Abstract
Protein-protein interactions (PPIs) are known to be involved in most cellular functions, and a detailed knowledge of such interactions is essential for studying their role in normal and pathological conditions. Significant progress is being made in the identification of PPIs through advances in computational methods. In particular, the AlphaFold2 machine learning-based model has been shown to accelerate drug discovery process by predicting the 3D structure of protein complexes. In this chapter, a straightforward protocol for predicting interprotein interactions between PAR-3 and its protein partner adapter molecule crk is provided. Such artificial intelligence-based and publicly available approaches can provide a resource for further investigation of therapeutic drug targets.
References
Durham J, Zhang J, Humphreys IR, Pei J, Cong Q (2023) Recent advances in predicting and modeling protein-protein interactions. Trends Biochem Sci 48:527–538
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, ŽĂdek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589
Zhou X, Chen Y, Cui L, Shi Y, Guo C (2022) Advances in the pathogenesis of psoriasis: from keratinocyte perspective. Cell Death Dis 13:81
Hou R, Li J, Niu X, Liu R, Chang W, Zhao X, Wang Q, Li X, Yin G, Zhang K (2017) Stem cells in psoriasis. J Dermatol Sci 86:181–186
Yan J, Zhang K, Guo T, Yang S, Jia H (2022) Par3 regulates the asymmetric division of basal stem cells in psoriasis via the Par3/mInsc/LGN signaling axis. Cell Immunol 373:104496
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H (2014) The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42(Database issue):D358–D363
Lopez ML, Lo M, Kung JE, Dudkiewicz M, Jang GM, Von Dollen J, Johnson JR, Krogan NJ, Pawłowski K, Jura N (2019) PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization. Proc Natl Acad Sci USA 116:15495–15504
Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE (2023) UCSF ChimeraX: tools for structure building and analysis. Protein Sci 32:e4792
Mirdita M, SchĂ¼tze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M (2022) ColabFold: making protein folding accessible to all. Nat Methods 19:679–682
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2024 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
D’Amico, F. (2024). Contribution of Artificial Intelligence to the Identification of Protein-Protein Interactions: A Case Study on PAR-3 and Its Partner Adapter Molecule Crk. In: Methods in Molecular Biology. Springer, New York, NY. https://doi.org/10.1007/7651_2024_530
Download citation
DOI: https://doi.org/10.1007/7651_2024_530
Published:
Publisher Name: Springer, New York, NY