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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]
  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:
Sponsoring Org.:
USDOE
OSTI Identifier:
1592514
Alternate Identifier(s):
OSTI ID: 1592515
Grant/Contract Number:  
Joint Design of Advanced Computing Solutions for Cancer (JDACS4C)
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

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.
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:10.7554/eLife.47654.
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:10.7554/eLife.47654.
@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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.7554/eLife.47654

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Works referenced in this record:

Regulating the regulator: post-translational modification of RAS
journal, December 2011

  • Ahearn, Ian M.; Haigis, Kevin; Bar-Sagi, Dafna
  • Nature Reviews Molecular Cell Biology, Vol. 13, Issue 1
  • DOI: 10.1038/nrm3255

Genetic analysis of Ras signalling pathways in cell proliferation, migration and survival
journal, February 2010

  • Drosten, Matthias; Dhawahir, Alma; Sum, Eleanor Y. M.
  • The EMBO Journal, Vol. 29, Issue 6
  • DOI: 10.1038/emboj.2010.7

Quantitative Measurement of Intrinsic GTP Hydrolysis for Carcinogenic Glutamine 61 Mutants in H-Ras
journal, October 2018


Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
journal, April 2011

  • Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart
  • Journal of Computational Chemistry, Vol. 32, Issue 9
  • DOI: 10.1002/jcc.21777

Stimulation of Membrane Ruffling and MAP Kinase Activation by Distinct Effectors of RAS
journal, February 1996


Distinct Binding Preferences between Ras and Raf Family Members and the Impact on Oncogenic Ras Signaling
journal, December 2019


TrackMate: An open and extensible platform for single-particle tracking
journal, February 2017


Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ
journal, October 2016

  • Dharmaiah, Srisathiyanarayanan; Bindu, Lakshman; Tran, Timothy H.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 44
  • DOI: 10.1073/pnas.1615316113

Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output
journal, January 2017


Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

Bright photoactivatable fluorophores for single-molecule imaging
journal, October 2016

  • Grimm, Jonathan B.; English, Brian P.; Choi, Heejun
  • Nature Methods, Vol. 13, Issue 12
  • DOI: 10.1038/nmeth.4034

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B
journal, October 2018


Brownian motion in biological membranes.
journal, August 1975

  • Saffman, P. G.; Delbruck, M.
  • Proceedings of the National Academy of Sciences, Vol. 72, Issue 8
  • DOI: 10.1073/pnas.72.8.3111

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy
journal, December 2012


Complexes of Ras.GTP with Raf-1 and mitogen-activated protein kinase kinase
journal, June 1993


Extracting intracellular diffusive states and transition rates from single-molecule tracking data
journal, February 2013

  • Persson, Fredrik; Lindén, Martin; Unoson, Cecilia
  • Nature Methods, Vol. 10, Issue 3
  • DOI: 10.1038/nmeth.2367

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes
journal, July 2008

  • Sergé, Arnauld; Bertaux, Nicolas; Rigneault, Hervé
  • Nature Methods, Vol. 5, Issue 8
  • DOI: 10.1038/nmeth.1233

Dragging Ras Back in the Ring
journal, March 2014


Single-molecule imaging analysis of Ras activation in living cells
journal, April 2004

  • Murakoshi, H.; Iino, R.; Kobayashi, T.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 19
  • DOI: 10.1073/pnas.0401354101

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

  • Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
  • The Journal of Physical Chemistry B, Vol. 114, Issue 23
  • DOI: 10.1021/jp101759q

Dynamic Organizing Principles of the Plasma Membrane that Regulate Signal Transduction: Commemorating the Fortieth Anniversary of Singer and Nicolson's Fluid-Mosaic Model
journal, November 2012


Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway
journal, June 2015

  • Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 26
  • DOI: 10.1073/pnas.1509123112

Direct interaction of Ras and the amino-terminal region of Raf-1 in vitro
journal, July 1993

  • Warne, Patricia H.; Vician, Pablo Rodrigueza; Downward, Julian
  • Nature, Vol. 364, Issue 6435
  • DOI: 10.1038/364352a0

RAS Proteins and Their Regulators in Human Disease
journal, June 2017


Complex formation between RAS and RAF and other protein kinases.
journal, July 1993

  • Van Aelst, L.; Barr, M.; Marcus, S.
  • Proceedings of the National Academy of Sciences, Vol. 90, Issue 13
  • DOI: 10.1073/pnas.90.13.6213