Reconstructing of the geometry of Atg13 and Atg101 molecules while assembling the complex

DOI: https://doi.org/10.7124/FEEO.v35.1676
Keywords: A. thaliana, ATG (AuTophaGy-related), Protein-protein docking, ATG101, ATG13

Abstract

Aim. Associated subproteins which constitute the ATG1 multi-protein complex in plants and mammals, including ULK1 in humans, are orchestral protein kinase atg-units in resistance to stress stimuli across their different nature. The goals of this endeavour were to characterize the molecular nature of the interaction of ATG13 with ATG101, followed by in silico docking to catch the plausible ensuing integration into a multimeric complex ULK1/ATG1, which initiates the assembly of a PAS-preautophagosomal structure in the first step of autophagy initiation. Methods. Protein structures were modeled by homology using AlphaFold, and molecular dynamics (MD) was performed using GROMACS 5.0 with the Charmm36. Results. By implementing computer modeling methods, a complex of protein kinase atg-units for both ATG13 and ATG101 proteins, reflecting the interaction interface and conformational properties, was constructed for detailed interpretation while forming the forthcoming assembly of the ULK1/ATG1 multi-protein platform. Conclusions. This study provides a high-quality model platform for further sequential studies of protein-protein docking and protein-protein interactions with the possibility of reconstructing a model of the full ULK1/ATG1 complex to identify ATG8 binding sites.

References

Zeng X., Liu C., Han N., Bian H., Zhu M. Progress on the autophagic regulators and receptors in plants. Yi chuan = Hereditas. 2016. Vol. 38 (7). P. 644–650. doi: 10.16288/j.yczz.15-525.

Kurusu T., Kuchitsu K. Autophagy, programmed cell death and reactive oxygen species in sexual reproduction in plants. Journal of plant research. 2017. Vol. 130 (3). P. 491–499. doi: 10.1007/s10265-017-0934-4.

Samperna S., Masi M., Vurro M., Evidente A., Marra M. Cyclopaldic Acid, the Main Phytotoxic Metabolite of Diplodia cupressi, Induces Programmed Cell Death and Autophagy in Arabidopsis thaliana. Toxins (Basel). 2022. Vol. 14 (7). P. 474. doi: 10.3390/toxins14070474.

Xie Z., Klionsky D. Autophagosome formation: core machinery and adaptations. Nature cell biology. 2007. Vol. 9 (10). P. 1102–1109. doi: 10.1038/ncb1007-1102.

Zhi X., Feng W., Rong Y., Liu R. Anatomy of autophagy: from the beginning to the end. Cellular and molecular life sciences : CMLS. 2018. Vol. 75 (5). P. 815–831. doi: 10.1007/s00018-017-2657-z.

Ke, P.-Y. Molecular Mechanism of Autophagosome–Lysosome Fusion in Mammalian Cells. Cells. 2024. Vol. 13 (6). P. 500. doi: 10.3390/cells13060500.

Stanley R., Ragusa M., Hurley J. The beginning of the end: how scaffolds nucleate autophagosome biogenesis. Trends in cell biology. 2014. Vol. 24 (1). P. 73–81. doi: 10.1016/j.tcb.2013.07.008.

Mercer C., Kaliappan A., Dennis P. A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy. Autophagy. 2009. Vol. 5 (5). P. 649–662. doi: 10.4161/auto.5.5.8249.

Hosokawa N., Sasaki T., Iemura S., Natsume T., Hara T., Mizushima N. Atg101, a novel mammalian autophagy protein interacting with Atg13. Autophagy. 2009. Vol. 5 (7). P. 973–979. doi: 10.4161/auto.5.7.9296.

Fujioka Y., Suzuki S., Yamamoto H., Kondo-Kakuta C., Kimura Y., Hirano H., Akada R., Inagaki F., Ohsumi Y., Noda N. Structural basis of starvation-induced assembly of the autophagy initiation complex. Nature structural & molecular biology. 2014. Vol. 21 (6). P. 513–521. doi: 10.1038/nsmb.2822.

Kabeya Y., Kamada Y., Baba M., Takikawa H., Sasaki M., Ohsumi Y. Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Molecular biology of the cell. 2005. Vol. 16 (5). P. 2544–2553. doi: 10.1091/mbc.e04-08-0669.

UniProt Consortium T. UniProt: the universal protein knowledgebase. Nucleic acids research. 2018. Vol. 46 (5) P. 2699. doi: 10.1093/nar/gky092.

Larkin M., Blackshields G., Brown N., Chenna R., McGettigan P., McWilliam H., Valentin F., Wallace I., Wilm A., Lopez R., Thompson J., Gibson T., Higgins D. Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England). 2007. Vol. 23 (21). P. 2947–2948. doi: 10.1093/bioinformatics/btm404.

Waterhouse A., Bertoni M., Bienert S., Studer G., Tauriello G., Gumienny R., Heer F., de Beer T., Rempfer C., Bordoli L., Lepore R., Schwede T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research. 2018. Vol. 46 (1). P. W296–W303. doi: 10.1093/nar/gky427.

Pronk S., Páll S., Schulz R., Larsson P., Bjelkmar P., Apostolov R., Shirts M., Smith J., Kasson P., van der Spoel D., Hess B., Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England). 2013. Vol. 29 (7). P. 845–854. doi: 10.1093/bioinformatics/btt055.

MacKerell A., Bashford D., Bellott M., Dunbrack L., Evanseck J., Field M., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F., Mattos C., Michnick S., Ngo T., Nguyen D., Prodhom B., Reiher W., Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The journal of physical chemistry. 1998. Vol. 102 (18). P. 3586–3616. doi: 10.1021/jp973084f.

Abraham M., Teemu M., Roland S., Szilárd P., Jeremy C S., Berk H., Erik L. Gromacs: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX. 2015. Vol. 1–2. P. 19–25.doi: 10.1016/j.softx.2015.06.001.

Suttangkakul A., Li F., Chung T., Vierstra R. The ATG1/ATG13 protein kinase complex is both a regulator and a target of autophagic recycling in Arabidopsis. The Plant Cell. 2011. Vol. 23 (10). P. 3761–3779. doi: 10.1105/tpc.111.090993.