Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

Shrestha, Rebika; Carpenter, Timothy S.; Van, Que N.; Agamasu, Constance; Tonelli, Marco; Aydin, Fikret; Chen, De; Gulten, Gulcin; Glosli, James N.; López Bautista, Cesar Augusto; Oppelstrup, Tomas; Neale, Chris; Gnanakaran, Sandrasegaram; Gillette, William K.; Ingólfsson, Helgi I.; Lightstone, Felice C.; Stephen, Andrew G.; Streitz, Frederick H.; Nissley, Dwight V.; Turbyville, Thomas J.

doi:10.1038/s42003-024-05916-0

Title: Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

Journal Article · 28 February 2024 · Communications Biology

DOI: https://doi.org/10.1038/s42003-024-05916-0 · OSTI ID:2340874

Shrestha, Rebika ^[1];

^[2];

^[1]; Agamasu, Constance ^[1]; Tonelli, Marco ^[3]; Aydin, Fikret ^[2]; Chen, De ^[1]; Gulten, Gulcin ^[1]; Glosli, James N. ^[2];

^[4]; Oppelstrup, Tomas ^[2];

^[4];

^[4]; Gillette, William K. ^[1];

^[2];

^[2]; Stephen, Andrew G. ^[1];

^[2]; Nissley, Dwight V. ^[1];

^[1]

Frederick National Lab. for Cancer Research, Frederick, MD (United States)
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Univ. of Wisconsin, Madison, WI (United States)
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

AbstractThe oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: 89233218CNA000001; AC52-07NA27344; AC52-06NA25396; AC05-00OR22725

OSTI ID:: 2340874

Alternate ID(s):: OSTI ID: 2375427

Report Number(s):: LA-UR-23-21911; LLNL-JRNL-845293

Journal Information:: Communications Biology, Vol. 7, Issue 1; ISSN 2399-3642

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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