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Principal Investigator: Mitchell Isaac Parker
Organization: DREXEL UNIVERSITY
Fiscal Year: 2024
Award: $40,487
Funding agency: National Institute of General Medical Sciences
Abstract: RAS proteins (KRAS, NRAS, and HRAS) are the most extensively studied set of mutationally activated
oncogenes. Yet we do not completely understand the structural impact of RAS mutations in cancer. As of August
2020, there are 333 experimentally solved wild-type (WT) and mutated RAS structures in the Protein Data Bank
(PDB), comprising 175 HRAS, 155 KRAS, and 3 NRAS structures. This growing structural ensemble provides a
valuable resource to discover novel insights into RAS activity through statistical analyses that enable quantitative
determination of biological correlates. In recent years, NMR studies and molecular dynamic (MD) simulations
(using experimental structures as templates) have shown that the conserved RAS switch 1 (SW1) and 2 (SW2)
regions display dynamic conformational behaviors that modify RAS activity. Conformational changes in
SW1/SW2 facilitate the concerted binding of regulator and effector proteins at these regional interfaces, in turn
promoting proper switching of RAS proteins from an active GTP-conformer to an inactive GDP-conformer. In
addition, biochemical studies have provided evidence for the existence of a GTP-bound RAS homodimer
required for activation of certain signaling pathways. While we know that RAS homodimerization occurs in a
GTP-bound state, we do not know if a specific RAS conformational arrangement is required for RAS homodimer
formation and associated protein-protein interaction (PPI) events. Further complicating this issue, there is no
consolidated understanding of how mutations on RAS proteins may shift SW1/SW2 conformation in ways
favoring or disfavoring RAS PPIs, including RAS homodimerization. The objective of this proposal is to create a
unified RAS structural classification to assess the impact of oncogenic mutations on KRAS, HRAS, and NRAS,
ligands (GTP, GDP, inhibitors, or none), and PPIs/homodimerization. In preliminary work, I created a unified
RAS structural nomenclature based on clustering SW1/SW2 conformations across experimental structures of
KRAS, HRAS, and NRAS. I have also performed a pan-cancer analysis of 18,841 RAS missense mutations from
a cohort of 100,707 patients, providing the most comprehensive existing resource for KRAS, NRAS, and HRAS
mutational patterns in human tumors. In Aim 1, I will compare the conformational and PPI preferences of RAS
mutated and WT forms with experimentally solved structures. Following this, in Aim 2, I will predict the
conformational and PPI preferences of RAS mutated and WT forms by examining energy distributions of
generated structural ensembles. If we can reproduce the effects of some known mutations, then we can
confidently predict the consequence for novel mutations that have not been experimentally studied. In completing
this proposal, I will present the unified RAS structural nomenclature, including the determined impact of RAS
mutations, in a database that will be continually updated upon solving of new experimental structures. This work
will serve as a biological resource, informing future studies stratifying RAS WT and mutated structures and efforts
to create drugs directly targeting RAS proteins for cancer treatment.
Terms: <3-D><3-Dimensional><3D><Agreement><Alanine><Antibodies><Behavior><Binding><Biochemical><Biological><C-K-RAS><Canada><Cancer Genes><Cancer Treatment><Cancer-Promoting Gene><Cancers><Classification><Complex><Computational toolkit><Computer software><Data Bases><Databases><Drugs><Europe><Event><Future><GTP><GTP Binding><GTP bound><Genes><Genetic Alteration><Genetic Change><Genetic defect><Guanosine Triphosphate><H-ras><H-ras Gene><H-ras Oncogene><HRAS><HRAS gene><HRAS1><Harvey Rat Sarcoma Viral Oncogene Homolog><Homodimerization><Human><K-RAS2A><K-RAS2B><K-Ras><K-Ras 2A><K-Ras-2 Oncogene><KRAS><KRAS2><KRAS2 gene><Ki-RAS><Kinases><Ligand Binding><Ligands><Malignant Neoplasm Therapy><Malignant Neoplasm Treatment><Malignant Neoplasms><Malignant Tumor><Mating Type Switch 1><Medication><Missense Mutation><Modern Man><Molecular Configuration><Molecular Conformation><Molecular Dynamics Simulation><Molecular Interaction><Molecular Stereochemistry><Mutate><Mutation><Mutation Analysis><Nomenclature><Oncogene K-Ras><Oncogenes><Oncogenic><Output><Patients><Pattern><Pharmaceutical Preparations><Phosphotransferase Gene><Phosphotransferases><Proteins><RAS genes><RASH1><RASK2><Research Resources><Resources><Roentgen Rays><SWI1><Scanning><Signal Pathway><Site><Software><Statistical Data Analyses><Statistical Data Analysis><Statistical Data Interpretation><Structure><Swi1/Adr6><Switch 1><Systematics><Testing><Transforming Genes><Transphosphorylases><United States><Update><Visualization><Work><X-Radiation><X-Ray Radiation><X-ray><Xray><anti-cancer therapy><biologic><cancer therapy><cancer-directed therapy><cohort><computational suite><computational toolbox><computational tools><computational toolset><computerized tools><conformation><conformational><conformational state><conformationally><conformations><conformer><data base><design><designing><drug/agent><electron density><experiment><experimental group><experimental research><experimental study><experiments><genome mutation><improved><inhibitor><insight><malignancy><molecular dynamics><mutation status><mutational status><neoplasm/cancer><novel><preference><protein data bank><protein databank><protein protein interaction><protein structure><protein structures><proteins structure><ras Gene Products><ras Proteins><statistical analysis><three dimensional><tumor><v-Ha-RAS Harvey Rat Sarcoma Viral Oncogene Homolog><v-Ki-RAS2 Kirsten Rat Sarcoma 2 Viral Oncogene Homolog><web server>