208947x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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