Ammar Shakir
Research Mentor: Yang Li
Mentor Department: Ecology and Evolutionary Biology, LSA
Author(s): Ammar Shakir, Yang Li
Session: Session 6 (3:00 PM – 3:50 PM)
Presentation Type: Poster 20
Abstract
Protein sequences diverge by mutations over evolution, yet many orthologous proteins retain their highly conserved structures. This pattern suggests strong evolutionary constraints acting on protein structure to preserve function, even as amino acid sequences accumulate mutations. In this project, we investigated the relationship between sequence divergence and structural conservation across the three domains of life: Bacteria, Archaea, and Eukarya. We focused on ribosomal proteins from both large and small subunits, as these proteins are universally conserved and essential for cellular function. Sequence divergence among orthologs was quantified using MMseqs2, while protein structures were predicted with ColabFold and compared using TM-scores. Despite substantial sequence divergence between domains, we observed strong conservation of overall protein structure across all orthologous groups analyzed. These results indicate that evolutionary constraints preserve protein structure despite significant sequence mutations, highlighting the difference between sequence evolution and structural conservation. Our findings demonstrate the limitations of sequence based approaches for inferring deep evolutionary relationships and emphasize the importance of structural comparison. This work provides a foundation for developing a scalable computational pipeline to study protein evolution through the lens of structural conservation. By allowing identification of proteins with low sequence similarity but conserved structural folds, allows for further identification of deeper evolutionary relationships.
