Related Experiment Video

Updated: Jul 17, 2025

Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods
07:49

Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods

Published on: July 17, 2019

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Mechanism-Based Redesign of GAP to Activate Oncogenic Ras

Dénes Berta1, Sascha Gehrke1, Kinga Nyíri2,3

  • 1Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom.

Journal of the American Chemical Society
|September 8, 2023
PubMed

Insights

Ras GTPases are key in cell signaling, but mutations cause cancer. This study reveals a GTP hydrolysis mechanism and designs novel Ras-GAP mutants to restore function in oncogenic Ras proteins.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Ras GTPases are critical regulators of cellular signaling pathways.
  • Mutations in Ras genes, particularly at Gly12, Gly13, and Gln61, are frequent in cancers and lead to impaired GTPase activity.
  • Understanding the mechanism of GTP hydrolysis is essential for developing targeted cancer therapies.

Purpose of the Study:

  • To elucidate the mechanism of GTP hydrolysis catalyzed by the Ras.GAP complex.
  • To validate the proposed mechanism using oncogenic Ras mutants (G12D, G12C).
  • To develop a computational strategy for designing Ras-GAP mutants that restore catalytic activity to oncogenic Ras.

Main Methods:

  • Quantum Mechanics/Molecular Mechanics (QM/MM) free energy calculations and minimizations were employed to study the reaction mechanism.
  • Computational screening of 190 single Ras-GAP mutants was performed by calculating activation barriers.
  • A machine learning model was developed for ultrafast screening of single and double Ras-GAP mutations.

Main Results:

  • A two-step mechanism for GTP hydrolysis by Ras.GAP was proposed, involving Gln61 as a transient Brønsted base.
  • The mechanism accurately predicted the loss of catalytic activity in G12D and G12C Ras mutants.
  • Computational screening identified several Ras-GAP mutations predicted to restore catalytic activity to G12D Ras.

Conclusions:

  • The study provides a validated mechanism for Ras GTP hydrolysis and a computational framework for designing protein catalysts.
  • The developed screening protocol enables fast and accurate design of protein sequences with enhanced catalytic activity.
  • Targeting Ras-GAP activity offers a potential therapeutic strategy to counteract aberrant Ras-driven signaling in cancer.

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