Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network
The ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in...
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MDPI AG
2020-10-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/20/4787 |
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| author | Dimitris G. Mintis Anastasia Chasapi Konstantinos Poulas George Lagoumintzis Christos T. Chasapis |
| author_facet | Dimitris G. Mintis Anastasia Chasapi Konstantinos Poulas George Lagoumintzis Christos T. Chasapis |
| author_sort | Dimitris G. Mintis |
| collection | DOAJ |
| description | The ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the pathway. Its RING domain binds both E2-Ub and free Ub with high affinity, resulting in a catalytic active Ub<sub>R</sub>-RING-E2-Ub<sub>D</sub> complex formation. We examined potential changes in the conformational plasticity of the Ark2C RING domain and its ligands in their complexed form within the ubiquitin pathway through molecular dynamics (MD). Three molecular mechanics force fields compared to previous NMR relaxation studies of RING domain of Arkadia were used for effective and accurate assessment of MDs. Our results suggest the Ark2C Ub-RING docking site has a substantial impact on maintaining the conformational rigidity of E2-E3 assembly, necessary for the E3’s catalytic activity. In the Ub<sub>R</sub>-RING-E2-Ub<sub>D</sub> catalytic complex, the Ub<sub>R</sub> molecule was found to have greater mobility than the other Ub, bound to E2. Furthermore, network-based bioinformatics helped us identify E3 RING ligase candidates which potentially exhibit similar structural modules as Ark2C, along with predicted substrates targeted by the Ub-binding RING Ark2C. Our findings could trigger a further exploration of related unrevealed functions of various other E3 RING ligases. |
| first_indexed | 2024-03-10T15:31:22Z |
| format | Article |
| id | doaj.art-3ac371b201284888a60d9e868b526546 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T15:31:22Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-3ac371b201284888a60d9e868b5265462023-11-20T17:36:52ZengMDPI AGMolecules1420-30492020-10-012520478710.3390/molecules25204787Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction NetworkDimitris G. Mintis0Anastasia Chasapi1Konstantinos Poulas2George Lagoumintzis3Christos T. Chasapis4Laboratory of Statistical Thermodynamics and Macromolecules, Department of Chemical Engineering, University of Patras & FORTH/ICE-HT, 26504 Patras, GreeceBiological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, 57001 Thessaloniki, GreeceLaboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26504 Patras, GreeceLaboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26504 Patras, GreeceNMR Center, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, GreeceThe ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the pathway. Its RING domain binds both E2-Ub and free Ub with high affinity, resulting in a catalytic active Ub<sub>R</sub>-RING-E2-Ub<sub>D</sub> complex formation. We examined potential changes in the conformational plasticity of the Ark2C RING domain and its ligands in their complexed form within the ubiquitin pathway through molecular dynamics (MD). Three molecular mechanics force fields compared to previous NMR relaxation studies of RING domain of Arkadia were used for effective and accurate assessment of MDs. Our results suggest the Ark2C Ub-RING docking site has a substantial impact on maintaining the conformational rigidity of E2-E3 assembly, necessary for the E3’s catalytic activity. In the Ub<sub>R</sub>-RING-E2-Ub<sub>D</sub> catalytic complex, the Ub<sub>R</sub> molecule was found to have greater mobility than the other Ub, bound to E2. Furthermore, network-based bioinformatics helped us identify E3 RING ligase candidates which potentially exhibit similar structural modules as Ark2C, along with predicted substrates targeted by the Ub-binding RING Ark2C. Our findings could trigger a further exploration of related unrevealed functions of various other E3 RING ligases.https://www.mdpi.com/1420-3049/25/20/4787E3 RING ligasesubiquitinmolecular dynamicsPPI network |
| spellingShingle | Dimitris G. Mintis Anastasia Chasapi Konstantinos Poulas George Lagoumintzis Christos T. Chasapis Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network Molecules E3 RING ligases ubiquitin molecular dynamics PPI network |
| title | Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network |
| title_full | Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network |
| title_fullStr | Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network |
| title_full_unstemmed | Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network |
| title_short | Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network |
| title_sort | assessing the direct binding of ark like e3 ring ligases to ubiquitin and its implication on their protein interaction network |
| topic | E3 RING ligases ubiquitin molecular dynamics PPI network |
| url | https://www.mdpi.com/1420-3049/25/20/4787 |
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