Document Type



Master of Science (MS)



First Advisor's Name

Jessica Siltberg-Liberles

First Advisor's Committee Title

Committee chair

Second Advisor's Name

Lidia Kos

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Yuk-Ching Tse-Dinh

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Prem Chapagain

Fourth Advisor's Committee Title

Committee member


Short Linear Motifs, SLiMs, ELM Database, Intrinsic Disordered Protein Regions, Molecular Mimicry, Protein Flexibility, Bioinformatics, Viruses, Host-Pathogen Interaction

Date of Defense



Short linear motifs (SLiMs), often found in intrinsically disordered regions (IDPs), can initiate protein-protein interactions in eukaryotes. Although pathogens tend to have less disorder than eukaryotes, their proteins alter host cellular function through molecular mimicry of SLiMs. The first objective was to study sequence-based structure properties of viral SLiMs in the ELM database and the conservation of selected viral motifs involved in the virus life cycle. The second objective was to compare the structural features for SliMs in pathogens and eukaryotes in the ELM database. Our analysis showed that many viral SliMs are not found in IDPs, particularly glycosylation motifs. Moreover, analysis of disorder and secondary structure properties in the same motif from pathogens and eukaryotes shed light on similarities and differences in motif properties between pathogens and their eukaryotic equivalents. Our results indicate that the interaction mechanism may differ between pathogens and their eukaryotic hosts for the same motif.




Previously Published In


Elkhaligy, H., Balbin, C. A., Gonzalez, J. L., Liberatore, T., & Siltberg-Liberles, J. (2021). Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins. Viruses, 13(12), 2369.


Elkhaligy, H., Balbin, C. A., & Siltberg-Liberles, J. (2022). Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions.Pathogens, 11(5), 583.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.



Rights Statement

Rights Statement

In Copyright. URI:
This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).