Specialty Molecular Biomedicine Mechanisms of Disease, Molecular and Cellular Therapies, and Bioinnovation
Library of the School of Health Sciences

2024-09-30

2024

Logiadi Maria-Eliza

Ζωή Κούρνια, Ερευνήτρια Α', ΙΙΒΕΑΑ
Δέσποινα Σανούδου, Καθηγήτρια, Ιατρική Σχολή, EKΠΑ
Γεώργιος Παυλόπουλος, Ερευνητής Α', ΕΚΕΒΕ "Αλεξανδρος Φλέμινγκ"

Δομική και δυναμική μελέτη διμερών της ογκογόνου πρωτεΐνης K-Ras4BG12D με προσομοιώσεις Μοριακής Δυναμικής

English

Structural and dynamical studies of K- Ras4BG12D dimers using Molecular Dynamics simulations

K-RAS mutations, particularly the G12D activating variant, play a central role in the pathogenesis of aggressive cancers. Current therapeutic options for these K-RAS - driven malignancies are limited, underlining the urgent need for innovative approaches to disrupt K-Ras activity. The active, GTP-bound K-Ras4BG12D variant can form dimers in the plasma membrane, which could then act as scaffold for the recruitment of C-Raf to the membrane and subsequent dimerization. These events lead to sustained activation of the MAPK signaling pathway, contributing to uncontrolled cell proliferation and tumorigenesis. However, the dimerization of K-Ras4BG12D remains largely uncharacterized. We have recently analyzed the dimerization free energy landscape of K-Ras4BG12D, using enhanced sampling Coarse-Grained Molecular Dynamics (CG- MD) simulations. We have extracted ten dimers that correspond to local minima of these free energy landscapes. This research project evaluates the structure and dynamics of selected K-Ras4BG12D dimers arising from the CG-MD simulations using all-atom MD simulations. Atomistic configurations of K-Ras4BG12D dimers in the presence and absence of the cysteine-rich and Ras-binding domains of C-Raf on a model membrane were obtained after backmapping the CG structures. All-atom MD simulations were then performed on these backmapped structures. During system equilibration, the system experienced instabilities that led to GTP-protein and protein- protein dissociation. Different strategies were explored to rectify these instability issues including the reconstruction of the GTP interaction network based on a crystal dimer structure of the wild type K-Ras4B and the use of gradually loosened restraints in combination with long equilibration time. GTP was finally stabilized with the use of restraints and the evolution of dimerization interfaces of K-Ras4BG12D with and without C-Raf were analyzed. These results may indicate inaccuracies in atom positions resulting from the backmapping procedure resulting in the loss of key intermolecular interactions, instability of the CG dimer structures, or a need for optimization in the employed atomistic simulation protocol. Future work is underway to shed light on these issues.

Health Sciences

K-Ras, G12D mutant, C-Raf, Cancer, Backmapping, Dimerization dynamics, Molecular Dynamics simulations

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https://pergamos.lib.uoa.gr/uoa/dl/object/3417933