Structural Insights into Yeast ATP Synthase

Multiple sequence alignment of Atp19 and Mco10 was performed using ClustalOmega^{54 (link)}. Hydropathy plots were generated by ProtScale on the ExPASy Server using Kate and Doolittle for predicted proteins of S. cerevisiae. Homology modelling of the ATP synthase complex was based on the atomic model built in the cryo-electron microscopy density map of S. cerevisiae ATP synthase, PDB: 6B8H^{6 (link)}, and Alphafold2 predicted structures of subunits in S. cerevisiae^{55 (link),56 (link)}. Structures of the homologs of Mco10 and Atp19 in Candida albicans and Pichia angusta were analyzed using the available structures in Alphafold2 database and also verified using ColabFold which offers an accelerated protein structure predictions by combining MMseqs2 with AlphaFold2 or RoseTTAFold⁵⁷. Structural visualization was carried out using PyMOL software.

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Panja C., Wiesyk A., Niedźwiecka K., Baranowska E, & Kucharczyk R. (2023). ATP synthase interactome analysis identifies a new subunit l as a modulator of permeability transition pore in yeast. Scientific Reports, 13, 3839.

Publication 2023

Candida albicans Cryo electron microscopy Pichia angusta Protein Proteins s Sequence alignment Subunits Synthase

Corresponding Organization : Institute of Biochemistry and Biophysics, Polish Academy of Sciences

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Variable analysis

independent variables

Multiple sequence alignment of Atp19 and Mco10 using ClustalOmega
Hydropathy plots generated by ProtScale on the ExPASy Server using Kate and Doolittle for predicted proteins of S. cerevisiae
Homology modelling of the ATP synthase complex based on the atomic model built in the cryo-electron microscopy density map of S. cerevisiae ATP synthase, PDB: 6B8H, and Alphafold2 predicted structures of subunits in S. cerevisiae
Structures of the homologs of Mco10 and Atp19 in Candida albicans and Pichia angusta analyzed using the available structures in Alphafold2 database and also verified using ColabFold

dependent variables

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control variables

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controls

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Negative control: Not mentioned

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