procoil

"PrOCoil" is a machine learning-based software tool developed to advance our understanding of the coiled-coil motif. A structural feature prevalent in proteins influences their oligomerization—the process by which multiple alpha-helices assemble to form a coiled-coil. Despite extensive characterization of coiled-coil structures, the specific rules governing their oligomerization, particularly the formation of two- and three-stranded coiled coils, remained elusive.

By analyzing weighted amino acid patterns, PrOCoil identifies and elucidates these rules, offering new insights into the determinants of coiled-coil stoichiometry. Notably, the tool highlights the significant role of sequence positions previously considered irrelevant to coiled-coil interactions, revealing their undeniable impact on oligomerization.

Additionally, PrOCoil provides a visualization feature demonstrating how each amino acid in a sequence contributes to the overall oligomeric tendency of a coiled-coil. This capability is instrumental in demystifying the oligomerization behavior of complex proteins, such as the yeast transcription factor GCN4. PrOCoil's analysis presents GCN4 as a hybrid entity with dimers and trimers characteristics supported by theoretical and experimental evidence.