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Title: Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

Abstract

The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.

Authors:
ORCiD logo [1];  [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]; ORCiD logo [2];  [1];  [3]; ORCiD logo [1]
+ Show Author Affiliations
  1. NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
  2. Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
  3. UCSF Helen Diller Family Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, San Francisco, United States
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); National Cancer Institute (NCI); National Institutes of Health (NIH); Joint Design of Advanced Computing Solutions for Cancer (JDACS4C)
OSTI Identifier:
1592514
Alternate Identifier(s):
OSTI ID: 1592515; OSTI ID: 1682527
Report Number(s):
LLNL-JRNL-771099
Journal ID: ISSN 2050-084X; e47654
Grant/Contract Number:  
AC52-07NA27344; HHSN261200800001E
Resource Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 9; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cancer Biology; Physics Of Living Systems; RAS Diffusion; Cancer; Single Molecule Tracking; Atomistic Simulation

Citation Formats

Goswami, Debanjan, Chen, De, Yang, Yue, Gudla, Prabhakar R., Columbus, John, Worthy, Karen, Rigby, Megan, Wheeler, Madeline, Mukhopadhyay, Suman, Powell, Katie, Burgan, William, Wall, Vanessa, Esposito, Dominic, Simanshu, Dhirendra K., Lightstone, Felice C., Nissley, Dwight V., McCormick, Frank, and Turbyville, Thomas. Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior. United States: N. p., 2020. Web. doi:10.7554/eLife.47654.
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Goswami, Debanjan, Chen, De, Yang, Yue, Gudla, Prabhakar R., Columbus, John, Worthy, Karen, Rigby, Megan, Wheeler, Madeline, Mukhopadhyay, Suman, Powell, Katie, Burgan, William, Wall, Vanessa, Esposito, Dominic, Simanshu, Dhirendra K., Lightstone, Felice C., Nissley, Dwight V., McCormick, Frank, & Turbyville, Thomas. Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior. United States. doi:https://doi.org/10.7554/eLife.47654
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Goswami, Debanjan, Chen, De, Yang, Yue, Gudla, Prabhakar R., Columbus, John, Worthy, Karen, Rigby, Megan, Wheeler, Madeline, Mukhopadhyay, Suman, Powell, Katie, Burgan, William, Wall, Vanessa, Esposito, Dominic, Simanshu, Dhirendra K., Lightstone, Felice C., Nissley, Dwight V., McCormick, Frank, and Turbyville, Thomas. Mon . "Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior". United States. doi:https://doi.org/10.7554/eLife.47654.
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@article{osti_1592514,
title = {Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior},
author = {Goswami, Debanjan and Chen, De and Yang, Yue and Gudla, Prabhakar R. and Columbus, John and Worthy, Karen and Rigby, Megan and Wheeler, Madeline and Mukhopadhyay, Suman and Powell, Katie and Burgan, William and Wall, Vanessa and Esposito, Dominic and Simanshu, Dhirendra K. and Lightstone, Felice C. and Nissley, Dwight V. and McCormick, Frank and Turbyville, Thomas},
abstractNote = {The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.},
doi = {10.7554/eLife.47654},
journal = {eLife},
number = ,
volume = 9,
place = {United States},
year = {2020},
month = {1}
}
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Journal Article:
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DOI: https://doi.org/10.7554/eLife.47654
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Figures / Tables:

Table 1 Table 1: Diffusion Rates and Percent Occupancy in Cancer Cell Lines
All figures and tables (16 total)
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    Figures / Tables found in this record:

    Table 1 (p. 31)table
    Table 2 (p. 31)table
    Table 3 (p. 32)table
    Figure-1 (p. 36)figure
    Figure 2 (p. 37)figure
    Figure 3 (p. 38)figure
    Figure 4 (p. 39)figure
    Figure 5 (p. 40)figure
    Figure 6 (p. 41)figure
    Supplementary Figure 1 (p. 42)figure
    Supplementary Figure 2 (p. 43)figure
    Supplementary Figure 3 (p. 44)figure
    Supplementary Figure 4 (p. 45)figure
    Supplementary Figure 5 (p. 46)figure
    Figure 1c (p. 47)figure
    Figure 1e (p. 47)figure
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