A Comprehensive Analysis of the Structural Recognition between KCTD Proteins and Cullin 3
Abstract
:1. Introduction
2. Results
2.1. The KCTD–Cul3 Interaction: An Overview of the Available Literature Data
2.2. Prediction of the KCTD7 and Cul3 Complex: Validation of the Approach
2.2.1. AlphaFold KCTD7BTB–Cul3 Predicted Structure
2.2.2. MD Analysis of the Predicted Model: A Dynamic View of the Interaction
2.3. Large-Scale Prediction of KCTD–Cul3 Interaction
2.3.1. Cluster 1—KCTD8, KCTD12, KCTD16, KCTD1, and KCTD15
2.3.2. Cluster 2—KCTD6, KCNRG, KCTD11, and KCTD21
2.3.3. Cluster 3—KCTD2, KCTD5, and KCTD17
2.3.4. Cluster 4—KCTD4, KCTD19, and KCTD18
2.3.5. Cluster 5—BTBD10, KCTD20, KCTD7, and KCTD14
2.3.6. Cluster 6—KCTD10, KCTD13, and TNFAP1
2.3.7. Non-Canonical KCTDs: Cluster 7—KCTD3, SHKBP1, and KCTD9
2.4. Common Traits and Differences in the Cul3 Recognition by KCTDs
3. Discussion
4. Methods and Materials
4.1. AlphaFold Predictions
4.2. Molecular Dynamics Simulations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cluster | Protein Complex | Selected Stoichiometry for the Prediction | AF Prediction |
---|---|---|---|
1A | KCTD8BTB(E44-L145)–Cul3 | 5:5 | No stable complex detected |
KCTD12BTB(P33-A131)–Cul3 | 5:5 | No stable complex detected | |
KCTD16BTB(E25-T123)–Cul3 | 5:5 | No stable complex detected | |
1B | KCTD1BTB(A30-T133)–Cul3 | 5:5 | No stable complex detected |
KCTD15BTB(A56-R162)–Cul3 | 5:5 | No stable complex detected | |
2A | KCTD6BTB(D12-D107)–Cul3 | 5:5 | Stable complex detected |
KCNRGBTB(E5-Q104)–Cul3 | 5:5 | No binding observed | |
2B | KCTD11BTB(G14-A123)–Cul3 | 5:5 | Stable complex detected * |
KCTD21BTB(P4-K108)–Cul3 | 5:5 | Stable complex detected | |
3 | KCTD2BTB(R72-T178)–Cul3 | 5:5 | Stable complex detected |
KCTD5BTB(V42-T149)–Cul3 | 5:5 | Stable complex detected | |
KCTD17BTB(G30-V135)–Cul3 | 5:5 | Stable complex detected | |
- | KCTD18BTB(D12-S118)–Cul3 | 1:1 | Stable complex detected |
4 | KCTD4BTB(T33-L135)–Cul3 | 5:5 | No stable complex detected |
KCTD19BTBa(D13-E107)–Cul3 | 1:1 | No stable complex detected | |
KCTD19BTBb(V172-M258)–Cul3 | 1:1 | No stable complex detected | |
KCTD19BTBc(Q396-Q487)–Cul3 | 1:1 | No stable complex detected | |
5A | BTBD10BTB(M149-C266)–Cul3 | 1:1 | Stable complex detected |
KCTD20BTB(E117-C216)–Cul3 | 1:1 | Stable complex detected | |
5B | KCTD7BTB(P50-N143)–Cul3 | 5:5 | Stable complex detected |
KCTD14BTB(T33-D124)–Cul3 | 5:5 | No stable complex detected | |
6 | KCTD10BTB(Y33-Q129)–Cul3 | 5:5 | Stable complex detected |
KCTD13BTB(K41-E142)–Cul3 | 5:5 | Stable complex detected | |
TNFAIP1BTB(K28-S130)–Cul3 | 5:5 | Stable complex detected | |
7 | KCTD3BTB(E18-L115)–Cul3 | 5:5 | Stable complex detected |
SHKBP1BTB(E19-R118)–Cul3 | 5:5 | Stable complex detected | |
- | KCTD9BTB(D89-S191)–Cul3 | 5:5 | Stable complex detected |
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Balasco, N.; Esposito, L.; Smaldone, G.; Salvatore, M.; Vitagliano, L. A Comprehensive Analysis of the Structural Recognition between KCTD Proteins and Cullin 3. Int. J. Mol. Sci. 2024, 25, 1881. https://doi.org/10.3390/ijms25031881
Balasco N, Esposito L, Smaldone G, Salvatore M, Vitagliano L. A Comprehensive Analysis of the Structural Recognition between KCTD Proteins and Cullin 3. International Journal of Molecular Sciences. 2024; 25(3):1881. https://doi.org/10.3390/ijms25031881
Chicago/Turabian StyleBalasco, Nicole, Luciana Esposito, Giovanni Smaldone, Marco Salvatore, and Luigi Vitagliano. 2024. "A Comprehensive Analysis of the Structural Recognition between KCTD Proteins and Cullin 3" International Journal of Molecular Sciences 25, no. 3: 1881. https://doi.org/10.3390/ijms25031881