Engineering Hydrophilic Analogs of Human ATP Synthase Fo Subunits Using the QTY Code
Independent Bioinformatics Research | 2025-Present
Under the mentorship of Dr. Shuguang Zhang, MIT Media Lab | Pending First-Author Publication
Protein Design & Sequence Analysis:
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QTY sequence conversion and protein redesign
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Transmembrane domain prediction and topology analysis
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Sequence alignment and residue-level comparison
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Amino-acid substitution analysis
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Hydrophobicity and hydrophilic surface analysis
Structural Bioinformatics & Comparison:
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AlphaFold 3 structural prediction
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Cryo-EM structural extraction and comparison
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PyMOL and ChimeraX structural visualization
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3D structural alignment and superpositioning
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RMSD and TM-score analysis
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Global and segment-based structural comparison
Model Confidence & Quantitative Analysis:
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pLDDT, pTM, PAE, and other confidence metrics analysis
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Secondary structure and alpha-helical analysis
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Quantitative comparison across eight subunits
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Python-based data analysis and visualization
Across all eight analysed subunits, QTY-modified AlphaFold3 models generally retained close structural similarity to their native counterparts while showing substantially reduced calculated surface hydrophobicity, indicating potential water solubility.
Membrane proteins play essential roles in cellular function, but their hydrophobic surfaces often make them difficult to study without special treatment. The QTY code, developed by Dr. Shuguang Zhang and colleagues, offers a way to redesign membrane proteins by systematically replacing hydrophobic amino acids with hydrophilic residues while still preserving overall structure.
At its core, my research asks whether these proteins could be made less hydrophobic (more water-soluble) while still preserving their predicted structures, potentially making difficult membrane proteins easier to study for applications ranging from basic biological research to drug discovery and protein engineering.
Under Dr. Zhang's mentorship, I applied the QTY code to eight membrane subunits of ATP synthase Fo, the key biological energy-generating system across nearly all cellular life. In humans, it is a big part of what makes the mitochondria the powerhouse of the cell.
The image on the left shows human ATP synthase, with the split between F1 and membrane-embedded Fo sector illustrated. The Fo sector subunits studied in this research are highlighted in red.
The below image is taken from a figure in the manuscript, showing native ATP6, an important protein subunit in ATP synthase Fo, with the QTY substituted analog. The close overlap between the experimental structure and predicted QTY analog suggests that QTY substitutions largely preserve ATP6's overall alpha-helical structure. The native structure is shown in magenta while the QTY structure is in cyan.
This study expands the current use of the QTY code, demonstrating its potential viability in rotary motor enzymes with ATP synthase.