Full Length Structural Modeling of Babesia bovis HAP2: Integration of AlphaFold2 Predictions with Experimental Ectodomain Benchmarking 

( 3.9.26  )                            Written and research done by Gio Kim                         

Food insecurity remains a global problem worldwide, with over total of 1,03,962 malnutrition related deaths being recorded between 1999 and 2020. One of the main sources of food, cattle, is significantly impacted by the tick born apicomplexan parasite Babesia bovis, which causes bovine babesiosis and lead to enormous food insecurity around the world. (Rahman et.al). HAP2, a protein in B.Bovis, plays a crucial role in gamete fusion of this parasite and is a strong candidate for developing a transmission blocking vaccine (Rahman et.al). 

While its structural homology is well-documented in model organisms like Chlamydomonas, its architecture in the bovine parasite Babesia bovis remains less characterized. This project sought to bridge that gap by generating a high-fidelity, full length computational model of B. bovis HAP2 using AlphaFold2 and validating its functional domains against recent experimental data. 

Methodology

The primary amino acid sequence of B.bovis Hap2 was extracted using UniProt. It was processed by AlphaFold2 to predict its tertiary structure. To ensure the reliability of this AI generated model, I performed a structural imposition with the experimental coordinates provided by (Rahman et al). The predicted protein was aligned with the ectodomain of Dr. Raman's predictions to calculate the Room Mean Square Deviation (RMSD).

Results

The superimposition yielded Global RMSD of 1.263 Å, which indicates a near atomic match between the predicted and experiemented models. This is significant given the primary sequence identity of only 27.3%. These results highlight a high degree in structural conservation as while the genetic diversity of B.Bovis has diverged, the tertiary fold and geospatial orientation of the fusion loops are functionally constrained. This suggests that the biophysical requirements for membrane bilayer disruption necessitate a specific protein geometry that evolution cannot significantly alter without loss of function. 

Full length architecture

Unliked the truncated ectodomains found in many studies, this model aimed to capture the full length model for more holistic view. The Global RMSD is based on the specific ectodomains of both proteins and more research must be done to grasp the entire nature of the protein. 

Additional Notes

This project was conducted as an independent student led investigations into parasitic structural biology. The objective of this research was not to claim a novel discovery, rather, it was to test the boundaries of predictive structural biology within a student led framework. While I am a student and this model is more of a structural hypothesis rather than a final discovery, it has allowed me to better understand the power of bioinformatics.

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References:

https://www.uniprot.org/uniprotkb/A7ANV4/entry#sequences (Uniprot database)

https://www.nature.com/articles/s41598-025-91359-4 (Dr. Rahman's research paper on the ectodomain of the B.bovis Hap2 protein's ectodomain)

https://pmc.ncbi.nlm.nih.gov/articles/PMC10990269/ (Food insecurity data by Chamanmoor)

https://www.nature.com/articles/s41586-021-03819-2 (AlphaFold citation)

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External Resources:

https://drive.google.com/file/d/1gZVdXAq1-hr011zSoy2-lYzas3nn3Qtl/view?usp=drive_link (The GLB file of the Hap2 protein)

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Acknowledgements:

Thank you so much to Dr. Rahman for inspiring me into the field of bioinformatics and teaching me how to use the bioinformatic software.

Thank you to Dr. Byung Kyu Kim for giving me the insight into the medical field and inspiring me to start this whole journey.

Thank you to Ohyoung Jang for teaching me how to programm in python and first introducing me to CS, giving me the opporuntiy to view the intersection of bio+cs.