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Updated: Oct 9, 2025
Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein
Published on: January 16, 2020
In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II
Michael Gerber1, Sanjay Goel2, Radhashree Maitra1
1Yeshiva University, Department of Biology, 500 W 185th Street, New York, NY, 10033, USA.
Abstract:
KRAS mutation is prevalent in around 30% of all cancers and is an undruggable molecular target. Of seven mutations at codon 12 and 13, only one, the G12C mutant is finally proven to be druggable, as evidenced by the recent USFDA approval of sotorasib. Investigation of other small molecules targeting G12C and G12D are undergoing clinical trials. Understanding the fine structural details is a prerequisite to design specific inhibitors which also requires in depth molecular exploration. We used bioinformatics as a tool to analyze the KRAS protein's GTP (guanosine triphosphate) binding dynamics when mutated. KRAS undergoes significant conformational changes, affecting GTP binding conformation within the active site pocket of KRAS due to high torsional strains, hydrophobicity, and altered Switch I and II regions. GTP molecule for wildtype had a low torsional strain of 10.71, and is the only molecule, in comparison to KRAS mutant bound GTP, to have a glycine at position 10 interacting with its nitrogenous base. All mutant KRAS proteins lacked the interaction of glycine with the nitrogenous base. The binding affinity of wildtype (WT) KRAS for the gamma-phosphate was lower in scoring compared to the mutated KRAS protein in multiple analyses. This study provides an insight to the GTP-KRAS protein binding details that are important to define parameters required to be explored to design the appropriate inhibitor for each different type of mutant KRAS protein.
Insights
KRAS mutations are common in cancer but hard to target. Bioinformatics analysis reveals key differences in how mutated KRAS proteins bind to GTP, offering insights for designing specific cancer inhibitors.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- KRAS mutations occur in ~30% of cancers, presenting a significant therapeutic challenge.
- While KRAS G12C is now druggable, other mutations require further investigation for targeted therapies.
- Understanding KRAS protein dynamics and GTP binding is crucial for designing specific inhibitors.
Purpose of the Study:
- To analyze the GTP binding dynamics of mutated KRAS proteins using bioinformatics.
- To elucidate the structural and energetic differences in GTP binding between wildtype and mutant KRAS.
- To identify key parameters for designing targeted inhibitors against various KRAS mutants.
Main Methods:
- Bioinformatic analysis of KRAS protein structure and dynamics.
- Computational investigation of GTP binding within the KRAS active site.
- Assessment of torsional strain, hydrophobicity, and molecular interactions.
Main Results:
- Mutated KRAS proteins exhibit significant conformational changes affecting GTP binding.
- Wildtype KRAS shows lower torsional strain and a unique glycine interaction with the GTP base compared to mutants.
- Mutant KRAS proteins demonstrated higher binding affinity for the gamma-phosphate of GTP.
Conclusions:
- Bioinformatics provides critical insights into KRAS-GTP binding mechanisms.
- Differences in GTP binding dynamics highlight the need for mutant-specific inhibitor design.
- This study lays the groundwork for developing tailored therapeutic strategies for KRAS-mutated cancers.
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