Dissertation
A comprehensive structural classification of RAS conformations
Doctor of Philosophy (Ph.D.), Drexel University
Apr 2022
DOI:
https://doi.org/10.17918/00001178
Abstract
For many human cancers and tumor-associated diseases, mutations in the RAS isoforms (KRAS, NRAS, and HRAS) are the most common oncogenic alterations, making these proteins high-priority therapeutic targets. Effectively targeting the RAS isoforms requires an exact understanding of their active, inactive, and druggable conformations. However, there is no structure-guided catalogue of RAS conformations to guide therapeutic targeting or examining the structural impact of RAS mutations. We present an expanded conformational classification of RAS conformations based on analyzing their catalytic switch 1 (SW1) and switch 2 (SW2) loops. From over 700 available human KRAS, NRAS, and HRAS structures in the Protein Data Bank (PDB), we first created a broad structural classification based on the spatial positions of residue Y32 in SW1 and residue Y71 in SW2. Subsequently, we defined further conformational subsets (some previously undescribed) by clustering all well modeled SW1 and SW2 loops using a density-based machine learning algorithm with a backbone dihedral-based distance metric. In all, we identified three SW1 conformations and nine SW2 conformations, each of which is associated with different nucleotide states (GTP-bound, nucleotide-free, and GDP-bound) and specific bound proteins or inhibitor sites. The GTP-bound SW1 conformation can be further subdivided based on the hydrogen (H)-bond type made between residue Y32 and the GTP [gamma]-phosphate: water-mediated, direct, or no H-bond. Further analyzing these structures clarified the catalytic impact of the most common RAS mutations, and the inhibitor chemistries that bind to each druggable RAS conformation. To facilitate future RAS structural analyses, we have created a web database, called Rascore, presenting an updated and searchable dataset of all human RAS structures in the PDB (http://dunbrack.fccc.edu/rascore/).
Metrics
42 File views/ downloads
39 Record Views
Details
- Title
- A comprehensive structural classification of RAS conformations
- Creators
- Mitchell Isaac Parker
- Contributors
- Roland L. Dunbrack Jr. (Advisor)Erica Golemis (Advisor)
- Awarding Institution
- Drexel University
- Degree Awarded
- Doctor of Philosophy (Ph.D.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Number of pages
- xiii, 108 pages
- Resource Type
- Dissertation
- Language
- English
- Academic Unit
- Biochemistry and Molecular Biology; College of Medicine; Drexel University
- Other Identifier
- 991017499584904721